mucin-17-like [Branchiostoma floridae]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | ||||||||||
| AP-like_stonins_MHD | cd09255 | Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of ... |
1436-1781 | 4.32e-172 | ||||||||||
Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonins, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonins is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin 1. Stonin 2, also known as stoned B, acts as an AP-2-dependent synaptotagmin-specific sorting adaptors for SV endocytosis. Stoned A is not a stonin. It is structurally unrelated to the adaptins and does not appear to have mammalian homologs. It is not included in this family. : Pssm-ID: 271163 [Multi-domain] Cd Length: 315 Bit Score: 528.13 E-value: 4.32e-172
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| TFIIA | pfam03153 | Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ... |
1813-2154 | 5.72e-52 | ||||||||||
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. : Pssm-ID: 460829 [Multi-domain] Cd Length: 344 Bit Score: 187.63 E-value: 5.72e-52
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| PHA03247 super family | cl33720 | large tegument protein UL36; Provisional |
662-1308 | 9.49e-12 | ||||||||||
large tegument protein UL36; Provisional The actual alignment was detected with superfamily member PHA03247: Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 71.12 E-value: 9.49e-12
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| PRK13335 super family | cl31400 | superantigen-like protein SSL3; Reviewed; |
218-322 | 3.36e-04 | ||||||||||
superantigen-like protein SSL3; Reviewed; The actual alignment was detected with superfamily member PRK13335: Pssm-ID: 139494 [Multi-domain] Cd Length: 356 Bit Score: 45.12 E-value: 3.36e-04
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| Atrophin-1 super family | cl38111 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
521-769 | 2.05e-03 | ||||||||||
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. The actual alignment was detected with superfamily member pfam03154: Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 43.22 E-value: 2.05e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||
| AP-like_stonins_MHD | cd09255 | Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of ... |
1436-1781 | 4.32e-172 | ||||||||||
Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonins, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonins is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin 1. Stonin 2, also known as stoned B, acts as an AP-2-dependent synaptotagmin-specific sorting adaptors for SV endocytosis. Stoned A is not a stonin. It is structurally unrelated to the adaptins and does not appear to have mammalian homologs. It is not included in this family. Pssm-ID: 271163 [Multi-domain] Cd Length: 315 Bit Score: 528.13 E-value: 4.32e-172
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| TFIIA | pfam03153 | Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ... |
1813-2154 | 5.72e-52 | ||||||||||
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Pssm-ID: 460829 [Multi-domain] Cd Length: 344 Bit Score: 187.63 E-value: 5.72e-52
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| Adap_comp_sub | pfam00928 | Adaptor complexes medium subunit family; This family also contains members which are coatomer ... |
1434-1777 | 1.72e-41 | ||||||||||
Adaptor complexes medium subunit family; This family also contains members which are coatomer subunits. Pssm-ID: 395742 Cd Length: 259 Bit Score: 154.38 E-value: 1.72e-41
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| TFIIA_alpha_beta_like | cd07976 | Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A ... |
2109-2154 | 5.39e-28 | ||||||||||
Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage). Pssm-ID: 199899 [Multi-domain] Cd Length: 102 Bit Score: 109.54 E-value: 5.39e-28
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| TOA1 | COG5149 | Transcription initiation factor IIA, large chain [Transcription]; |
1811-2154 | 3.89e-12 | ||||||||||
Transcription initiation factor IIA, large chain [Transcription]; Pssm-ID: 227478 [Multi-domain] Cd Length: 293 Bit Score: 69.32 E-value: 3.89e-12
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
662-1308 | 9.49e-12 | ||||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 71.12 E-value: 9.49e-12
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| Herpes_BLLF1 | pfam05109 | Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
648-980 | 5.14e-05 | ||||||||||
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 48.76 E-value: 5.14e-05
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| PRK13335 | PRK13335 | superantigen-like protein SSL3; Reviewed; |
218-322 | 3.36e-04 | ||||||||||
superantigen-like protein SSL3; Reviewed; Pssm-ID: 139494 [Multi-domain] Cd Length: 356 Bit Score: 45.12 E-value: 3.36e-04
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
521-769 | 2.05e-03 | ||||||||||
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 43.22 E-value: 2.05e-03
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| COG5373 | COG5373 | Uncharacterized membrane protein [Function unknown]; |
693-763 | 5.53e-03 | ||||||||||
