hypothetical protein CB1_000487037 [Camelus ferus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| Motor_domain super family | cl22853 | Myosin and Kinesin motor domain; Myosin and Kinesin motor domain. These ATPases belong to the ... |
369-641 | 7.66e-132 | |||||
Myosin and Kinesin motor domain; Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes. Some of the names do not match with what is given in the sequence list. This is because they are based on the current nomenclature by Kollmar/Sebe-Pedros. The actual alignment was detected with superfamily member cd01366: Pssm-ID: 473979 [Multi-domain] Cd Length: 329 Bit Score: 400.82 E-value: 7.66e-132
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| PHD2_PHF1 | cd15582 | PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 ... |
771-822 | 1.98e-36 | |||||
PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the second PHD finger. : Pssm-ID: 277057 Cd Length: 52 Bit Score: 130.84 E-value: 1.98e-36
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| PHD1_PHF1 | cd15500 | PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ... |
672-722 | 4.61e-27 | |||||
PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger. : Pssm-ID: 276975 Cd Length: 51 Bit Score: 104.14 E-value: 4.61e-27
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| Smc super family | cl34174 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
202-344 | 1.62e-14 | |||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; The actual alignment was detected with superfamily member COG1196: Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 78.44 E-value: 1.62e-14
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| Tudor_SF super family | cl02573 | Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ... |
636-665 | 9.87e-12 | |||||
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain. The actual alignment was detected with superfamily member cd20449: Pssm-ID: 470623 Cd Length: 54 Bit Score: 60.61 E-value: 9.87e-12
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| Mtf2_C super family | cl16580 | Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with ... |
964-993 | 1.89e-07 | |||||
Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics. The actual alignment was detected with superfamily member pfam14061: Pssm-ID: 464077 Cd Length: 48 Bit Score: 48.58 E-value: 1.89e-07
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| PHA03247 super family | cl33720 | large tegument protein UL36; Provisional |
73-190 | 8.33e-03 | |||||
large tegument protein UL36; Provisional The actual alignment was detected with superfamily member PHA03247: Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 40.31 E-value: 8.33e-03
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| Name | Accession | Description | Interval | E-value | |||||
| KISc_C_terminal | cd01366 | Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins; Kinesin motor domain, ... |
369-641 | 7.66e-132 | |||||
Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins; Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276817 [Multi-domain] Cd Length: 329 Bit Score: 400.82 E-value: 7.66e-132
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| Kinesin | pfam00225 | Kinesin motor domain; |
390-637 | 3.44e-85 | |||||
Kinesin motor domain; Pssm-ID: 459720 [Multi-domain] Cd Length: 326 Bit Score: 277.53 E-value: 3.44e-85
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| KISc | smart00129 | Kinesin motor, catalytic domain. ATPase; Microtubule-dependent molecular motors that play ... |
379-637 | 2.42e-84 | |||||
Kinesin motor, catalytic domain. ATPase; Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division. Pssm-ID: 214526 [Multi-domain] Cd Length: 335 Bit Score: 275.61 E-value: 2.42e-84
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| KIP1 | COG5059 | Kinesin-like protein [Cytoskeleton]; |
392-636 | 9.16e-53 | |||||
Kinesin-like protein [Cytoskeleton]; Pssm-ID: 227392 [Multi-domain] Cd Length: 568 Bit Score: 194.57 E-value: 9.16e-53
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| PHD2_PHF1 | cd15582 | PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 ... |
771-822 | 1.98e-36 | |||||
PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the second PHD finger. Pssm-ID: 277057 Cd Length: 52 Bit Score: 130.84 E-value: 1.98e-36
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| PLN03188 | PLN03188 | kinesin-12 family protein; Provisional |
437-655 | 1.05e-28 | |||||
kinesin-12 family protein; Provisional Pssm-ID: 215621 [Multi-domain] Cd Length: 1320 Bit Score: 124.66 E-value: 1.05e-28
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| PHD1_PHF1 | cd15500 | PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ... |
672-722 | 4.61e-27 | |||||
PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger. Pssm-ID: 276975 Cd Length: 51 Bit Score: 104.14 E-value: 4.61e-27
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
202-344 | 1.62e-14 | |||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 78.44 E-value: 1.62e-14
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-339 | 7.23e-12 | |||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 69.70 E-value: 7.23e-12
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| Tudor_PHF1 | cd20449 | Tudor domain found in PHD finger protein1 (PHF1) and similar proteins; PHF1, also called ... |
636-665 | 9.87e-12 | |||||
Tudor domain found in PHD finger protein1 (PHF1) and similar proteins; PHF1, also called Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis, through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t. Moreover, PHF1 is required for efficient H3-K27 trimethylation (H3K27me3) and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. PHF1 consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Pssm-ID: 410520 Cd Length: 54 Bit Score: 60.61 E-value: 9.87e-12
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| PHD | pfam00628 | PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ... |
673-725 | 1.49e-10 | |||||
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 57.12 E-value: 1.49e-10
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| Crescentin | pfam19220 | Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament ... |
192-342 | 6.49e-10 | |||||
Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament proteins, named crescentin, whose cytoskeletal function is required for the vibrioid and helical shapes of Caulobacter crescentus. Without crescentin, the cells adopt a straight-rod morphology. Crescentin has characteriztic features of IF proteins including the ability to assemble into filaments in vitro without energy or cofactor requirements. In vivo, crescentin forms a helical structure that colocalizes with the inner cell curvatures beneath the cytoplasmic membrane. Pssm-ID: 437057 [Multi-domain] Cd Length: 401 Bit Score: 62.39 E-value: 6.49e-10
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| PHD | smart00249 | PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ... |
673-722 | 6.70e-09 | |||||
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 52.60 E-value: 6.70e-09
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| mukB | PRK04863 | chromosome partition protein MukB; |
193-322 | 1.71e-07 | |||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 55.73 E-value: 1.71e-07
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| Mtf2_C | pfam14061 | Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with ... |
964-993 | 1.89e-07 | |||||
Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics. Pssm-ID: 464077 Cd Length: 48 Bit Score: 48.58 E-value: 1.89e-07
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| Atg16_CCD | cd22887 | Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ... |
269-329 | 6.13e-05 | |||||
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. Pssm-ID: 439196 [Multi-domain] Cd Length: 91 Bit Score: 42.55 E-value: 6.13e-05
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| growth_prot_Scy | NF041483 | polarized growth protein Scy; |
227-346 | 2.31e-04 | |||||
polarized growth protein Scy; Pssm-ID: 469371 [Multi-domain] Cd Length: 1293 Bit Score: 45.20 E-value: 2.31e-04
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| PHD | smart00249 | PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ... |
771-820 | 4.86e-03 | |||||
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 36.04 E-value: 4.86e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
73-190 | 8.33e-03 | |||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 40.31 E-value: 8.33e-03
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| Name | Accession | Description | Interval | E-value | ||||||
| KISc_C_terminal | cd01366 | Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins; Kinesin motor domain, ... |
369-641 | 7.66e-132 | ||||||
Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins; Kinesin motor domain, KIFC2/KIFC3/ncd-like carboxy-terminal kinesins. Ncd is a spindle motor protein necessary for chromosome segregation in meiosis. KIFC2/KIFC3-like kinesins have been implicated in motility of the Golgi apparatus as well as dentritic and axonal transport in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found at the C-terminus (C-type). C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276817 [Multi-domain] Cd Length: 329 Bit Score: 400.82 E-value: 7.66e-132
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| Kinesin | pfam00225 | Kinesin motor domain; |
390-637 | 3.44e-85 | ||||||
Kinesin motor domain; Pssm-ID: 459720 [Multi-domain] Cd Length: 326 Bit Score: 277.53 E-value: 3.44e-85
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| KISc | smart00129 | Kinesin motor, catalytic domain. ATPase; Microtubule-dependent molecular motors that play ... |
379-637 | 2.42e-84 | ||||||
Kinesin motor, catalytic domain. ATPase; Microtubule-dependent molecular motors that play important roles in intracellular transport of organelles and in cell division. Pssm-ID: 214526 [Multi-domain] Cd Length: 335 Bit Score: 275.61 E-value: 2.42e-84
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| KISc | cd00106 | Kinesin motor domain; Kinesin motor domain. This catalytic (head) domain has ATPase activity ... |
388-637 | 2.13e-75 | ||||||
Kinesin motor domain; Kinesin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), in some its is found in the middle (M-type), or C-terminal (C-type). N-type and M-type kinesins are (+) end-directed motors, while C-type kinesins are (-) end-directed motors, i.e. they transport cargo towards the (-) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276812 [Multi-domain] Cd Length: 326 Bit Score: 251.02 E-value: 2.13e-75
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| KISc_KIF4 | cd01372 | Kinesin motor domain, KIF4-like subfamily; Kinesin motor domain, KIF4-like subfamily. Members ... |
388-641 | 3.84e-56 | ||||||
Kinesin motor domain, KIF4-like subfamily; Kinesin motor domain, KIF4-like subfamily. Members of this group seem to perform a variety of functions, and have been implicated in neuronal organelle transport and chromosome segregation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276823 [Multi-domain] Cd Length: 341 Bit Score: 197.94 E-value: 3.84e-56
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| KISc_KIF3 | cd01371 | Kinesin motor domain, kinesins II or KIF3_like proteins; Kinesin motor domain, kinesins II or ... |
367-636 | 6.38e-56 | ||||||
Kinesin motor domain, kinesins II or KIF3_like proteins; Kinesin motor domain, kinesins II or KIF3_like proteins. Subgroup of kinesins, which form heterotrimers composed of 2 kinesins and one non-motor accessory subunit. Kinesins II play important roles in ciliary transport, and have been implicated in neuronal transport, melanosome transport, the secretory pathway, and mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this group the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276822 [Multi-domain] Cd Length: 334 Bit Score: 196.91 E-value: 6.38e-56
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| KIP1 | COG5059 | Kinesin-like protein [Cytoskeleton]; |
392-636 | 9.16e-53 | ||||||
Kinesin-like protein [Cytoskeleton]; Pssm-ID: 227392 [Multi-domain] Cd Length: 568 Bit Score: 194.57 E-value: 9.16e-53
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| KISc_KHC_KIF5 | cd01369 | Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup; Kinesin motor domain, ... |
370-636 | 1.73e-52 | ||||||
Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup; Kinesin motor domain, kinesin heavy chain (KHC) or KIF5-like subgroup. Members of this group have been associated with organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276820 [Multi-domain] Cd Length: 325 Bit Score: 186.77 E-value: 1.73e-52
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| KISc_KIF1A_KIF1B | cd01365 | Kinesin motor domain, KIF1_like proteins; Kinesin motor domain, KIF1_like proteins. KIF1A ... |
390-646 | 9.00e-51 | ||||||
Kinesin motor domain, KIF1_like proteins; Kinesin motor domain, KIF1_like proteins. KIF1A (Unc104) transports synaptic vesicles to the nerve terminal, KIF1B has been implicated in transport of mitochondria. Both proteins are expressed in neurons. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. In contrast to the majority of dimeric kinesins, most KIF1A/Unc104 kinesins are monomeric motors. A lysine-rich loop in KIF1A binds to the negatively charged C-terminus of tubulin and compensates for the lack of a second motor domain, allowing KIF1A to move processively. Pssm-ID: 276816 [Multi-domain] Cd Length: 361 Bit Score: 183.32 E-value: 9.00e-51
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| KISc_BimC_Eg5 | cd01364 | Kinesin motor domain, BimC/Eg5 spindle pole proteins; Kinesin motor domain, BimC/Eg5 spindle ... |
382-636 | 9.91e-49 | ||||||
Kinesin motor domain, BimC/Eg5 spindle pole proteins; Kinesin motor domain, BimC/Eg5 spindle pole proteins, participate in spindle assembly and chromosome segregation during cell division. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type), N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276815 [Multi-domain] Cd Length: 353 Bit Score: 177.13 E-value: 9.91e-49
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| KISc_CENP_E | cd01374 | Kinesin motor domain, CENP-E/KIP2-like subgroup; Kinesin motor domain, CENP-E/KIP2-like ... |
392-636 | 2.97e-48 | ||||||