Uncharacterized membrane protein [Function unknown]; Pssm-ID: 444140 [Multi-domain] Cd Length: 854 Bit Score: 41.91 E-value: 5.53e-03
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| Name | Accession | Description | Interval | E-value | ||||||||||
| AP-like_stonins_MHD | cd09255 | Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of ... |
1436-1781 | 4.32e-172 | ||||||||||
Mu homology domain (MHD) of adaptor-like proteins (AP-like), stonins; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonins, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonins is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin 1. Stonin 2, also known as stoned B, acts as an AP-2-dependent synaptotagmin-specific sorting adaptors for SV endocytosis. Stoned A is not a stonin. It is structurally unrelated to the adaptins and does not appear to have mammalian homologs. It is not included in this family. Pssm-ID: 271163 [Multi-domain] Cd Length: 315 Bit Score: 528.13 E-value: 4.32e-172
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| AP_stonin-2_MHD | cd09263 | Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2; A small family of ... |
1440-1781 | 4.59e-87 | ||||||||||
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-2; A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 2, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-2 is unable to recognize tyrosine-based endocytic sorting signals. It acts as an AP-2-dependent synaptotagmin-specific sorting adaptor for SV endocytosis. Pssm-ID: 271169 Cd Length: 318 Bit Score: 287.68 E-value: 4.59e-87
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| TFIIA | pfam03153 | Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a ... |
1813-2154 | 5.72e-52 | ||||||||||
Transcription factor IIA, alpha/beta subunit; Transcription initiation factor IIA (TFIIA) is a heterotrimer, the three subunits being known as alpha, beta, and gamma, in order of molecular weight. The N and C-terminal domains of the gamma subunit are represented in pfam02268 and pfam02751, respectively. This family represents the precursor that yields both the alpha and beta subunits. The TFIIA heterotrimer is an essential general transcription initiation factor for the expression of genes transcribed by RNA polymerase II. Together with TFIID, TFIIA binds to the promoter region; this is the first step in the formation of a pre-initiation complex (PIC). Binding of the rest of the transcription machinery follows this step. After initiation, the PIC does not completely dissociate from the promoter. Some components, including TFIIA, remain attached and re-initiate a subsequent round of transcription. Pssm-ID: 460829 [Multi-domain] Cd Length: 344 Bit Score: 187.63 E-value: 5.72e-52
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| AP_stonin-1_MHD | cd09262 | Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned ... |
1443-1781 | 1.87e-51 | ||||||||||
Mu homology domain (MHD) of adaptor-like protein (AP-like), stonin-1 (also called Stoned B-like factor); A small family of proteins named stonins has been characterized as clathrin-dependent AP-2 mu2 chain related factors, which may act as cargo-specific sorting adaptors in endocytosis. Stonins include stonin 1 and stonin 2, which are the only mammalian homologs of Drosophila stoned B, a presynaptic protein implicated in neurotransmission and synaptic vesicle (SV) recycling. They are conserved from C. elegans to humans, but are not found in prokaryotes or yeasts. This family corresponds to the mu homology domain of stonin 1, which is distantly related to the C-terminal domain of mu chains among AP complexes. Due to the low degree of sequence conservation of the corresponding binding site, the mu homology domain of stonin-1 is unable to recognize tyrosine-based endocytic sorting signals. To data, little is known about the localization and function of stonin-1. Pssm-ID: 271168 Cd Length: 314 Bit Score: 185.15 E-value: 1.87e-51
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| Adap_comp_sub | pfam00928 | Adaptor complexes medium subunit family; This family also contains members which are coatomer ... |
1434-1777 | 1.72e-41 | ||||||||||
Adaptor complexes medium subunit family; This family also contains members which are coatomer subunits. Pssm-ID: 395742 Cd Length: 259 Bit Score: 154.38 E-value: 1.72e-41
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| AP_MHD_Cterm | cd07954 | C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); ... |
1447-1778 | 6.27e-31 | ||||||||||