Kinesin motor domain, CENP-E/KIP2-like subgroup; Kinesin motor domain, CENP-E/KIP2-like subgroup, involved in chromosome movement and/or spindle elongation during mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276825 [Multi-domain] Cd Length: 321 Bit Score: 174.83 E-value: 2.97e-48
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| KISc_KIP3_like | cd01370 | Kinesin motor domain, KIP3-like subgroup; Kinesin motor domain, KIP3-like subgroup. The yeast ... |
392-636 | 5.70e-46 | ||||||
Kinesin motor domain, KIP3-like subgroup; Kinesin motor domain, KIP3-like subgroup. The yeast kinesin KIP3 plays a role in positioning the mitotic spindle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276821 [Multi-domain] Cd Length: 345 Bit Score: 168.68 E-value: 5.70e-46
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| KISc_KIF23_like | cd01368 | Kinesin motor domain, KIF23-like subgroup; Kinesin motor domain, KIF23-like subgroup. Members ... |
390-634 | 1.59e-43 | ||||||
Kinesin motor domain, KIF23-like subgroup; Kinesin motor domain, KIF23-like subgroup. Members of this group may play a role in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276819 [Multi-domain] Cd Length: 345 Bit Score: 161.79 E-value: 1.59e-43
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| KISc_KIF9_like | cd01375 | Kinesin motor domain, KIF9-like subgroup; Kinesin motor domain, KIF9-like subgroup; might play ... |
369-637 | 7.90e-40 | ||||||
Kinesin motor domain, KIF9-like subgroup; Kinesin motor domain, KIF9-like subgroup; might play a role in cell shape remodeling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276826 [Multi-domain] Cd Length: 334 Bit Score: 150.81 E-value: 7.90e-40
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| KISc_KLP2_like | cd01373 | Kinesin motor domain, KIF15-like subgroup; Kinesin motor domain, KIF15-like subgroup. Members ... |
392-637 | 3.50e-39 | ||||||
Kinesin motor domain, KIF15-like subgroup; Kinesin motor domain, KIF15-like subgroup. Members of this subgroup seem to play a role in mitosis and meiosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276824 [Multi-domain] Cd Length: 347 Bit Score: 149.20 E-value: 3.50e-39
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| KISc_KID_like | cd01376 | Kinesin motor domain, KIF22/Kid-like subgroup; Kinesin motor domain, KIF22/Kid-like subgroup. ... |
392-636 | 1.25e-38 | ||||||
Kinesin motor domain, KIF22/Kid-like subgroup; Kinesin motor domain, KIF22/Kid-like subgroup. Members of this group might play a role in regulating chromosomal movement along microtubules in mitosis. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In most kinesins, the motor domain is found at the N-terminus (N-type). N-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second. To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276827 [Multi-domain] Cd Length: 319 Bit Score: 146.88 E-value: 1.25e-38
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| PHD2_PHF1 | cd15582 | PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 ... |
771-822 | 1.98e-36 | ||||||
PHD finger 2 found in PHD finger protein1 (PHF1); PHF1, also termed Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the second PHD finger. Pssm-ID: 277057 Cd Length: 52 Bit Score: 130.84 E-value: 1.98e-36
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| KISc_KIF2_like | cd01367 | Kinesin motor domain, KIF2-like group; Kinesin motor domain, KIF2-like group. KIF2 is a ... |
388-637 | 2.24e-35 | ||||||
Kinesin motor domain, KIF2-like group; Kinesin motor domain, KIF2-like group. KIF2 is a protein expressed in neurons, which has been associated with axonal transport and neuron development; alternative splice forms have been implicated in lysosomal translocation. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Kinesins are microtubule-dependent molecular motors that play important roles in intracellular transport and in cell division. In this subgroup the motor domain is found in the middle (M-type) of the protein chain. M-type kinesins are (+) end-directed motors, i.e. they transport cargo towards the (+) end of the microtubule. Kinesin motor domains hydrolyze ATP at a rate of about 80 per second, and move along the microtubule at a speed of about 6400 Angstroms per second (KIF2 may be slower). To achieve that, kinesin head groups work in pairs. Upon replacing ADP with ATP, a kinesin motor domain increases its affinity for microtubule binding and locks in place. Also, the neck linker binds to the motor domain, which repositions the other head domain through the coiled-coil domain close to a second tubulin dimer, about 80 Angstroms along the microtubule. Meanwhile, ATP hydrolysis takes place, and when the second head domain binds to the microtubule, the first domain again replaces ADP with ATP, triggering a conformational change that pulls the first domain forward. Pssm-ID: 276818 [Multi-domain] Cd Length: 328 Bit Score: 137.43 E-value: 2.24e-35
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| PHD2_MTF2_PHF19_like | cd15503 | PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ... |
771-822 | 3.77e-35 | ||||||
PHD finger 2 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The PCL family includes PHD finger protein1 (PHF1) and its homologs metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD finger of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the second PHD finger. Pssm-ID: 276978 Cd Length: 52 Bit Score: 127.13 E-value: 3.77e-35
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| PLN03188 | PLN03188 | kinesin-12 family protein; Provisional |
437-655 | 1.05e-28 | ||||||
kinesin-12 family protein; Provisional Pssm-ID: 215621 [Multi-domain] Cd Length: 1320 Bit Score: 124.66 E-value: 1.05e-28
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| PHD2_PHF19 | cd15581 | PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ... |
771-820 | 1.21e-27 | ||||||
PHD finger 2 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. It binds H3K36me3 through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the second PHD finger. Pssm-ID: 277056 Cd Length: 52 Bit Score: 105.76 E-value: 1.21e-27
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| PHD2_MTF2 | cd15580 | PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ... |
771-820 | 1.69e-27 | ||||||
PHD finger 2 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or Polycomb-like protein 2 (PCL2), complexes with the Polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two plant homeodomain (PHD) fingers, and a C-terminal MTF2 domain. This model corresponds to the second PHD finger. Pssm-ID: 277055 Cd Length: 52 Bit Score: 105.36 E-value: 1.69e-27
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| PHD1_PHF1 | cd15500 | PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 ... |
672-722 | 4.61e-27 | ||||||
PHD finger 1 found in PHD finger protein1 (PHF1); PHF1, also termed polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of Lysine trimethylation at Lysine 36 of Histone H3 and Lysine 27 of Histone variant H3t. PHF1 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Moreover, PHF1 is required for efficient H3K27me3 and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. This model corresponds to the first PHD finger. Pssm-ID: 276975 Cd Length: 51 Bit Score: 104.14 E-value: 4.61e-27
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| Microtub_bd | pfam16796 | Microtubule binding; This motor homology domain binds microtubules and lacks an ATP-binding ... |
390-450 | 1.23e-18 | ||||||
Microtubule binding; This motor homology domain binds microtubules and lacks an ATP-binding site. Pssm-ID: 465274 [Multi-domain] Cd Length: 144 Bit Score: 83.42 E-value: 1.23e-18
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
202-344 | 1.62e-14 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 78.44 E-value: 1.62e-14
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
208-344 | 1.41e-13 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 75.36 E-value: 1.41e-13
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
214-345 | 2.52e-13 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 74.59 E-value: 2.52e-13
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
192-344 | 2.61e-13 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 74.59 E-value: 2.61e-13
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
208-345 | 4.20e-13 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 73.82 E-value: 4.20e-13
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
192-345 | 1.02e-12 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 71.09 E-value: 1.02e-12
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| Motor_domain | cd01363 | Myosin and Kinesin motor domain; Myosin and Kinesin motor domain. These ATPases belong to the ... |
394-582 | 1.36e-12 | ||||||
Myosin and Kinesin motor domain; Myosin and Kinesin motor domain. These ATPases belong to the P-loop NTPase family and provide the driving force in myosin and kinesin mediated processes. Some of the names do not match with what is given in the sequence list. This is because they are based on the current nomenclature by Kollmar/Sebe-Pedros. Pssm-ID: 276814 [Multi-domain] Cd Length: 170 Bit Score: 66.98 E-value: 1.36e-12
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
199-345 | 2.98e-12 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 71.12 E-value: 2.98e-12
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-339 | 7.23e-12 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 69.70 E-value: 7.23e-12
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| PHD1_MTF2 | cd15578 | PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also ... |
672-724 | 8.87e-12 | ||||||
PHD finger 1 found in metal-response element-binding transcription factor 2 (MTF2); MTF2, also termed metal regulatory transcription factor 2, or metal-response element DNA-binding protein M96, or polycomb-like protein 2 (PCL2), complexes with the polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. This model corresponds to the first PHD finger. Pssm-ID: 277053 Cd Length: 53 Bit Score: 60.87 E-value: 8.87e-12
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| Tudor_PHF1 | cd20449 | Tudor domain found in PHD finger protein1 (PHF1) and similar proteins; PHF1, also called ... |
636-665 | 9.87e-12 | ||||||
Tudor domain found in PHD finger protein1 (PHF1) and similar proteins; PHF1, also called Polycomb-like protein 1 (PCL1), together with JARID2 and AEBP2, associates with the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis, through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF1 is essential in epigenetic regulation and genome maintenance. It acts as a dual reader of lysine trimethylation at lysine 36 of histone H3 and lysine 27 of histone variant H3t. Moreover, PHF1 is required for efficient H3-K27 trimethylation (H3K27me3) and Hox gene silencing. It can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response. PHF1 consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. Its Tudor domain selectively binds to histone H3K36me3. Pssm-ID: 410520 Cd Length: 54 Bit Score: 60.61 E-value: 9.87e-12
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
199-344 | 1.90e-11 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 68.42 E-value: 1.90e-11
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
199-346 | 2.72e-11 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 67.65 E-value: 2.72e-11
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| PHD1_MTF2_PHF19_like | cd15499 | PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ... |
673-724 | 2.91e-11 | ||||||
PHD finger 1 found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins MTF2, PHF19, and similar proteins; The family includes two PCL family proteins, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are homologs of PHD finger protein1 (PHF1). PCL family proteins are accessory components of the polycomb repressive complex 2 (PRC2) core complex and all contain an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. They specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD finger-containing proteins, the first PHD fingers of PCL proteins do not display histone H3K4 binding affinity and they do not affect the Tudor domain binding to histones. This model corresponds to the first PHD finger. Pssm-ID: 276974 Cd Length: 53 Bit Score: 59.44 E-value: 2.91e-11
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
200-346 | 3.82e-11 | ||||||
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]; Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 64.18 E-value: 3.82e-11
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
208-344 | 4.06e-11 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 67.27 E-value: 4.06e-11
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
193-346 | 5.07e-11 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 66.88 E-value: 5.07e-11
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
191-346 | 6.44e-11 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 66.48 E-value: 6.44e-11
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
195-343 | 1.08e-10 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 66.09 E-value: 1.08e-10
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| PHD | pfam00628 | PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar ... |
673-725 | 1.49e-10 | ||||||
PHD-finger; PHD folds into an interleaved type of Zn-finger chelating 2 Zn ions in a similar manner to that of the RING and FYVE domains. Several PHD fingers have been identified as binding modules of methylated histone H3. Pssm-ID: 425785 [Multi-domain] Cd Length: 51 Bit Score: 57.12 E-value: 1.49e-10
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| PHD1_PHF19 | cd15579 | PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein ... |
673-724 | 1.69e-10 | ||||||
PHD finger 1 found in PHD finger protein 19 (PHF19); PHF19, also termed Polycomb-like protein 3 (PCL3), is a component of the polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD fingers, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. This model corresponds to the first PHD finger. Pssm-ID: 277054 Cd Length: 53 Bit Score: 57.20 E-value: 1.69e-10
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
208-344 | 1.74e-10 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 65.34 E-value: 1.74e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-344 | 2.00e-10 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 65.08 E-value: 2.00e-10