C-terminal domain of adaptor protein (AP) complexes medium mu subunits and its homologs (MHD); This family corresponds to the C-terminal domain of heterotetrameric AP complexes medium mu subunits and its homologs existing in monomeric stonins, delta-subunit of the heteroheptameric coat protein I (delta-COPI), a protein encoded by a pro-death gene referred as MuD (also known as MUDENG, mu-2 related death-inducing gene), an endocytic adaptor syp1, the mammalian FCH domain only proteins (FCHo1/2), SH3-containing GRB2-like protein 3-interacting protein 1 (SGIP1), and related proteins. AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. Stonins have been characterized as clathrin-dependent AP-2 mu chain related factors and may act as cargo-specific sorting adaptors in endocytosis. Coat protein complex I (COPI)-coated vesicles function in the early secretory pathway. They mediate the retrograde transport from the Golgi to the ER, and intra-Golgi transport. MuD is distantly related to the C-terminal domain of mu2 subunit of AP-2. It is able to induce cell death by itself and plays an important role in cell death in various tissues. Syp1 represents a novel type of endocytic adaptor protein that participates in endocytosis, promotes vesicle tabulation, and contributes to cell polarity and stress responses. It shares the same domain architecture with its two ubiquitously expressed mammalian counterparts, FCHo1/2, which represent key initial proteins ultimately controlling cellular nutrient uptake, receptor regulation, and synaptic vesicle retrieval. They bind specifically to the plasma membrane and recruit the scaffold proteins eps15 and intersectin, which subsequently engage the adaptor complex AP2 and clathrin, leading to coated vesicle formation. Another mammalian neuronal-specific protein SGIP1 does have a C-terminal MHD and has been classified into this family as well. It is an endophilin-interacting protein that plays an obligatory role in the regulation of energy homeostasis. It is also involved in clathrin-mediated endocytosis by interacting with phospholipids and eps15. Pssm-ID: 271157 Cd Length: 245 Bit Score: 123.28 E-value: 6.27e-31
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| TFIIA_alpha_beta_like | cd07976 | Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A ... |
2109-2154 | 5.39e-28 | ||||||||||
Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage). Pssm-ID: 199899 [Multi-domain] Cd Length: 102 Bit Score: 109.54 E-value: 5.39e-28
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| TFIIA_alpha_beta_like | cd07976 | Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A ... |
1811-1864 | 3.13e-23 | ||||||||||
Precursor of TFIIA alpha and beta subunits and similar proteins; Transcription factor II A (TFIIA) is one of the general transcription factors for RNA polymerase II. TFIIA increases the affinity of TATA-binding protein (TBP) for DNA in order to assemble the initiation complex. TFIIA also functions as an activator during development and differentiation, and is involved in transcription from TATA-less promoters. TFIIA is composed of more than one subunit in various organisms. Mammalian TFIIA large subunits (TFIIA alpha and beta) and the smaller subunit (TFIIA gamma) form a heterotrimer. TFIIA alpha and beta are encoded by a single gene (TFIIA_alpha_beta), its protein product is post-translationally processed and cleaved. TOA1 and TOA2 are the two subunits of Yeast TFIIA which correspond to Mammalian TFIIA_alpha_beta and TFIIA gamma, respectively. TOA1 and TOA2 form a heterodimeric protein complex. TFIIA_alpha_beta alone is sufficient for transcription in early embryogenesis, but the cleaved forms, TFIIA alpha and TFIIA beta, represent the vast majority of TFIIA in most differentiated cells. The exact functional differences between cleaved and uncleaved forms are not yet clear. This model also contains paralogs of the canonical TFIIA_alpha_beta, such as the human ALF, which may be involved in gametogenesis and early embryogenesis (and is also subject to proteolytic cleavage). Pssm-ID: 199899 [Multi-domain] Cd Length: 102 Bit Score: 96.05 E-value: 3.13e-23
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| AP-1_Mu1_Cterm | cd09250 | C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex ... |
1437-1770 | 5.89e-21 | ||||||||||
C-terminal domain of medium Mu1 subunit in clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1 subunit, which includes two closely related homologs, mu1A (encoded by ap1m1) and mu1B (encoded by ap1m2). Mu1A is ubiquitously expressed, but mu1B is expressed exclusively in polarized epithelial cells. AP-1 has been implicated in bi-directional transport between the trans-Golgi network (TGN) and endosomes. It plays an essential role in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Epithelial cell-specific AP-1 is also involved in sorting to the basolateral surface of polarized epithelial cells. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 271158 Cd Length: 272 Bit Score: 94.98 E-value: 5.89e-21
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| AP-2_Mu2_Cterm | cd09251 | C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor ... |
1443-1777 | 2.39e-20 | ||||||||||
C-terminal domain of medium Mu2 subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-2; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, -2, -3, and -4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 2 (AP-2) medium mu2 subunit. Mu2 is ubiquitously expressed in mammals. In higher eukaryotes, AP-2 plays a critical role in clathrin-mediated endocytosis from the plasma membrane in different cells. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-2. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-2 mu2 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Since the Y-X-X-Phi binding site is buried in the core structure of AP-2, a phosphorylation induced conformational change is required when the cargo molecules binds to AP-2. In addition, the C-terminal domain of mu2 subunit has been shown to bind other molecules. For instance, it can bind phosphoinositides, in particular PI[4,5]P2, which might be involved in the recognition process of the tyrosine-based signals. It can also interact with synaptotagmins, a family of important modulators of calcium-dependent neurosecretion within the synaptic vesicle (SV) membrane. Since many of the other endocytic adaptors responsible for biogenesis of synaptic vesicles exist, in the absence of AP-2, clathrin-mediated endocytosis can still occur. However, the cells may not survive in the complete absence of clathrin as well as AP-2. Pssm-ID: 271159 Cd Length: 263 Bit Score: 93.04 E-value: 2.39e-20
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| AP-1_Mu1B_Cterm | cd09259 | C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated ... |
1435-1769 | 2.38e-16 | ||||||||||
C-terminal domain of medium Mu1B subunit in epithelial cell-specific clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1B subunit encoded by ap1m2 gene exclusively expressed in polarized epithelial cells. Epithelial cell-specific AP-1 is used to sort proteins to the basolateral plasma membrane, which involves the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). The phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic reside-binding. Besides, AP-1 mu1B subunit mediates the basolateral recycling of low-density lipoprotein receptor (LDLR) and transferrin receptor (TfR) from the sorting endosomes, where the basolateral sorting signal does not belong to the tyrosine-based signals. Thus, the binding site in mu1B subunit of AP-1 for the signals of LDLR and TfR might be distinct from that for YXXPhi signals. Pssm-ID: 271167 Cd Length: 268 Bit Score: 81.61 E-value: 2.38e-16
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| AP-3_Mu3_Cterm | cd09252 | C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3; AP complexes ... |
1437-1769 | 1.48e-14 | ||||||||||
C-terminal domain of medium Mu3 subunit in adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3 subunit, which includes two closely related homologs, mu3A (P47A, encoded by ap3m1) and mu1B (P47B, encoded by ap3m2). Mu3A is ubiquitously expressed, but mu3B is specifically expressed in neurons and neuroendocrine cells. AP-3 is particularly important for targeting integral membrane proteins to lysosomes and lysome-related organelles at trans-Golgi network (TGN) and/or endosomes, such as the yeast vacuole, fly pigment granules and mammalian melanosomes, platelet dense bodies and the secretory lysosomes of cytotoxic T lymphocytes. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3 subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 271160 Cd Length: 251 Bit Score: 75.70 E-value: 1.48e-14
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| AP-1_Mu1A_Cterm | cd09258 | C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor ... |
1435-1769 | 2.02e-13 | ||||||||||
C-terminal domain of medium Mu1A subunit in ubiquitously expressed clathrin-associated adaptor protein (AP) complex AP-1; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric clathrin-associated adaptor protein complex 1 (AP-1) medium mu1A subunit encoded by ap1m1 gene, which is ubiquitously expressed in all mammalian tissues and cells. AP-1 has been implicated in bidirectional transport between the trans-Golgi network (TGN) and endosomes. It is involved in the formation of clathrin-coated vesicles (CCVs) from the trans-Golgi network (TGN). The ubiquitous AP-1 is recruited to the TGN membrane, as well as to immature secretory granules. Recruitment of AP-1 to the TGN membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1). Phosphorylation/dephosphorylation events can also regulate the function of AP-1. The membrane-anchored cargo molecules can be linked to the outer lattice of CCVs by AP-1. Those cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-1 mu1A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 271166 Cd Length: 270 Bit Score: 72.61 E-value: 2.02e-13
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| TOA1 | COG5149 | Transcription initiation factor IIA, large chain [Transcription]; |
1811-2154 | 3.89e-12 | ||||||||||
Transcription initiation factor IIA, large chain [Transcription]; Pssm-ID: 227478 [Multi-domain] Cd Length: 293 Bit Score: 69.32 E-value: 3.89e-12
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
662-1308 | 9.49e-12 | ||||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 71.12 E-value: 9.49e-12
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| AP-4_Mu4_Cterm | cd09253 | C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4; AP complexes ... |
1446-1777 | 1.90e-09 | ||||||||||