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
208-345 | 2.01e-10 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 64.94 E-value: 2.01e-10
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| PHD_Int12 | cd15501 | PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also ... |
673-722 | 2.66e-10 | ||||||
PHD finger found in integrator complex subunit 12 (Int12) and similar proteins; Int12, also termed IntS12, or PHD finger protein 22, is a component of integrator, a multi-protein mediator of small nuclear RNA processing. The integrator complex directly interacts with the C-terminal domain of RNA polymerase II (RNAPII) largest subunit and mediates the 3' end processing of small nuclear RNAs (snRNAs) U1 and U2. Different from other components of integrator, Int12 contains a PHD finger, which is not required for snRNA 3' end cleavage. Instead, Int12 harbors a small microdomain at its N-terminus which is necessary and sufficient for Int12 function; this microdomain facilitates Int12 binding to Int1 and promotes snRNA 3' end formation. Pssm-ID: 276976 Cd Length: 52 Bit Score: 56.58 E-value: 2.66e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
214-342 | 2.83e-10 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 64.69 E-value: 2.83e-10
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
192-344 | 3.35e-10 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 63.00 E-value: 3.35e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
201-342 | 3.71e-10 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 64.31 E-value: 3.71e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
193-344 | 6.45e-10 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 63.54 E-value: 6.45e-10
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| Crescentin | pfam19220 | Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament ... |
192-342 | 6.49e-10 | ||||||
Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament proteins, named crescentin, whose cytoskeletal function is required for the vibrioid and helical shapes of Caulobacter crescentus. Without crescentin, the cells adopt a straight-rod morphology. Crescentin has characteriztic features of IF proteins including the ability to assemble into filaments in vitro without energy or cofactor requirements. In vivo, crescentin forms a helical structure that colocalizes with the inner cell curvatures beneath the cytoplasmic membrane. Pssm-ID: 437057 [Multi-domain] Cd Length: 401 Bit Score: 62.39 E-value: 6.49e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-343 | 7.64e-10 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 63.15 E-value: 7.64e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-344 | 8.46e-10 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 63.15 E-value: 8.46e-10
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-345 | 1.48e-09 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 62.38 E-value: 1.48e-09
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
183-343 | 3.01e-09 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 60.94 E-value: 3.01e-09
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| DR0291 | COG1579 | Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ... |
219-343 | 4.83e-09 | ||||||
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only]; Pssm-ID: 441187 [Multi-domain] Cd Length: 236 Bit Score: 58.01 E-value: 4.83e-09
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
215-343 | 4.98e-09 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 60.46 E-value: 4.98e-09
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| GumC | COG3206 | Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]; |
208-344 | 6.26e-09 | ||||||
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 60.03 E-value: 6.26e-09
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
192-345 | 6.50e-09 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 59.78 E-value: 6.50e-09
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| PHD | smart00249 | PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ... |
673-722 | 6.70e-09 | ||||||
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 52.60 E-value: 6.70e-09
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
192-385 | 7.45e-09 | ||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 59.01 E-value: 7.45e-09
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| Tudor_PCL | cd20385 | Tudor domain found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) ... |
636-665 | 9.94e-09 | ||||||
Tudor domain found in polycomb repressive complex 2 (PRC2)-associated polycomb-like (PCL) family proteins; The PCL family includes PHD finger protein1 (PHF1) and its homologs, metal-response element-binding transcription factor 2 (MTF2/PCL2) and PHF19/PCL3, which are accessory components of the Polycomb repressive complex 2 (PRC2) core complex. Members contain an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. The interaction between their Tudor domains and H3K36me3 is critical for both the targeting and spreading of PRC2 into active chromatin regions and for the maintenance of optimal repression of poised developmental genes where PCL proteins, H3K36me3, and H3K27me3 coexist. Moreover, unlike other PHD domain-containing proteins, the first PHD domains of PCL proteins do not display histone H3K4 binding affinity and they do not affect the binding of the Tudor domain to histones. Pssm-ID: 410456 Cd Length: 54 Bit Score: 52.25 E-value: 9.94e-09
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
203-429 | 2.09e-08 | ||||||
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]; Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 57.53 E-value: 2.09e-08
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-343 | 2.61e-08 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 58.14 E-value: 2.61e-08
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| Tudor_PHF19 | cd20451 | Tudor domain found in PHD finger protein1 (PHF19) and similar proteins; PHF19, also called ... |
636-669 | 2.94e-08 | ||||||
Tudor domain found in PHD finger protein1 (PHF19) and similar proteins; PHF19, also called Polycomb-like protein 3 (PCL3), is a component of the Polycomb repressive complex 2 (PRC2), which is the major H3K27 methyltransferase that regulates pluripotency, differentiation, and tumorigenesis through catalysis of histone H3 lysine 27 trimethylation (H3K27me3) on chromatin. PHF19 consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. It binds trimethylated histone H3 Lys36 (H3K36me3) through its Tudor domain and recruits the PRC2 complex and the H3K36me3 demethylase NO66 to embryonic stem cell genes during differentiation. Moreover, PHF19 and its upstream regulator, Akt, play roles in the phenotype switch of melanoma cells from proliferative to invasive states. Pssm-ID: 410522 Cd Length: 57 Bit Score: 51.16 E-value: 2.94e-08
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| GumC | COG3206 | Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]; |
209-337 | 2.96e-08 | ||||||
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 57.72 E-value: 2.96e-08
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| PHD_Phf1p_Phf2p_like | cd15502 | PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 ... |
672-722 | 3.12e-08 | ||||||
PHD finger found in Schizosaccharomyces pombe SWM histone demethylase complex subunits Phf1 (Phf1p) and Phf2 (Phf2p); Phf1p and Phf2p are components of the SWM histone demethylase complex that specifically demethylates histone H3 at lysine 9 (H3K9me2), a specific tag for epigenetic transcriptional activation. They function as corepressors and play roles in regulating heterochromatin propagation and euchromatic transcription. Both Phf1p and Phf2p contain a plant homeodomain (PHD) finger. Pssm-ID: 276977 Cd Length: 52 Bit Score: 50.90 E-value: 3.12e-08
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
196-345 | 3.51e-08 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 57.76 E-value: 3.51e-08
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
209-343 | 3.77e-08 | ||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 56.70 E-value: 3.77e-08
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| PspA | COG1842 | Phage shock protein A [Transcription, Signal transduction mechanisms]; |
213-333 | 7.38e-08 | ||||||
Phage shock protein A [Transcription, Signal transduction mechanisms]; Pssm-ID: 441447 [Multi-domain] Cd Length: 217 Bit Score: 54.06 E-value: 7.38e-08
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| SH3_and_anchor | TIGR04211 | SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved ... |
210-314 | 1.24e-07 | ||||||
SH3 domain protein; Members of this protein family have a signal peptide, a strongly conserved SH3 domain, a variable region, and then a C-terminal hydrophobic transmembrane alpha helix region. Pssm-ID: 275056 [Multi-domain] Cd Length: 198 Bit Score: 53.09 E-value: 1.24e-07
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| PHD_BRPF_JADE_like | cd15492 | PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; ... |
672-722 | 1.31e-07 | ||||||
PHD finger found in BRPF proteins, Jade proteins, protein AF-10, AF-17, and similar proteins; The family includes BRPF proteins, Jade proteins, protein AF-10 and AF-17. BRPF proteins are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. Jade proteins are required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6, to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor that has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is a putative transcription factor that may play a role in multiple signaling pathways. All Jade proteins, AF-10, and AF-17 contain a canonical PHD finger followed by a non-canonical ePHD finger. This model corresponds to the canonical PHD finger. Pssm-ID: 276967 [Multi-domain] Cd Length: 46 Bit Score: 48.77 E-value: 1.31e-07
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
192-344 | 1.35e-07 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 55.84 E-value: 1.35e-07
|
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
192-336 | 1.53e-07 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 55.84 E-value: 1.53e-07
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| mukB | PRK04863 | chromosome partition protein MukB; |
193-322 | 1.71e-07 | ||||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 55.73 E-value: 1.71e-07
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| PHD_SF | cd15489 | PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ... |
771-820 | 1.77e-07 | ||||||
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies. Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 48.47 E-value: 1.77e-07
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-343 | 1.85e-07 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 55.45 E-value: 1.85e-07
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| Mtf2_C | pfam14061 | Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with ... |
964-993 | 1.89e-07 | ||||||
Polycomb-like MTF2 factor 2; Mammalian Polycomb-like gene MTF2/PCL2 forms a complex with Polycomb repressive complex-2 (PRC2) and collaborates with PRC1 to achieve repression of Hox gene expression. The human MTF2 gene is expressed in three splicing variants, each of them contains the short C-terminal domain defined here. The domain is subject to structure determination by the Joint Center of Structural Genomics. Pssm-ID: 464077 Cd Length: 48 Bit Score: 48.58 E-value: 1.89e-07
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| EnvC | COG4942 | Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ... |
192-346 | 1.91e-07 | ||||||
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 443969 [Multi-domain] Cd Length: 377 Bit Score: 54.38 E-value: 1.91e-07
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
189-329 | 2.74e-07 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 54.92 E-value: 2.74e-07
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| HAP1_N | pfam04849 | HAP1 N-terminal conserved region; This family represents an N-terminal conserved region found ... |
193-329 | 3.22e-07 | ||||||
HAP1 N-terminal conserved region; This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologs. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34. Pssm-ID: 461455 [Multi-domain] Cd Length: 309 Bit Score: 53.11 E-value: 3.22e-07
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
212-346 | 3.26e-07 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 54.57 E-value: 3.26e-07
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| COG1340 | COG1340 | Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; |
192-342 | 3.29e-07 | ||||||
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 52.99 E-value: 3.29e-07
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| GAS | pfam13851 | Growth-arrest specific micro-tubule binding; This family is the highly conserved central ... |
193-337 | 3.43e-07 | ||||||
Growth-arrest specific micro-tubule binding; This family is the highly conserved central region of a number of metazoan proteins referred to as growth-arrest proteins. In mouse, Gas8 is predominantly a testicular protein, whose expression is developmentally regulated during puberty and spermatogenesis. In humans, it is absent in infertile males who lack the ability to generate gametes. The localization of Gas8 in the motility apparatus of post-meiotic gametocytes and mature spermatozoa, together with the detection of Gas8 also in cilia at the apical surfaces of epithelial cells lining the pulmonary bronchi and Fallopian tubes suggests that the Gas8 protein may have a role in the functioning of motile cellular appendages. Gas8 is a microtubule-binding protein localized to regions of dynein regulation in mammalian cells. Pssm-ID: 464001 [Multi-domain] Cd Length: 200 Bit Score: 51.83 E-value: 3.43e-07
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| PHD_SF | cd15489 | PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) ... |
673-722 | 4.62e-07 | ||||||
PHD finger superfamily; The PHD finger superfamily includes a canonical plant homeodomain (PHD) finger typically characterized as Cys4HisCys3, and a non-canonical extended PHD finger, characterized as Cys2HisCys5HisCys2His. Variations include the RAG2 PHD finger characterized by Cys3His2Cys2His and the PHD finger 5 found in nuclear receptor-binding SET domain-containing proteins characterized by Cys4HisCys2His. The PHD finger is also termed LAP (leukemia-associated protein) motif or TTC (trithorax consensus) domain. Single or multiple copies of PHD fingers have been found in a variety of eukaryotic proteins involved in the control of gene transcription and chromatin dynamics. PHD fingers can recognize the unmodified and modified histone H3 tail, and some have been found to interact with non-histone proteins. They also function as epigenome readers controlling gene expression through molecular recruitment of multi-protein complexes of chromatin regulators and transcription factors. The PHD finger domain SF is structurally similar to the RING and FYVE_like superfamilies. Pssm-ID: 276966 [Multi-domain] Cd Length: 48 Bit Score: 47.31 E-value: 4.62e-07
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| MAD | pfam05557 | Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint ... |
221-346 | 4.69e-07 | ||||||
Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated. Pssm-ID: 461677 [Multi-domain] Cd Length: 660 Bit Score: 53.98 E-value: 4.69e-07
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
215-339 | 4.79e-07 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 54.15 E-value: 4.79e-07
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
193-339 | 5.20e-07 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 53.91 E-value: 5.20e-07
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| PHD_ash2p_like | cd15583 | PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and ... |
771-820 | 5.51e-07 | ||||||
PHD finger found in Schizosaccharomyces pombe Set1 complex component ash2 (spAsh2p) and similar proteins; spAsh2p, also termed Set1C component ash2, or COMPASS component ash2, or complex proteins associated with set1 protein ash2, or Lid2 complex component ash2, or Lid2C component ash2, is orthologous to Drosophila melanogaster Ash2 protein. Both spAsh2p and D. melanogaster Ash2 contain a plant homeodomain (PHD) finger and a SPRY domain. In contrast, its counterpart in Saccharomyces cerevisiae, Bre2p, has no PHD finger and is not included in this family. spAsh2p shows histone H3 Lys4 (H3K4) methyltransferase activity through its PHD finger. It also interacts with Lid2p in S. pombe. Human Ash2L contains an atypical PHD finger that lacks part of the Cys4HisCys3 signature characteristic of PHD fingers, it binds to only one zinc ion through the second half of the motif and does not have histone tail binding activity. Pssm-ID: 277058 Cd Length: 50 Bit Score: 46.96 E-value: 5.51e-07
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
190-326 | 6.50e-07 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 53.23 E-value: 6.50e-07
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
193-345 | 6.57e-07 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 52.60 E-value: 6.57e-07
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| PHD_ATX3_4_5_like | cd15495 | PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ... |
673-722 | 8.38e-07 | ||||||
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX3, ATX4, ATX5, and similar proteins; The family includes A. thaliana ATX3 (also termed protein SET domain group 14, or trithorax-homolog protein 3), ATX4 (also termed protein SET domain group 16, or trithorax-homolog protein 4) and ATX5 (also termed protein SET domain group 29, or trithorax-homolog protein 5), which belong to the histone-lysine methyltransferase family. They show distinct phylogenetic origins from the ATX1 and ATX2 family. They are multi-domain containing proteins that consist of an N-terminal PWWP domain, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger. Pssm-ID: 276970 [Multi-domain] Cd Length: 47 Bit Score: 46.60 E-value: 8.38e-07
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| PRK06975 | PRK06975 | bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed |
130-284 | 1.04e-06 | ||||||
bifunctional uroporphyrinogen-III synthetase/uroporphyrin-III C-methyltransferase; Reviewed Pssm-ID: 235899 [Multi-domain] Cd Length: 656 Bit Score: 52.80 E-value: 1.04e-06
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| CwlO1 | COG3883 | Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ... |
171-439 | 1.22e-06 | ||||||
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown]; Pssm-ID: 443091 [Multi-domain] Cd Length: 379 Bit Score: 51.75 E-value: 1.22e-06
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
192-345 | 1.41e-06 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 52.38 E-value: 1.41e-06
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
208-345 | 2.16e-06 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 51.86 E-value: 2.16e-06
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
210-344 | 3.72e-06 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 50.92 E-value: 3.72e-06
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-311 | 3.98e-06 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 51.21 E-value: 3.98e-06
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| MscS_porin | pfam12795 | Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part ... |
219-345 | 4.72e-06 | ||||||
Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. Pssm-ID: 432790 [Multi-domain] Cd Length: 238 Bit Score: 48.84 E-value: 4.72e-06
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-329 | 6.13e-06 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 50.44 E-value: 6.13e-06
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
223-344 | 6.40e-06 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 50.44 E-value: 6.40e-06
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| PHD_JADE3 | cd15681 | PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger ... |
672-726 | 8.41e-06 | ||||||
PHD finger found in protein Jade-3 and similar proteins; Jade-3, also termed PHD finger protein 16 (PHF16), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-3 is required for ING4 and ING5 to associate with histone acetyl transferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-3 contains a canonical Cys4HisCys3 PHD domain followed by a non-canonical extended PHD (ePHD) domain, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277151 [Multi-domain] Cd Length: 50 Bit Score: 43.81 E-value: 8.41e-06
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| YhaN | COG4717 | Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; |
190-343 | 8.67e-06 | ||||||
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown]; Pssm-ID: 443752 [Multi-domain] Cd Length: 641 Bit Score: 49.77 E-value: 8.67e-06
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| sbcc | TIGR00618 | exonuclease SbcC; All proteins in this family for which functions are known are part of an ... |
186-342 | 8.80e-06 | ||||||
exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 49.97 E-value: 8.80e-06
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
217-334 | 8.97e-06 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 50.07 E-value: 8.97e-06
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| PHD_TIF1_like | cd15541 | PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar ... |
673-722 | 1.06e-05 | ||||||
PHD finger found in the transcriptional intermediary factor 1 (TIF1) family and similar proteins; The TIF1 family of transcriptional cofactors includes TIF1alpha (TRIM24), TIF1beta (TRIM28), TIF1gamma (TRIM33), and TIF1delta (TRIM66), which are characterized by an N-terminal RING-finger B-box coiled-coil (RBCC/TRIM) motif and plant homeodomain (PHD) finger followed by a bromodomain in the C-terminal region. TIF1 proteins couple chromatin modifications to transcriptional regulation, signaling, and tumor suppression. They exert a deacetylase-dependent silencing effect when tethered to a promoter region. TIF1alpha, TIF1beta, and TIF1delta can homodimerize and contain a PXVXL motif necessary and sufficient for heterochromatin protein 1(HP1) binding. TIF1alpha and TIF1beta bind nuclear receptors and Kruppel-associated boxes (KRAB) specifically and respectively. In contrast, TIF1delta appears to lack nuclear receptor- and KRAB-binding activity. Moreover, TIF1delta is specifically involved in heterochromatin-mediated gene silencing during postmeiotic phases of spermatogenesis. TIF1gamma is structurally closely related to TIF1alpha and TIF1beta, but has very little functional features in common with them. It does not interact with the KRAB silencing domain of KOX1 or the heterochromatinic proteins HP1alpha, beta, and gamma. It cannot bind to nuclear receptors (NRs). This family also includes Sp100/Sp140 family proteins, the nuclear body SP100 and SP140. Sp110 is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. SP140 is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus viral infectivity factor (Vif) protein. Both Sp110 and Sp140 contain a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). Pssm-ID: 277016 [Multi-domain] Cd Length: 43 Bit Score: 43.49 E-value: 1.06e-05
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| GumC | COG3206 | Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]; |
219-343 | 1.07e-05 | ||||||
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442439 [Multi-domain] Cd Length: 687 Bit Score: 49.63 E-value: 1.07e-05
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| KIP1 | COG5059 | Kinesin-like protein [Cytoskeleton]; |
390-583 | 1.09e-05 | ||||||
Kinesin-like protein [Cytoskeleton]; Pssm-ID: 227392 [Multi-domain] Cd Length: 568 Bit Score: 49.35 E-value: 1.09e-05
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| Crescentin | pfam19220 | Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament ... |
192-336 | 1.29e-05 | ||||||
Crescentin protein; This entry represents a bacterial equivalent to Intermediate Filament proteins, named crescentin, whose cytoskeletal function is required for the vibrioid and helical shapes of Caulobacter crescentus. Without crescentin, the cells adopt a straight-rod morphology. Crescentin has characteriztic features of IF proteins including the ability to assemble into filaments in vitro without energy or cofactor requirements. In vivo, crescentin forms a helical structure that colocalizes with the inner cell curvatures beneath the cytoplasmic membrane. Pssm-ID: 437057 [Multi-domain] Cd Length: 401 Bit Score: 48.91 E-value: 1.29e-05
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| PRK09039 | PRK09039 | peptidoglycan -binding protein; |
196-329 | 2.02e-05 | ||||||
peptidoglycan -binding protein; Pssm-ID: 181619 [Multi-domain] Cd Length: 343 Bit Score: 48.04 E-value: 2.02e-05
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| ATG16 | pfam08614 | Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for ... |
209-336 | 2.05e-05 | ||||||
Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. Pssm-ID: 462536 [Multi-domain] Cd Length: 176 Bit Score: 46.08 E-value: 2.05e-05
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
192-346 | 2.29e-05 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 48.50 E-value: 2.29e-05
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| mukB | PRK04863 | chromosome partition protein MukB; |
212-335 | 2.46e-05 | ||||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 48.41 E-value: 2.46e-05
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
192-340 | 3.04e-05 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 48.14 E-value: 3.04e-05
|
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
193-334 | 3.12e-05 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 48.14 E-value: 3.12e-05
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| PHD2_KMT2B | cd15591 | PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed ... |
672-722 | 3.38e-05 | ||||||
PHD domain 2 found in Histone-lysine N-methyltransferase 2B (KMT2B); KMT2B, also termed trithorax homolog 2 or WW domain-binding protein 7 (WBP-7), is encoded by the gene that was first named myeloid/lymphoid or mixed-lineage leukemia 2 (MLL2), a second human homolog of Drosophila trithorax, located on chromosome 19. It belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2) and is vital for normal mammalian embryonic development. KMT2B functions as the catalytic subunit in the MLL2 complex, which contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL2 complex is highly active and specific for histone 3lysine 4 (H3K4) methylation, which stimulates chromatin transcription in a SAM- and H3K4-dependent manner. Moreover, KMT2B plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. KMT2B contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD), an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger. Pssm-ID: 277066 Cd Length: 50 Bit Score: 42.23 E-value: 3.38e-05
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
208-329 | 3.49e-05 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 47.86 E-value: 3.49e-05
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
201-309 | 3.52e-05 | ||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 44.14 E-value: 3.52e-05
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| mukB | PRK04863 | chromosome partition protein MukB; |
199-321 | 3.56e-05 | ||||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 48.03 E-value: 3.56e-05
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| CALCOCO1 | pfam07888 | Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ... |
186-344 | 3.68e-05 | ||||||
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region. Pssm-ID: 462303 [Multi-domain] Cd Length: 488 Bit Score: 47.58 E-value: 3.68e-05
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
214-339 | 3.82e-05 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 47.99 E-value: 3.82e-05
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| PHD2_KMT2A_like | cd15507 | PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ... |
687-722 | 5.02e-05 | ||||||
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger. Pssm-ID: 276982 Cd Length: 50 Bit Score: 41.68 E-value: 5.02e-05
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| PHD_PRHA_like | cd15504 | PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and ... |
672-722 | 5.07e-05 | ||||||