C-terminal domain of medium Mu4 subunit in adaptor protein (AP) complex AP-4; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This family corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 4 (AP-4) medium mu4 subunit. AP-4 plays a role in signal-mediated trafficking of integral membrane proteins in mammalian cells. Unlike other AP complexes, AP-4 is found only in mammals and plants. It is believed to be part of a nonclathrin coat, since it might function independently of clathrin, a scaffolding protein participating in the formation of coated vesicles. Recruitment of AP-4 to the trans-Golgi network (TGN) membrane is regulated by a small GTPase, ADP-ribosylation factor 1 (ARF1) or a related protein. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. One of the most important sorting signals binding to mu subunits of AP complexes are tyrosine-based endocytotic signals, which are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. However, AP-4 does not bind most canonical tyrosine-based signals except for two naturally occurring ones from the lysosomal membrane proteins CD63 and LAMP-2a. It binds YX [FYL][FL]E motif, where X can be any residue, from the cytosolic tails of amyloid precursor protein (APP) family members in a distinct way. Pssm-ID: 271161 Cd Length: 271 Bit Score: 60.66 E-value: 1.90e-09
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
662-872 | 4.37e-09 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 61.82 E-value: 4.37e-09
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| PHA03247 | PHA03247 | large tegument protein UL36; Provisional |
525-1083 | 5.42e-09 | ||||||||||
large tegument protein UL36; Provisional Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 61.88 E-value: 5.42e-09
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| PRK07994 | PRK07994 | DNA polymerase III subunits gamma and tau; Validated |
695-848 | 3.39e-08 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236138 [Multi-domain] Cd Length: 647 Bit Score: 58.72 E-value: 3.39e-08
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
649-851 | 4.37e-08 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 58.35 E-value: 4.37e-08
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| PRK14950 | PRK14950 | DNA polymerase III subunits gamma and tau; Provisional |
670-779 | 4.52e-08 | ||||||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 58.28 E-value: 4.52e-08
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| PHA03378 | PHA03378 | EBNA-3B; Provisional |
496-829 | 7.33e-08 | ||||||||||
EBNA-3B; Provisional Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 58.15 E-value: 7.33e-08
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| PTZ00449 | PTZ00449 | 104 kDa microneme/rhoptry antigen; Provisional |
667-951 | 7.94e-08 | ||||||||||
104 kDa microneme/rhoptry antigen; Provisional Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 57.78 E-value: 7.94e-08
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| PRK14951 | PRK14951 | DNA polymerase III subunits gamma and tau; Provisional |
648-822 | 2.15e-07 | ||||||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 56.26 E-value: 2.15e-07
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
612-985 | 6.21e-07 | ||||||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 55.18 E-value: 6.21e-07
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| PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
650-1200 | 1.04e-06 | ||||||||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 54.32 E-value: 1.04e-06
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
666-854 | 1.65e-06 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 53.31 E-value: 1.65e-06
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
674-912 | 5.23e-06 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 51.80 E-value: 5.23e-06
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| PLN03209 | PLN03209 | translocon at the inner envelope of chloroplast subunit 62; Provisional |
632-853 | 5.64e-06 | ||||||||||
translocon at the inner envelope of chloroplast subunit 62; Provisional Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 51.47 E-value: 5.64e-06
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
563-810 | 7.22e-06 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 51.42 E-value: 7.22e-06
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
706-879 | 9.43e-06 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 51.00 E-value: 9.43e-06
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| kgd | PRK12270 | multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ... |
694-786 | 1.10e-05 | ||||||||||
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit; Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 51.04 E-value: 1.10e-05
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| PRK10263 | PRK10263 | DNA translocase FtsK; Provisional |
638-1278 | 1.31e-05 | ||||||||||
DNA translocase FtsK; Provisional Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 50.85 E-value: 1.31e-05
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| PRK14951 | PRK14951 | DNA polymerase III subunits gamma and tau; Provisional |
704-845 | 1.32e-05 | ||||||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 50.48 E-value: 1.32e-05
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| Herpes_BLLF1 | pfam05109 | Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 ... |
648-980 | 5.14e-05 | ||||||||||
Herpes virus major outer envelope glycoprotein (BLLF1); This family consists of the BLLF1 viral late glycoprotein, also termed gp350/220. It is the most abundantly expressed glycoprotein in the viral envelope of the Herpesviruses and is the major antigen responsible for stimulating the production of neutralising antibodies in vivo. Pssm-ID: 282904 [Multi-domain] Cd Length: 886 Bit Score: 48.76 E-value: 5.14e-05