PHD finger found in Arabidopsis thaliana pathogenesis-related homeodomain protein (PRHA) and similar proteins; PRHA is a homeodomain protein encoded by a single-copy Arabidopsis thaliana homeobox gene, prha. It shows the capacity to bind to TAATTG core sequence elements but requires additional adjacent bases for high-affinity binding. PRHA contains a plant homeodomain (PHD) finger, a homeodomain, peptide repeats and a putative leucine zipper dimerization domain. Pssm-ID: 276979 Cd Length: 53 Bit Score: 41.65 E-value: 5.07e-05
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
223-339 | 5.14e-05 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 47.37 E-value: 5.14e-05
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| PHD_BRPF | cd15572 | PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF ... |
672-723 | 5.16e-05 | ||||||
PHD finger found in bromodomain and PHD finger-containing (BRPF) proteins; The family of BRPF proteins includes BRPF1, BRD1/BRPF2, and BRPF3. They are scaffold proteins that form monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complexes with other regulatory subunits, such as inhibitor of growth 5 (ING5) and Esa1-associated factor 6 ortholog (EAF6). BRPF proteins have multiple domains, including a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277047 [Multi-domain] Cd Length: 54 Bit Score: 41.83 E-value: 5.16e-05
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
192-343 | 5.51e-05 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 47.36 E-value: 5.51e-05
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| CusB_dom_1 | pfam00529 | Cation efflux system protein CusB domain 1; The cation efflux system protein CusB from E. coli ... |
219-345 | 5.88e-05 | ||||||
Cation efflux system protein CusB domain 1; The cation efflux system protein CusB from E. coli can be divided into four different domains, the first three domains of the protein are mostly beta-strands and the fourth forms an all alpha-helical domain. This entry represents the first beta-domain (domain 1) of CusB and it is formed by the N and C-terminal ends of the polypeptide (residues 89-102 and 324-385). CusB is part of the copper-transporting efflux system CusCFBA. This domain can also be found in other membrane-fusion proteins, such as HlyD, MdtN, MdtE and AaeA. HlyD is a component of the prototypical alpha-haemolysin (HlyA) bacterial type I secretion system, along with the other components HlyB and TolC. HlyD is anchored in the cytoplasmic membrane by a single transmembrane domain and has a large periplasmic domain within the carboxy-terminal 100 amino acids, HlyB and HlyD form a stable complex that binds the recombinant protein bearing a C-terminal HlyA signal sequence and ATP in the cytoplasm. HlyD, HlyB and TolC combine to form the three-component ABC transporter complex that forms a trans-membrane channel or pore through which HlyA can be transferred directly to the extracellular medium. Cutinase has been shown to be transported effectively through this pore. Pssm-ID: 425733 [Multi-domain] Cd Length: 322 Bit Score: 46.26 E-value: 5.88e-05
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
192-346 | 6.07e-05 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 46.43 E-value: 6.07e-05
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| Atg16_CCD | cd22887 | Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ... |
269-329 | 6.13e-05 | ||||||
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. Pssm-ID: 439196 [Multi-domain] Cd Length: 91 Bit Score: 42.55 E-value: 6.13e-05
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| CENP-F_leu_zip | pfam10473 | Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Cenp-F, a centromeric kinetochore, ... |
209-294 | 6.75e-05 | ||||||
Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance. Pssm-ID: 463102 [Multi-domain] Cd Length: 140 Bit Score: 43.82 E-value: 6.75e-05
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| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
208-342 | 7.71e-05 | ||||||
Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related proteins, ezrin, radixin and moesin. Ezrin was first identified as a constituent of microvilli, radixin as a barbed, end-capping actin-modulating protein from isolated junctional fractions, and moesin as a heparin binding protein. A tumour suppressor molecule responsible for neurofibromatosis type 2 (NF2) is highly similar to ERM proteins and has been designated merlin (moesin-ezrin-radixin-like protein). ERM molecules contain 3 domains, an N-terminal globular domain, an extended alpha-helical domain and a charged C-terminal domain (pfam00769). Ezrin, radixin and merlin also contain a polyproline linker region between the helical and C-terminal domains. The N-terminal domain is highly conserved and is also found in merlin, band 4.1 proteins and members of the band 4.1 superfamily, designated the FERM domain. ERM proteins crosslink actin filaments with plasma membranes. They co-localize with CD44 at actin filament plasma membrane interaction sites, associating with CD44 via their N-terminal domains and with actin filaments via their C-terminal domains. This is the alpha-helical domain, which is involved in intramolecular masking of protein-protein interaction sites, regulating the activity of this proteins. Pssm-ID: 466641 [Multi-domain] Cd Length: 120 Bit Score: 42.98 E-value: 7.71e-05
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
192-345 | 9.47e-05 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 46.57 E-value: 9.47e-05
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
200-343 | 1.03e-04 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 46.32 E-value: 1.03e-04
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| PHD_BRPF2 | cd15677 | PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar ... |
672-723 | 1.04e-04 | ||||||
PHD finger found in bromodomain and PHD finger-containing protein 2 (BRPF2) and similar proteins; BRPF2, also termed bromodomain-containing protein 1 (BRD1), or BR140-like protein, is encoded by BRL (BR140 Like gene). It is responsible for the bulk of the acetylation of H3K14 and forms a novel monocytic leukemic zinc-finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with HBO1 and ING4. The complex is required for full transcriptional activation of the erythroid-specific regulator genes essential for terminal differentiation and survival of erythroblasts in fetal liver. BRPF2 shows widespread expression and localizes to the nucleus within spermatocytes. It contains a cysteine rich region harboring a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277147 [Multi-domain] Cd Length: 54 Bit Score: 40.77 E-value: 1.04e-04
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| PHD_SP110_140 | cd15626 | PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family ... |
673-722 | 1.05e-04 | ||||||
PHD finger found in the Sp100/Sp140 family of nuclear body components; The Sp100/Sp140 family includes nuclear body proteins SP100, SP140, and similar proteins. Sp110, also termed interferon-induced protein 41/75, or speckled 110 kDa, or transcriptional coactivator Sp110, is a leukocyte-specific component of the nuclear body. It may function as a nuclear hormone receptor transcriptional coactivator that may play a role in inducing differentiation of myeloid cells. It is also involved in resisting intracellular pathogens and functions as an important drug target for preventing intracellular pathogen diseases, such as tuberculosis, hepatic veno-occlusive disease, and intracellular cancers. Sp110 gene polymorphisms may be associated with susceptibility to tuberculosis in Chinese population. Sp110 contains a Sp100-like domain, a SAND domain, a plant homeodomain (PHD) finger, and a bromodomain (BRD). SP140, also termed lymphoid-restricted homolog of Sp100 (LYSp100), or nuclear autoantigen Sp-140, or speckled 140 kDa, is an interferon inducible nuclear leukocyte-specific protein involved in primary biliary cirrhosis and a risk factor in chronic lymphocytic leukemia. It is also implicated in innate immune response to human immunodeficiency virus type 1 (HIV-1) by binding to the virus's viral infectivity factor (Vif) protein. Sp140 contains a nuclear localization signal, a dimerization domain (HSR or CARD domain), a SAND domain, a PHD finger, and a BRD. Pssm-ID: 277096 Cd Length: 42 Bit Score: 40.49 E-value: 1.05e-04
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
208-318 | 1.11e-04 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 46.08 E-value: 1.11e-04
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
209-339 | 1.23e-04 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 46.19 E-value: 1.23e-04
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| PHD_UBR7 | cd15542 | PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, ... |
771-820 | 1.35e-04 | ||||||
PHD finger found in putative E3 ubiquitin-protein ligase UBR7; UBR7, also termed N-recognin-7, is a UBR box-containing protein that belongs to the E3 ubiquitin ligase family that recognizes N-degrons or structurally related molecules for ubiquitin-dependent proteolysis or related processes through the UBR box motif. In addition to the UBR box, UBR7 also harbors a plant homeodomain (PHD) finger. The biochemical properties of UBR7 remain unclear. Pssm-ID: 277017 Cd Length: 54 Bit Score: 40.43 E-value: 1.35e-04
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| sbcc | TIGR00618 | exonuclease SbcC; All proteins in this family for which functions are known are part of an ... |
220-313 | 1.52e-04 | ||||||
exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 45.73 E-value: 1.52e-04
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
215-344 | 1.57e-04 | ||||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 45.42 E-value: 1.57e-04
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
214-342 | 1.84e-04 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 45.71 E-value: 1.84e-04
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| PHD_BRPF1 | cd15676 | PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar ... |
665-723 | 2.03e-04 | ||||||
PHD finger found in bromodomain and PHD finger-containing protein 1 (BRPF1) and similar proteins; BRPF1, also termed peregrin or protein Br140, is a multi-domain protein that binds histones, mediates monocytic leukemic zinc-finger protein (MOZ)-dependent histone acetylation, and is required for Hox gene expression and segmental identity. It is a close partner of the MOZ histone acetyltransferase (HAT) complex and a novel Trithorax group (TrxG) member with a central role during development. BRPF1 is primarily a nuclear protein that has a broad tissue distribution and is abundant in testes and spermatogonia. It contains a canonical Cys4HisCys3 plant homeodomain (PHD) zinc finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain and a proline-tryptophan-tryptophan-proline (PWWP) domain. PHD and ePHD fingers both bind to lysine 4 of histone H3 (K4H3), bromodomains interact with acetylated lysines on N-terminal tails of histones and other proteins, and PWWP domains show histone-binding and chromatin association properties. BRPF1 may be involved in chromatin remodeling. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277146 [Multi-domain] Cd Length: 62 Bit Score: 40.42 E-value: 2.03e-04
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
197-345 | 2.04e-04 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 45.55 E-value: 2.04e-04
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| growth_prot_Scy | NF041483 | polarized growth protein Scy; |
227-346 | 2.31e-04 | ||||||
polarized growth protein Scy; Pssm-ID: 469371 [Multi-domain] Cd Length: 1293 Bit Score: 45.20 E-value: 2.31e-04
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
196-344 | 2.35e-04 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 45.03 E-value: 2.35e-04
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
193-322 | 2.44e-04 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 45.33 E-value: 2.44e-04
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| PHD_JADE1 | cd15679 | PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger ... |
672-722 | 2.57e-04 | ||||||
PHD finger found in protein Jade-1 and similar proteins; Jade-1, also termed PHD finger protein 17 (PHF17), is a novel binding partner of von Hippel-Lindau (VHL) tumor suppressor Pvhl, a key regulator of the cellular oxygen sensing pathway. It is highly expressed in renal proximal tubules. Jade-1 functions as an essential regulator of multiple cell signaling pathways. It may be involved in the serine/threonine kinase AKT/AKT1 pathway during renal cancer pathogenesis and normally prevents renal epithelial cell proliferation and transformation. It also acts as a pro-apoptotic and growth suppressive ubiquitin ligase to inhibit canonical Wnt downstream effector beta-catenin for proteasomal degradation, and as a transcription factor associated with histone acetyltransferase activity and with increased abundance of cyclin-dependent kinase inhibitor p21. Moreover, Jade-1 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex, and plays a role in epithelial cell regeneration. It has also been identified as a novel component of the nephrocystin protein (NPHP) complex and interacts with the ciliary protein nephrocystin-4 (NPHP4). Jade-1 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277149 [Multi-domain] Cd Length: 46 Bit Score: 39.67 E-value: 2.57e-04
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
192-342 | 2.74e-04 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 45.17 E-value: 2.74e-04
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| GOLGA2L5 | pfam15070 | Putative golgin subfamily A member 2-like protein 5; The function of the GOLGA2L5 protein ... |
203-332 | 2.83e-04 | ||||||
Putative golgin subfamily A member 2-like protein 5; The function of the GOLGA2L5 protein family remains unknown. This family of proteins is thought to be found in the Golgi apparatus of eukaryotes. Pssm-ID: 464485 [Multi-domain] Cd Length: 521 Bit Score: 44.67 E-value: 2.83e-04
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| MAD | pfam05557 | Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint ... |
209-339 | 2.86e-04 | ||||||
Mitotic checkpoint protein; This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in yeast and higher eukaryotes. In S.cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated. Pssm-ID: 461677 [Multi-domain] Cd Length: 660 Bit Score: 44.73 E-value: 2.86e-04
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| PHD_JADE2 | cd15680 | PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger ... |
672-722 | 3.34e-04 | ||||||
PHD finger found in protein Jade-2 and similar proteins; Jade-2, also termed PHD finger protein 15 (PHF15), is a plant homeodomain (PHD) zinc finger protein that is closely related to Jade-1, which functions as an essential regulator of multiple cell signaling pathways. Like Jade-1, Jade-2 is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and Eaf6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. Jade-2 contains a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277150 [Multi-domain] Cd Length: 46 Bit Score: 39.22 E-value: 3.34e-04
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| PHD2_KMT2A | cd15590 | PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, ... |
686-722 | 3.60e-04 | ||||||
PHD finger 2 found in histone-lysine N-methyltransferase 2A (KMT2A); KMT2A (also termed ALL-1, CXXC-type zinc finger protein 7, myeloid/lymphoid or mixed-lineage leukemia protein 1 (MLL1), trithorax-like protein (Htrx), or zinc finger protein HRX) is a histone methyltransferase that belongs to the MLL subfamily of H3K4-specific histone lysine methyltransferases (KMT2). It regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex, which also contains WDR5, RbBP5, ASH2L and DPY30 as integral core subunits required for the efficient methylation activity of the complex. The MLL1 complex is highly active and specific for H3K4 methylation. KMT2A contains a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, a Bromodomain domain, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the second PHD finger. Pssm-ID: 277065 Cd Length: 50 Bit Score: 39.24 E-value: 3.60e-04
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| Tudor_MTF2 | cd20450 | Tudor domain found in metal-response element-binding transcription factor 2 (MTF2) and similar ... |
625-665 | 3.93e-04 | ||||||
Tudor domain found in metal-response element-binding transcription factor 2 (MTF2) and similar proteins; MTF2, also called metal regulatory transcription factor 2, metal-response element DNA-binding protein M96, or Polycomb-like protein 2 (PCL2), complexes with the Polycomb repressive complex-2 (PRC2) in embryonic stem cells and regulates the transcriptional networks during embryonic stem cell self-renewal and differentiation. It recruits the PRC2 complex to the inactive X chromosome and target loci in embryonic stem cells. Moreover, MTF2 is required for PRC2-mediated Hox cluster repression. It activates the Cdkn2a gene and promotes cellular senescence, thus suppressing the catalytic activity of PRC2 locally. MTF2, like other PCL family proteins, consists of an N-terminal Tudor domain followed by two PHD domains, and a C-terminal MTF2 domain. PCL proteins specifically recognize tri-methylated H3K36 (H3K36me3) through their N-terminal Tudor domains. Pssm-ID: 410521 Cd Length: 54 Bit Score: 39.24 E-value: 3.93e-04
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| DUF4686 | pfam15742 | Domain of unknown function (DUF4686); This family of proteins is found in eukaryotes. Proteins ... |
201-329 | 4.12e-04 | ||||||
Domain of unknown function (DUF4686); This family of proteins is found in eukaryotes. Proteins in this family are typically between 498 and 775 amino acids in length. There is a conserved DLK sequence motif. Pssm-ID: 464838 [Multi-domain] Cd Length: 384 Bit Score: 43.90 E-value: 4.12e-04
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| MscS_porin | pfam12795 | Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part ... |
209-343 | 4.44e-04 | ||||||
Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. Pssm-ID: 432790 [Multi-domain] Cd Length: 238 Bit Score: 43.06 E-value: 4.44e-04
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| rad50 | TIGR00606 | rad50; All proteins in this family for which functions are known are involvedin recombination, ... |
182-346 | 4.44e-04 | ||||||
rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). Pssm-ID: 129694 [Multi-domain] Cd Length: 1311 Bit Score: 44.27 E-value: 4.44e-04
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| MscS_porin | pfam12795 | Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part ... |
199-345 | 5.82e-04 | ||||||
Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. Pssm-ID: 432790 [Multi-domain] Cd Length: 238 Bit Score: 42.67 E-value: 5.82e-04
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| PRK09039 | PRK09039 | peptidoglycan -binding protein; |
192-334 | 6.14e-04 | ||||||
peptidoglycan -binding protein; Pssm-ID: 181619 [Multi-domain] Cd Length: 343 Bit Score: 43.03 E-value: 6.14e-04
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
216-343 | 6.23e-04 | ||||||
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 43.40 E-value: 6.23e-04
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| ATG16 | pfam08614 | Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for ... |
218-341 | 6.63e-04 | ||||||
Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. Pssm-ID: 462536 [Multi-domain] Cd Length: 176 Bit Score: 41.46 E-value: 6.63e-04
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| PHD_PHF2_like | cd15554 | PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar ... |
771-798 | 7.62e-04 | ||||||
PHD finger found in PHF2, PHF8 and KDM7; This family includes PHF2, PHF8, KDM7, and similar proteins. PHF2, also termed GRC5, or PHD finger protein 2, is a histone lysine demethylase ubiquitously expressed in various tissues. PHF8, also termed PHD finger protein 8, or KDM7B, is a monomethylated histone H4 lysine 20(H4K20me1) demethylase that transcriptionally regulates many cell cycle genes. It also preferentially acts on H3K9me2 and H3K9me1. PHF8 is modulated by CDC20-containing anaphase-promoting complex (APC (cdc20)) and plays an important role in the G2/M transition. It acts as a critical molecular sensor for mediating retinoic acid (RA) treatment response in RAR alpha-fusion-induced leukemia. Moreover, PHF8 is essential for cytoskeleton dynamics and is associated with X-linked mental retardation. KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. All family members contain a plant homeodomain (PHD) finger and a JmjC domain. Pssm-ID: 277029 Cd Length: 47 Bit Score: 38.13 E-value: 7.62e-04
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
214-346 | 8.26e-04 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 43.63 E-value: 8.26e-04
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| KpsE | COG3524 | Capsule polysaccharide export protein KpsE/RkpR [Cell wall/membrane/envelope biogenesis]; |
218-345 | 8.37e-04 | ||||||
Capsule polysaccharide export protein KpsE/RkpR [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442746 [Multi-domain] Cd Length: 370 Bit Score: 42.92 E-value: 8.37e-04
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
190-345 | 8.63e-04 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 43.49 E-value: 8.63e-04
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| Laminin_I | pfam06008 | Laminin Domain I; coiled-coil structure. It has been suggested that the domains I and II from ... |
194-343 | 9.78e-04 | ||||||
Laminin Domain I; coiled-coil structure. It has been suggested that the domains I and II from laminin A, B1 and B2 may come together to form a triple helical coiled-coil structure. Pssm-ID: 310534 [Multi-domain] Cd Length: 258 Bit Score: 42.01 E-value: 9.78e-04
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| COG4372 | COG4372 | Uncharacterized protein, contains DUF3084 domain [Function unknown]; |
190-344 | 9.82e-04 | ||||||
Uncharacterized protein, contains DUF3084 domain [Function unknown]; Pssm-ID: 443500 [Multi-domain] Cd Length: 370 Bit Score: 42.58 E-value: 9.82e-04
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| mukB | PRK04863 | chromosome partition protein MukB; |
199-334 | 1.01e-03 | ||||||
chromosome partition protein MukB; Pssm-ID: 235316 [Multi-domain] Cd Length: 1486 Bit Score: 43.41 E-value: 1.01e-03
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
196-299 | 1.02e-03 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 43.40 E-value: 1.02e-03
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| COG1340 | COG1340 | Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; |
214-314 | 1.04e-03 | ||||||
Uncharacterized coiled-coil protein, contains DUF342 domain [Function unknown]; Pssm-ID: 440951 [Multi-domain] Cd Length: 297 Bit Score: 42.21 E-value: 1.04e-03
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| PRK10929 | PRK10929 | putative mechanosensitive channel protein; Provisional |
208-339 | 1.07e-03 | ||||||
putative mechanosensitive channel protein; Provisional Pssm-ID: 236798 [Multi-domain] Cd Length: 1109 Bit Score: 43.12 E-value: 1.07e-03
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| PHD_JADE | cd15573 | PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family ... |
672-722 | 1.08e-03 | ||||||
PHD finger found in proteins Jade-1, Jade-2, Jade-3, and similar proteins; This family includes proteins Jade-1 (PHF17), Jade-2 (PHF15), and Jade-3 (PHF16), each of which is required for ING4 and ING5 to associate with histone acetyltransferase (HAT) HBO1 and EAF6 to form a HBO1 complex that has a histone H4-specific acetyltransferase activity, a reduced activity toward histone H3, and is responsible for the bulk of histone H4 acetylation in vivo. This family also contains Drosophila melanogaster PHD finger protein rhinoceros (RNO). It is a novel plant homeodomain (PHD)-containing nuclear protein that may function as a transcription factor that antagonizes Ras signaling by regulating transcription of key EGFR/Ras pathway regulators in the Drosophila eye. All Jade proteins contain a canonical Cys4HisCys3 PHD finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, both of which are zinc-binding motifs. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277048 [Multi-domain] Cd Length: 46 Bit Score: 37.77 E-value: 1.08e-03
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| GBP_C | cd16269 | Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ... |
224-329 | 1.20e-03 | ||||||
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines. Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 42.18 E-value: 1.20e-03
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| Smc | COG1196 | Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ... |
192-343 | 1.25e-03 | ||||||
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 440809 [Multi-domain] Cd Length: 983 Bit Score: 43.00 E-value: 1.25e-03
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| PHD2_KAT6A_6B | cd15527 | PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, ... |
673-722 | 1.39e-03 | ||||||
PHD finger 2 found in monocytic leukemia zinc-finger protein (MOZ) and its factor (MORF); MOZ, also termed histone acetyltransferase KAT6A, YBF2/SAS3, SAS2 and TIP60 protein 3 (MYST-3), or runt-related transcription factor-binding protein 2, or zinc finger protein 220, is a MYST-type histone acetyltransferase (HAT) that functions as a coactivator for acute myeloid leukemia 1 protein (AML1)- and p53-dependent transcription. It possesses intrinsic HAT activity to acetylate both itself and lysine (K) residues on histone H2B, histone H3 (K14) and histone H4 (K5, K8, K12 and K16) in vitro and H3K9 in vivo. MOZ-related factor (MORF), also termed MOZ2, or histone acetyltransferase KAT6B, or MOZ, YBF2/SAS3, SAS2 and TIP60 protein 4 (MYST4), is a ubiquitously expressed transcriptional regulator with intrinsic HAT activity. It can interact with the Runt-domain transcription factor Runx2 and form a tetrameric complex with BRPFs, ING5, and EAF6. Both MOZ and MORF are catalytic subunits of HAT complexes that are required for normal developmental programs, such as hematopoiesis, neurogenesis, and skeletogenesis, and are also implicated in human leukemias. MOZ is also the catalytic subunit of a tetrameric inhibitor of growth 5 (ING5) complex, which specifically acetylates nucleosomal histone H3K14. Moreover, MOZ and MORF are involved in regulating transcriptional activation mediated by Runx2 (or Cbfa1), a Runt-domain transcription factor known to play important roles in T cell lymphomagenesis and bone development, and its homologs. MOZ contains a linker histone 1 and histone 5 domains and two plant homeodomain (PHD) fingers. In contrast, MORF contains an N-terminal region containing two PHD fingers, a putative HAT domain, an acidic region, and a C-terminal Ser/Met-rich domain. The family corresponds to the first PHD finger. Pssm-ID: 277002 Cd Length: 46 Bit Score: 37.36 E-value: 1.39e-03
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| TPR_MLP1_2 | pfam07926 | TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of ... |
193-304 | 1.41e-03 | ||||||
TPR/MLP1/MLP2-like protein; The sequences featured in this family are similar to a region of human TPR protein and to yeast myosin-like proteins 1 (MLP1) and 2 (MLP2). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores. TPR is thought to be a component of nuclear pore complex- attached intra-nuclear filaments, and is implicated in nuclear protein import. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerization of kinase domains or by targeting these kinases to the nuclear pore complex. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity. Pssm-ID: 462316 [Multi-domain] Cd Length: 129 Bit Score: 39.93 E-value: 1.41e-03
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
199-339 | 1.41e-03 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 42.72 E-value: 1.41e-03
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| PRK10246 | PRK10246 | exonuclease subunit SbcC; Provisional |
214-345 | 1.42e-03 | ||||||
exonuclease subunit SbcC; Provisional Pssm-ID: 182330 [Multi-domain] Cd Length: 1047 Bit Score: 42.87 E-value: 1.42e-03
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| PHD_TIF1alpha | cd15622 | PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also ... |
673-722 | 1.46e-03 | ||||||