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
714-916 | 5.27e-05 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 48.33 E-value: 5.27e-05
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| PRK07003 | PRK07003 | DNA polymerase III subunit gamma/tau; |
620-882 | 5.40e-05 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 48.31 E-value: 5.40e-05
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
713-1131 | 1.29e-04 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 47.29 E-value: 1.29e-04
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| PRK14950 | PRK14950 | DNA polymerase III subunits gamma and tau; Provisional |
702-850 | 1.48e-04 | ||||||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 46.73 E-value: 1.48e-04
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| PRK07994 | PRK07994 | DNA polymerase III subunits gamma and tau; Validated |
722-875 | 1.60e-04 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236138 [Multi-domain] Cd Length: 647 Bit Score: 46.78 E-value: 1.60e-04
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
624-779 | 1.61e-04 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 46.90 E-value: 1.61e-04
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| AP-3_Mu3B_Cterm | cd09261 | C-terminal domain of medium Mu3B subunit in neuron-specific adaptor protein (AP) complex AP-3; ... |
1436-1567 | 1.67e-04 | ||||||||||
C-terminal domain of medium Mu3B subunit in neuron-specific adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3B subunit encoded by ap3m2 gene. Mu3B is specifically expressed in neurons and neuroendocrine cells. Neuron-specific AP-3 appears to be involved in synaptic vesicle biogenesis from endosomes in neurons and plays an important role in synaptic transmission in the central nervous system. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of neuron-specific AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3B subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 211372 Cd Length: 254 Bit Score: 45.42 E-value: 1.67e-04
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| PHA02682 | PHA02682 | ORF080 virion core protein; Provisional |
702-791 | 1.83e-04 | ||||||||||
ORF080 virion core protein; Provisional Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 45.62 E-value: 1.83e-04
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
638-849 | 1.91e-04 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 46.52 E-value: 1.91e-04
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| AP-3_Mu3A_Cterm | cd09260 | C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) ... |
1436-1567 | 2.32e-04 | ||||||||||
C-terminal domain of medium Mu3A subunit in ubiquitously expressed adaptor protein (AP) complex AP-3; AP complexes participate in the formation of intracellular coated transport vesicles and select cargo molecules for incorporation into the coated vesicles in the late secretory and endocytic pathways. There are four AP complexes, AP-1, AP-2, AP-3, and AP-4, described in various eukaryotic organisms. Each AP complex consists of four subunits: two large chains (one each of gamma/alpha/delta/epsilon and beta1-4, respectively), a medium mu chain (mu1-4), and a small sigma chain (sigma1-4). Each of the four subunits from the different AP complexes exhibits similarity with each other. This subfamily corresponds to the C-terminal domain of heterotetrameric adaptor protein complex 3 (AP-3) medium mu3A subunit encoded by ap3m1gene. Mu3A is ubiquitously expressed in all mammalian tissues and cells. It appears to be localized to the trans-Golgi network (TGN) and/or endosomes and participates in trafficking to the vacuole/lysosome in yeast, flies, and mammals. Unlike AP-1 and AP-2, which function in conjunction with clathrin which is a scaffolding protein participating in the formation of coated vesicles, the nature of the outer shell of ubiquitous AP-3 containing coats remains to be elucidated. Membrane-anchored cargo molecules interact with adaptors through short sorting signals in their cytosolic segments. Tyrosine-based endocytotic signals are one of the most important sorting signals. They are of the form Y-X-X-Phi, where Y is tyrosine, X is any amino acid and Phi is a bulky hydrophobic residue that can be Leu, Ile, Met, Phe, or Val. These kinds of sorting signals can be recognized by the C-terminal domain of AP-3 mu3A subunit, also known as Y-X-X-Phi signal-binding domain that contains two hydrophobic pockets, one for the tyrosine-binding and one for the bulky hydrophobic residue-binding. Pssm-ID: 211371 Cd Length: 254 Bit Score: 45.09 E-value: 2.32e-04
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| PLN02983 | PLN02983 | biotin carboxyl carrier protein of acetyl-CoA carboxylase |
683-757 | 3.10e-04 | ||||||||||
biotin carboxyl carrier protein of acetyl-CoA carboxylase Pssm-ID: 215533 [Multi-domain] Cd Length: 274 Bit Score: 44.83 E-value: 3.10e-04
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| PRK14971 | PRK14971 | DNA polymerase III subunit gamma/tau; |
699-832 | 3.25e-04 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 45.92 E-value: 3.25e-04