PHD finger found in transcription intermediary factor 1-alpha (TIF1-alpha); TIF1-alpha, also termed tripartite motif-containing protein 24 (TRIM24), or E3 ubiquitin-protein ligase TRIM24, or RING finger protein 82, belongs to the TRIM/RBCC protein family. It interacts specifically and in a ligand-dependent manner with the ligand binding domain (LBD) of several nuclear receptors (NRs), including retinoid X (RXR), retinoic acid (RAR), vitamin D3 (VDR), estrogen (ER), and progesterone (PR) receptors. It also associates with heterochromatin-associated factors HP1alpha, MOD1 (HP1beta) and MOD2 (HP1gamma), as well as vertebrate Kruppel-type (C2H2) zinc finger proteins that contain transcriptional silencing domain KRAB. TIF1-alpha is a ligand-dependent co-repressor of retinoic acid receptor (RAR) that interacts with multiple nuclear receptors in vitro via an LXXLL motif, and further acts as a gatekeeper of liver carcinogenesis. It also functions as an E3-ubiquitin ligase targeting p53 and is broadly associated with chromatin silencing. Moreover, it is a chromatin regulator that recognizes specific, combinatorial histone modifications through its C-terminal plant homeodomain (PHD)-Bromodomain (Bromo) region. In addition, it interacts with chromatin and estrogen receptor to activate estrogen-dependent genes associated with cellular proliferation and tumor development. TIF1-alpha contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region. Pssm-ID: 277092 Cd Length: 43 Bit Score: 37.35 E-value: 1.46e-03
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| PHD_BRPF3 | cd15678 | PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar ... |
672-723 | 1.46e-03 | ||||||
PHD finger found in bromodomain and PHD finger-containing protein 3 (BRPF3) and similar proteins; BRPF3 is a homolog of BRPF1 and BRPF2. It is a scaffold protein that forms a novel monocytic leukemic zinc finger protein (MOZ)/MOZ-related factor (MORF) H3 histone acetyltransferase (HAT) complex with other regulatory subunits. BRPF3 contains a canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, a bromodomain, and a proline-tryptophan-tryptophan-proline (PWWP) domain. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277148 [Multi-domain] Cd Length: 55 Bit Score: 37.69 E-value: 1.46e-03
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
226-343 | 1.49e-03 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 42.74 E-value: 1.49e-03
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| PHD3_PHF14 | cd15563 | PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel ... |
673-722 | 1.52e-03 | ||||||
PHD finger 3 found in PHD finger protein 14 (PHF14) and similar proteins; PHF14 is a novel nuclear transcription factor that controls the proliferation of mesenchymal cells by directly repressing platelet-derived growth factor receptor-alpha (PDGFRalpha) expression. It also acts as an epigenetic regulator and plays an important role in the development of multiple organs in mammals. PHF14 contains three canonical plant homeodomain (PHD) fingers and a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. It can interact with histones through its PHD fingers. The model corresponds to the third PHD finger. Pssm-ID: 277038 Cd Length: 49 Bit Score: 37.37 E-value: 1.52e-03
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
199-343 | 1.53e-03 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 42.63 E-value: 1.53e-03
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| COG5141 | COG5141 | PHD zinc finger-containing protein [General function prediction only]; |
591-725 | 1.59e-03 | ||||||
PHD zinc finger-containing protein [General function prediction only]; Pssm-ID: 227470 [Multi-domain] Cd Length: 669 Bit Score: 42.28 E-value: 1.59e-03
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| PHD_KDM7 | cd15640 | PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC ... |
771-800 | 1.65e-03 | ||||||
PHD finger found in lysine-specific demethylase 7 (KDM7); KDM7, also termed JmjC domain-containing histone demethylation protein 1D (JHDM1D), or KIAA1718, is a dual histone demethylase that catalyzes demethylation of monomethylated and dimethylated H3K9 (H3K9me2/me1) and H3K27 (H3K27me2/me1), which functions as an eraser of silencing marks on chromatin during brain development. It also plays a tumor-suppressive role by regulating angiogenesis. KDM7 contains a plant homeodomain (PHD) that binds Lys4-trimethylated histone 3 (H3K4me3) and a jumonji domain that demethylates either H3K9me2 or H3K27me2. Pssm-ID: 277110 Cd Length: 50 Bit Score: 37.27 E-value: 1.65e-03
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| PRK04778 | PRK04778 | septation ring formation regulator EzrA; Provisional |
216-308 | 1.70e-03 | ||||||
septation ring formation regulator EzrA; Provisional Pssm-ID: 179877 [Multi-domain] Cd Length: 569 Bit Score: 42.13 E-value: 1.70e-03
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| PHD_AF10_AF17 | cd15574 | PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. ... |
673-722 | 1.73e-03 | ||||||
PHD finger found in protein AF-10 and AF-17; This family includes protein AF-10 and AF-17. AF-10, also termed ALL1 (acute lymphoblastic leukemia)-fused gene from chromosome 10 protein, is a transcription factor encoded by gene AF10, a translocation partner of the MLL (mixed-lineage leukemia) oncogene in leukemia. AF-10 has been implicated in the development of leukemia following chromosomal rearrangements between the AF10 gene and one of at least two other genes, MLL and CALM. It plays a key role in the survival of uncommitted hematopoietic cells. Moreover, AF-10 functions as a follistatin-related gene (FLRG)-interacting protein. The interaction with FLRG enhances AF10-dependent transcription. It interacts with the human counterpart of the yeast Dot1, hDOT1L, and may act as a bridge for the recruitment of hDOT1L to the genes targeted by MLL-AF10. It also interacts with the synovial sarcoma associated SYT protein and may play a role in synovial sarcomas and acute leukemias. AF-17, also termed ALL1-fused gene from chromosome 17 protein, is encoded by gene AF17 that has been identified in hematological malignancies as translocation partners of the mixed lineage leukemia gene MLL. It is a putative transcription factor that may play a role in multiple signaling pathways. It is involved in chromatin-mediated gene regulation mechanisms. It functions as a component of the multi-subunit Dot1 complex (Dotcom) and plays a role in the Wnt/Wingless signaling pathway. It also seems to be a downstream target of the beta-catenin/T-cell factor pathway, and participates in G2-M progression. Moreover, it may function as an important regulator of ENaC-mediated Na+ transport and thus blood pressure. Both AF-10 and AF-17 contain an N-terminal canonical Cys4HisCys3 plant homeodomain (PHD) finger followed by a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His. The PHD finger is involved in their homo-oligomerization. In the C-terminal region, they possess a leucine zipper domain and a glutamine-rich region. This family also includes ZFP-1, the Caenorhabditis elegans AF10 homolog. It was originally identified as a factor promoting RNAi interference in C. elegans. It also acts as a Dot1-interacting protein that opposes H2B ubiquitination to reduce polymerase II (Pol II) transcription. This model corresponds to the canonical Cys4HisCys3 PHD finger. Pssm-ID: 277049 [Multi-domain] Cd Length: 48 Bit Score: 37.11 E-value: 1.73e-03
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| sbcc | TIGR00618 | exonuclease SbcC; All proteins in this family for which functions are known are part of an ... |
193-345 | 1.87e-03 | ||||||
exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair] Pssm-ID: 129705 [Multi-domain] Cd Length: 1042 Bit Score: 42.26 E-value: 1.87e-03
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| PRK10246 | PRK10246 | exonuclease subunit SbcC; Provisional |
193-340 | 2.13e-03 | ||||||
exonuclease subunit SbcC; Provisional Pssm-ID: 182330 [Multi-domain] Cd Length: 1047 Bit Score: 42.09 E-value: 2.13e-03
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| PRK11281 | PRK11281 | mechanosensitive channel MscK; |
192-340 | 2.14e-03 | ||||||
mechanosensitive channel MscK; Pssm-ID: 236892 [Multi-domain] Cd Length: 1113 Bit Score: 42.21 E-value: 2.14e-03
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| CALCOCO1 | pfam07888 | Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are ... |
209-333 | 2.52e-03 | ||||||
Calcium binding and coiled-coil domain (CALCOCO1) like; Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein coexpressed by Mus musculus (CoCoA/CALCOCO1). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1, and thus enhances transcriptional activation by a number of nuclear receptors. CALCOCO1 has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region. Pssm-ID: 462303 [Multi-domain] Cd Length: 488 Bit Score: 41.42 E-value: 2.52e-03
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| DUF3584 | pfam12128 | Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. ... |
207-339 | 2.57e-03 | ||||||
Protein of unknown function (DUF3584); This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 943 to 1234 amino acids in length. This family contains a P-loop motif suggesting it is a nucleotide binding protein. It may be involved in replication. Pssm-ID: 432349 [Multi-domain] Cd Length: 1191 Bit Score: 41.75 E-value: 2.57e-03
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| DUF5401 | pfam17380 | Family of unknown function (DUF5401); This is a family of unknown function found in ... |
205-344 | 2.58e-03 | ||||||
Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea. Pssm-ID: 375164 [Multi-domain] Cd Length: 722 Bit Score: 41.65 E-value: 2.58e-03
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| DUF4670 | pfam15709 | Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins ... |
208-333 | 2.61e-03 | ||||||
Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length. Pssm-ID: 464815 [Multi-domain] Cd Length: 522 Bit Score: 41.48 E-value: 2.61e-03
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
193-342 | 2.68e-03 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 41.70 E-value: 2.68e-03
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| GimC | COG1382 | Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]; |
214-310 | 2.69e-03 | ||||||
Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440992 [Multi-domain] Cd Length: 121 Bit Score: 38.72 E-value: 2.69e-03
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| PHD1_KMT2A_like | cd15506 | PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This ... |
672-722 | 2.85e-03 | ||||||
PHD finger 1 found in histone-lysine N-methyltransferase 2A (KMT2A) and 2B (KMT2B); This family includes histone-lysine N-methyltransferase trithorax (Trx) like proteins, KMT2A (MLL1) and KMT2B (MLL2), which comprise the mammalian Trx branch of the COMPASS family, and are both essential for mammalian embryonic development. KMT2A regulates chromatin-mediated transcription through the catalysis of methylation of histone 3 lysine 4 (H3K4), and is frequently rearranged in acute leukemia. KMT2A functions as the catalytic subunit in the MLL1 complex. KMT2B is a second human homolog of Drosophila trithorax, located on chromosome 19 and functions as the catalytic subunit in the MLL2 complex. It plays a critical role in memory formation through mediating hippocampal H3K4 di- and trimethylation. It is also required for RNA polymerase II association and protection from DNA methylation at the MagohB CpG island promoter. Both KMT2A and KMT2B contain a CxxC (x for any residue) zinc finger domain, three plant homeodomain (PHD) fingers, an extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, two FY (phenylalanine tyrosine)-rich domains, and a SET (Suppressor of variegation, Enhancer of zeste, Trithorax) domain. This model corresponds to the first PHD finger. Pssm-ID: 276981 Cd Length: 47 Bit Score: 36.57 E-value: 2.85e-03
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| Borrelia_P83 | pfam05262 | Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins. |
194-333 | 2.86e-03 | ||||||
Borrelia P83/100 protein; This family consists of several Borrelia P83/P100 antigen proteins. Pssm-ID: 114011 [Multi-domain] Cd Length: 489 Bit Score: 41.53 E-value: 2.86e-03
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| PHD_ATX1_2_like | cd15494 | PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis ... |
673-722 | 3.10e-03 | ||||||
PHD finger found in Arabidopsis thaliana histone-lysine N-methyltransferase arabidopsis trithorax-like protein ATX1, ATX2, and similar proteins; The family includes A. thaliana ATX1 and ATX2, both of which are sister paralogs originating from a segmental chromosomal duplication. They are plant counterparts of the Drosophila melanogaster trithorax (TRX) and mammalian mixed-lineage leukemia (MLL1) proteins. ATX1, also termed protein SET domain group 27, or trithorax-homolog protein 1 (TRX-homolog protein 1), is a methyltransferase that trimethylates histone H3 at lysine 4 (H3K4me3). It also acts as a histone modifier and as a positive effector of gene expression. ATX1regulates transcription from diverse classes of genes implicated in biotic and abiotic stress responses. It is involved in dehydration stress signaling in both abscisic acid (ABA)-dependent and ABA-independent pathways. ATX2, also termed protein SET domain group 30, or trithorax-homolog protein 2 (TRX-homolog protein 2), is involved in dimethylating histone H3 at lysine 4 (H3K4me2). Both ATX1 and ATX2 are multi-domain containing proteins that consist of an N-terminal PWWP domain, FYRN- and FYRC (DAST, domain associated with SET in trithorax) domains, a canonical Cys4HisCys3 plant homeodomain (PHD) finger, a non-canonical extended PHD (ePHD) finger, Cys2HisCys5HisCys2His, and a C-terminal SET domain; this model corresponds to the Cys4HisCys3 canonical PHD finger. Pssm-ID: 276969 Cd Length: 47 Bit Score: 36.66 E-value: 3.10e-03
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| UPF0242 | pfam06785 | Uncharacterized protein family (UPF0242) N-terminus; This region includes an N-terminal ... |
221-309 | 3.59e-03 | ||||||
Uncharacterized protein family (UPF0242) N-terminus; This region includes an N-terminal transmembrane region and a C-terminal coiled-coil. Pssm-ID: 429117 [Multi-domain] Cd Length: 194 Bit Score: 39.80 E-value: 3.59e-03
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| SMC_N | pfam02463 | RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ... |
193-345 | 3.66e-03 | ||||||
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination. Pssm-ID: 426784 [Multi-domain] Cd Length: 1161 Bit Score: 41.50 E-value: 3.66e-03
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| RpnC | COG5464 | Recombination-promoting DNA endonuclease RpnC/YadD [Replication, recombination and repair]; |
215-337 | 3.77e-03 | ||||||
Recombination-promoting DNA endonuclease RpnC/YadD [Replication, recombination and repair]; Pssm-ID: 444215 [Multi-domain] Cd Length: 301 Bit Score: 40.33 E-value: 3.77e-03
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
208-345 | 3.84e-03 | ||||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 40.79 E-value: 3.84e-03
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
199-311 | 3.94e-03 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 41.48 E-value: 3.94e-03
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| HMMR_N | pfam15905 | Hyaluronan mediated motility receptor N-terminal; HMMR_N is the N-terminal region of ... |
219-339 | 4.14e-03 | ||||||
Hyaluronan mediated motility receptor N-terminal; HMMR_N is the N-terminal region of eukaryotic hyaluronan-mediated motility receptor proteins. The protein is functionally associated with BRCA1 and thus predicted to be a common, low-penetrance breast cancer candidate. Pssm-ID: 464932 [Multi-domain] Cd Length: 329 Bit Score: 40.56 E-value: 4.14e-03
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| GBP_C | pfam02841 | Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral ... |
228-328 | 4.19e-03 | ||||||
Guanylate-binding protein, C-terminal domain; Transcription of the anti-viral guanylate-binding protein (GBP) is induced by interferon-gamma during macrophage induction. This family contains GBP1 and GPB2, both GTPases capable of binding GTP, GDP and GMP. Pssm-ID: 460721 [Multi-domain] Cd Length: 297 Bit Score: 40.35 E-value: 4.19e-03
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| MscS_porin | pfam12795 | Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part ... |
192-339 | 4.20e-03 | ||||||
Mechanosensitive ion channel porin domain; The small mechanosensitive channel, MscS, is a part of the turgor-driven solute efflux system that protects bacteria from lysis in the event of osmotic shock. The MscS protein alone is sufficient to form a functional mechanosensitive channel gated directly by tension in the lipid bilayer. The MscS proteins are heptamers of three transmembrane subunits with seven converging M3 domains, and this MscS_porin is towards the N-terminal of the molecules. The high concentration of negative charges at the extracellular entrance of the pore helps select the cations for efflux. Pssm-ID: 432790 [Multi-domain] Cd Length: 238 Bit Score: 39.98 E-value: 4.20e-03
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| ClpA | COG0542 | ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ... |
202-306 | 4.25e-03 | ||||||
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones]; Pssm-ID: 440308 [Multi-domain] Cd Length: 836 Bit Score: 41.22 E-value: 4.25e-03
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| SMC_prok_B | TIGR02168 | chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ... |
224-344 | 4.29e-03 | ||||||
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274008 [Multi-domain] Cd Length: 1179 Bit Score: 41.20 E-value: 4.29e-03
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| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
209-343 | 4.80e-03 | ||||||
MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is presumably controlled by tissue-specific microtubule-associated proteins (MAPs). The 115-kDa epithelial MAP (E-MAP-115/MAP7) has been identified as a microtubule-stabilising protein predominantly expressed in cell lines of epithelial origin. The binding of this microtubule associated protein is nucleotide independent. Pssm-ID: 461709 [Multi-domain] Cd Length: 153 Bit Score: 38.87 E-value: 4.80e-03
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| PHD | smart00249 | PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in ... |
771-820 | 4.86e-03 | ||||||
PHD zinc finger; The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the RING finger and the FYVE finger. It is not yet known if PHD fingers have a common molecular function. Several reports suggest that it can function as a protein-protein interacton domain and it was recently demonstrated that the PHD finger of p300 can cooperate with the adjacent BROMO domain in nucleosome binding in vitro. Other reports suggesting that the PHD finger is a ubiquitin ligase have been refuted as these domains were RING fingers misidentified as PHD fingers. Pssm-ID: 214584 [Multi-domain] Cd Length: 47 Bit Score: 36.04 E-value: 4.86e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
210-344 | 4.92e-03 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 41.05 E-value: 4.92e-03
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| DUF3450 | pfam11932 | Protein of unknown function (DUF3450); This family of proteins are functionally ... |
209-340 | 4.95e-03 | ||||||
Protein of unknown function (DUF3450); This family of proteins are functionally uncharacterized. This protein is found in bacteria and eukaryotes. Proteins in this family are about 260 amino acids in length. Pssm-ID: 432198 [Multi-domain] Cd Length: 238 Bit Score: 39.91 E-value: 4.95e-03
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| GBP_C | cd16269 | Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ... |
208-310 | 5.14e-03 | ||||||
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines. Pssm-ID: 293879 [Multi-domain] Cd Length: 291 Bit Score: 39.87 E-value: 5.14e-03
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| PRK03918 | PRK03918 | DNA double-strand break repair ATPase Rad50; |
203-342 | 5.41e-03 | ||||||
DNA double-strand break repair ATPase Rad50; Pssm-ID: 235175 [Multi-domain] Cd Length: 880 Bit Score: 40.82 E-value: 5.41e-03
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| FliJ | pfam02050 | Flagellar FliJ protein; |
254-345 | 5.65e-03 | ||||||
Flagellar FliJ protein; Pssm-ID: 426581 [Multi-domain] Cd Length: 123 Bit Score: 38.03 E-value: 5.65e-03
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| Apolipoprotein | pfam01442 | Apolipoprotein A1/A4/E domain; These proteins contain several 22 residue repeats which form a ... |
199-340 | 5.73e-03 | ||||||
Apolipoprotein A1/A4/E domain; These proteins contain several 22 residue repeats which form a pair of alpha helices. This family includes: Apolipoprotein A-I. Apolipoprotein A-IV. Apolipoprotein E. Pssm-ID: 460211 [Multi-domain] Cd Length: 175 Bit Score: 38.78 E-value: 5.73e-03
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| PRK02224 | PRK02224 | DNA double-strand break repair Rad50 ATPase; |
207-346 | 5.88e-03 | ||||||
DNA double-strand break repair Rad50 ATPase; Pssm-ID: 179385 [Multi-domain] Cd Length: 880 Bit Score: 40.79 E-value: 5.88e-03
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| Atg16_CCD | cd22887 | Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family ... |
242-310 | 5.99e-03 | ||||||
Coiled-coiled domain of autophagy-related 16 (Atg16) family proteins; The Atg16 family includes Saccharomyces cerevisiae Atg16 (also called cytoplasm to vacuole targeting protein 11, CVT11, or SAP18), human autophagy-related protein 16-1 (also called APG16-like 1, ATG16L1, or APG16L) and autophagy-related protein 16-2 (also called APG16-like 2, ATG16L2, WD repeat-containing protein 80 or WDR80), and similar proteins. Atg16 stabilizes the Atg5-Atg12 conjugate and mediates the formation of the 350 kDa complex, which is necessary for autophagy. The Atg5-Atg12/Atg16 complex is required for efficient promotion of Atg8-conjugation to phosphatidylethanolamine and Atg8 localization to the pre-autophagosomal structure (PAS). Similarly, human ATG16L1 plays an essential role in autophagy and acts as a molecular scaffold which mediates protein-protein interactions essential for autophagosome formation. ATG16L2, though structurally similar to ATG16L1 and able to form a complex with the autophagy proteins Atg5 and Atg12, is not essential for autophagy. Single-nucleotide polymorphisms in ATG16L1 is associated with an increased risk of developing Crohn disease. Saccharomyces cerevisiae Atg16 contains an N-terminal domain (NTD) that interacts with the Atg5-Atg12 protein conjugate and a coiled-coil domain (CCD) that dimerizes and mediates self-assembly. Human ATG16L1 and ATG16L2 also contains an N-terminal region that binds Atg5, a CCD homologous to the yeast CCD, and a WD40 domain that represents approximately 50% of the full-length protein. This model corresponds to the CCD of Atg16 family proteins. Pssm-ID: 439196 [Multi-domain] Cd Length: 91 Bit Score: 37.16 E-value: 5.99e-03
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| PHD_TIF1gamma | cd15624 | PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also ... |
673-722 | 6.01e-03 | ||||||
PHD finger found in transcriptional intermediary factor 1 gamma (TIF1gamma); TIF1gamma, also termed tripartite motif-containing 33 (trim33), or ectodermin, or RFG7, or PTC7, is an E3-ubiquitin ligase that functions as a regulator of transforming growth factor beta (TGFbeta) signaling; it inhibits the Smad4-mediated TGFbeta response by interaction with Smad2/3 or ubiquitylation of Smad4. Moreover, TIF1gamma is an important regulator of transcription during hematopoiesis, as well as a key factor of tumorigenesis. Like other TIF1 family members, TIF1gamma also contains an intrinsic transcriptional silencing function. It can control erythroid cell fate by regulating transcription elongation. It can bind to the anaphase-promoting complex/cyclosome (APC/C) and promotes mitosis. TIF1gamma contains an N-terminal RBCC (RING finger, B-box zinc-fingers, coiled-coil), a plant homeodomain (PHD) finger, followed by a bromodomain in the C-terminal region. Pssm-ID: 277094 Cd Length: 46 Bit Score: 35.79 E-value: 6.01e-03
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| PHD2_KDM5B | cd15607 | PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis ... |
674-722 | 6.07e-03 | ||||||
PHD finger 2 found in lysine-specific demethylase 5B (KDM5B); KDM5B (also termed Cancer/testis antigen 31 (CT31), Histone demethylase JARID1B, Jumonji/ARID domain-containing protein 1B (JARID1B), retinoblastoma-binding protein 2 homolog 1 (RBP2-H1 or RBBP2H1A), or PLU-1) is a member of the JARID subfamily within the JmjC proteins. It has a restricted expression pattern in the testis, ovary, and transiently in the mammary gland of the pregnant female and has been shown to be upregulated in breast cancer, prostate cancer, and lung cancer, suggesting a potential role in tumorigenesis. KDM5B acts as a histone demethylase that catalyzes the removal of trimethylation of lysine 4 on histone H3 (H3K4me3), induced by polychlorinated biphenyls (PCBs). It also mediates demethylation of H3K4me2 and H3K4me1. Moreover, KDM5B functions as a negative regulator of hematopoietic stem cell (HSC) self-renewal and progenitor cell activity. KDM5B has also been shown to interact with the DNA binding transcription factors BF-1 and PAX9, as well as TIEG1/KLF10 (transforming growth factor-beta inducible early gene-1/Kruppel-like transcription factor 10), and possibly function as a transcriptional corepressor. KDM5B contains the catalytic JmjC domain, JmjN, the BRIGHT domain, which is an AT-rich interacting domain (ARID), and a Cys5HisCys2 zinc finger, as well as three plant homeodomain (PHD) fingers. This model corresponds to the second PHD finger. Pssm-ID: 277080 Cd Length: 44 Bit Score: 35.58 E-value: 6.07e-03
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| Myosin_tail_1 | pfam01576 | Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ... |
199-342 | 6.54e-03 | ||||||
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament. Pssm-ID: 460256 [Multi-domain] Cd Length: 1081 Bit Score: 40.54 E-value: 6.54e-03
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
192-284 | 7.18e-03 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 40.44 E-value: 7.18e-03
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| DUF4472 | pfam14739 | Domain of unknown function (DUF4472); This family is specific to the Chordates. Some members ... |
248-328 | 7.55e-03 | ||||||
Domain of unknown function (DUF4472); This family is specific to the Chordates. Some members also carry Kinesin-motor domains at their N-terminus, Kinesin, pfam00225. Pssm-ID: 464291 [Multi-domain] Cd Length: 107 Bit Score: 37.28 E-value: 7.55e-03
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
73-190 | 8.33e-03 | ||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 40.31 E-value: 8.33e-03
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| COG4913 | COG4913 | Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; |
192-321 | 8.98e-03 | ||||||
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown]; Pssm-ID: 443941 [Multi-domain] Cd Length: 1089 Bit Score: 39.90 E-value: 8.98e-03
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| PRK11281 | PRK11281 | mechanosensitive channel MscK; |
208-338 | 9.26e-03 | ||||||
mechanosensitive channel MscK; Pssm-ID: 236892 [Multi-domain] Cd Length: 1113 Bit Score: 39.89 E-value: 9.26e-03
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| MukB | COG3096 | Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell ... |
202-343 | 9.58e-03 | ||||||
Chromosome condensin MukBEF, ATPase and DNA-binding subunit MukB [Cell cycle control, cell division, chromosome partitioning]; Pssm-ID: 442330 [Multi-domain] Cd Length: 1470 Bit Score: 39.94 E-value: 9.58e-03
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| SMC_prok_A | TIGR02169 | chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ... |
192-307 | 9.58e-03 | ||||||
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins] Pssm-ID: 274009 [Multi-domain] Cd Length: 1164 Bit Score: 40.05 E-value: 9.58e-03
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| ATG16 | pfam08614 | Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for ... |
196-309 | 9.66e-03 | ||||||
Autophagy protein 16 (ATG16); Autophagy is a ubiquitous intracellular degradation system for eukaryotic cells. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. ATG16 (also known as Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway. Pssm-ID: 462536 [Multi-domain] Cd Length: 176 Bit Score: 38.37 E-value: 9.66e-03
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