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| PRK10819 | PRK10819 | transport protein TonB; Provisional |
649-770 | 3.26e-04 | ||||||||||
transport protein TonB; Provisional Pssm-ID: 236768 [Multi-domain] Cd Length: 246 Bit Score: 44.67 E-value: 3.26e-04
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| PRK13335 | PRK13335 | superantigen-like protein SSL3; Reviewed; |
218-322 | 3.36e-04 | ||||||||||
superantigen-like protein SSL3; Reviewed; Pssm-ID: 139494 [Multi-domain] Cd Length: 356 Bit Score: 45.12 E-value: 3.36e-04
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| PHA02682 | PHA02682 | ORF080 virion core protein; Provisional |
687-798 | 4.19e-04 | ||||||||||
ORF080 virion core protein; Provisional Pssm-ID: 177464 [Multi-domain] Cd Length: 280 Bit Score: 44.47 E-value: 4.19e-04
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
664-781 | 4.33e-04 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 45.36 E-value: 4.33e-04
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| flhF | PRK06995 | flagellar biosynthesis protein FlhF; |
694-815 | 5.35e-04 | ||||||||||
flagellar biosynthesis protein FlhF; Pssm-ID: 235904 [Multi-domain] Cd Length: 484 Bit Score: 44.96 E-value: 5.35e-04
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| DUF3729 | pfam12526 | Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins ... |
691-772 | 8.65e-04 | ||||||||||
Protein of unknown function (DUF3729); This family of proteins is found in viruses. Proteins in this family are typically between 145 and 1707 amino acids in length. The family is found in association with pfam01443, pfam01661, pfam05417, pfam01660, pfam00978. There is a single completely conserved residue L that may be functionally important. Pssm-ID: 372164 [Multi-domain] Cd Length: 115 Bit Score: 41.22 E-value: 8.65e-04
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| kgd | PRK12270 | multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ... |
713-795 | 8.66e-04 | ||||||||||
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit; Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 44.50 E-value: 8.66e-04
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| PTZ00449 | PTZ00449 | 104 kDa microneme/rhoptry antigen; Provisional |
684-956 | 9.69e-04 | ||||||||||
104 kDa microneme/rhoptry antigen; Provisional Pssm-ID: 185628 [Multi-domain] Cd Length: 943 Bit Score: 44.30 E-value: 9.69e-04
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| PRK14971 | PRK14971 | DNA polymerase III subunit gamma/tau; |
691-811 | 1.10e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237874 [Multi-domain] Cd Length: 614 Bit Score: 44.00 E-value: 1.10e-03
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| PHA03379 | PHA03379 | EBNA-3A; Provisional |
587-830 | 1.13e-03 | ||||||||||
EBNA-3A; Provisional Pssm-ID: 223066 [Multi-domain] Cd Length: 935 Bit Score: 44.28 E-value: 1.13e-03
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| PRK11633 | PRK11633 | cell division protein DedD; Provisional |
695-772 | 1.27e-03 | ||||||||||
cell division protein DedD; Provisional Pssm-ID: 236940 [Multi-domain] Cd Length: 226 Bit Score: 42.68 E-value: 1.27e-03
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
1062-1263 | 1.30e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 43.71 E-value: 1.30e-03
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| PTZ00144 | PTZ00144 | dihydrolipoamide succinyltransferase; Provisional |
705-769 | 1.57e-03 | ||||||||||
dihydrolipoamide succinyltransferase; Provisional Pssm-ID: 240289 [Multi-domain] Cd Length: 418 Bit Score: 43.13 E-value: 1.57e-03
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| FAP | pfam07174 | Fibronectin-attachment protein (FAP); This family contains bacterial fibronectin-attachment ... |
699-774 | 1.59e-03 | ||||||||||
Fibronectin-attachment protein (FAP); This family contains bacterial fibronectin-attachment proteins (FAP). Family members are rich in alanine and proline, are approximately 300 long, and seem to be restricted to mycobacteria. These proteins contain a fibronectin-binding motif that allows mycobacteria to bind to fibronectin in the extracellular matrix. Pssm-ID: 429334 Cd Length: 301 Bit Score: 42.99 E-value: 1.59e-03
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| PRK10819 | PRK10819 | transport protein TonB; Provisional |
676-772 | 1.62e-03 | ||||||||||
transport protein TonB; Provisional Pssm-ID: 236768 [Multi-domain] Cd Length: 246 Bit Score: 42.36 E-value: 1.62e-03
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| Atrophin-1 | pfam03154 | Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian ... |
521-769 | 2.05e-03 | ||||||||||
Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity. Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 43.22 E-value: 2.05e-03
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| rne | PRK10811 | ribonuclease E; Reviewed |
676-848 | 2.96e-03 | ||||||||||
ribonuclease E; Reviewed Pssm-ID: 236766 [Multi-domain] Cd Length: 1068 Bit Score: 42.72 E-value: 2.96e-03
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| PRK14950 | PRK14950 | DNA polymerase III subunits gamma and tau; Provisional |
661-764 | 2.97e-03 | ||||||||||
DNA polymerase III subunits gamma and tau; Provisional Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 42.49 E-value: 2.97e-03
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| PRK14948 | PRK14948 | DNA polymerase III subunit gamma/tau; |
700-772 | 3.06e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237862 [Multi-domain] Cd Length: 620 Bit Score: 42.64 E-value: 3.06e-03
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| PRK14948 | PRK14948 | DNA polymerase III subunit gamma/tau; |
701-786 | 3.66e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237862 [Multi-domain] Cd Length: 620 Bit Score: 42.26 E-value: 3.66e-03
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| PRK12373 | PRK12373 | NADH-quinone oxidoreductase subunit E; |
636-782 | 3.78e-03 | ||||||||||
NADH-quinone oxidoreductase subunit E; Pssm-ID: 237082 [Multi-domain] Cd Length: 400 Bit Score: 42.10 E-value: 3.78e-03
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| kgd | PRK12270 | multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ... |
657-742 | 4.22e-03 | ||||||||||
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit; Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 42.57 E-value: 4.22e-03
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| PRK14948 | PRK14948 | DNA polymerase III subunit gamma/tau; |
695-766 | 4.92e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237862 [Multi-domain] Cd Length: 620 Bit Score: 41.87 E-value: 4.92e-03
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| COG5373 | COG5373 | Uncharacterized membrane protein [Function unknown]; |
693-763 | 5.53e-03 | ||||||||||
Uncharacterized membrane protein [Function unknown]; Pssm-ID: 444140 [Multi-domain] Cd Length: 854 Bit Score: 41.91 E-value: 5.53e-03
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| PLN03209 | PLN03209 | translocon at the inner envelope of chloroplast subunit 62; Provisional |
634-772 | 5.71e-03 | ||||||||||
translocon at the inner envelope of chloroplast subunit 62; Provisional Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 41.84 E-value: 5.71e-03
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| kgd | PRK12270 | multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine ... |
687-769 | 5.92e-03 | ||||||||||
multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit; Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 41.80 E-value: 5.92e-03
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| PTZ00436 | PTZ00436 | 60S ribosomal protein L19-like protein; Provisional |
682-848 | 7.28e-03 | ||||||||||
60S ribosomal protein L19-like protein; Provisional Pssm-ID: 185616 [Multi-domain] Cd Length: 357 Bit Score: 41.09 E-value: 7.28e-03
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| PRK07764 | PRK07764 | DNA polymerase III subunits gamma and tau; Validated |
662-1012 | 7.77e-03 | ||||||||||
DNA polymerase III subunits gamma and tau; Validated Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.51 E-value: 7.77e-03
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| PHA03307 | PHA03307 | transcriptional regulator ICP4; Provisional |
1001-1301 | 8.61e-03 | ||||||||||
transcriptional regulator ICP4; Provisional Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 41.31 E-value: 8.61e-03
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| SOBP | pfam15279 | Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual ... |
645-741 | 9.04e-03 | ||||||||||
Sine oculis-binding protein; SOBP is associated with syndromic and nonsyndromic intellectual disability. It carries a zinc-finger of the zf-C2H2 type at the N-terminus, and a highly characteriztic C-terminal PhPhPhPhPhPh motif. The deduced 873-amino acid protein contains an N-terminal nuclear localization signal (NLS), followed by 2 FCS-type zinc finger motifs, a proline-rich region (PR1), a putative RNA-binding motif region, and a C-terminal NLS embedded in a second proline-rich motif. SOBP is expressed in various human tissues, including developing mouse brain at embryonic day 14. In postnatal and adult mouse brain SOBP is expressed in all neurons, with intense staining in the limbic system. Highest expression is in layer V cortical neurons, hippocampus, pyriform cortex, dorsomedial nucleus of thalamus, amygdala, and hypothalamus. Postnatal expression of SOBP in the limbic system corresponds to a time of active synaptogenesis. the family is also referred to as Jackson circler, JXC1. In seven affected siblings from a consanguineous Israeli Arab family with mental retardation, anterior maxillary protrusion, and strabismus mutations were found in this protein. Pssm-ID: 464609 [Multi-domain] Cd Length: 325 Bit Score: 40.57 E-value: 9.04e-03
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| PRK12323 | PRK12323 | DNA polymerase III subunit gamma/tau; |
1101-1305 | 9.48e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 41.01 E-value: 9.48e-03
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| PRK14948 | PRK14948 | DNA polymerase III subunit gamma/tau; |
695-774 | 9.89e-03 | ||||||||||
DNA polymerase III subunit gamma/tau; Pssm-ID: 237862 [Multi-domain] Cd Length: 620 Bit Score: 41.10 E-value: 9.89e-03
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| Blast search parameters | ||||
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