polyprotein, partial [Pennisetum mosaic virus]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Potyviridae_RdRp | cd23175 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ... |
1-204 | 3.60e-159 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. : Pssm-ID: 438025 Cd Length: 236 Bit Score: 455.76 E-value: 3.60e-159
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| Poty_coat super family | cl02961 | Potyvirus coat protein; |
395-627 | 1.50e-102 | |||||
Potyvirus coat protein; The actual alignment was detected with superfamily member pfam00767: Pssm-ID: 279151 Cd Length: 243 Bit Score: 311.46 E-value: 1.50e-102
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-389 | 8.74e-10 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] : Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 60.63 E-value: 8.74e-10
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| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Potyviridae_RdRp | cd23175 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ... |
1-204 | 3.60e-159 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438025 Cd Length: 236 Bit Score: 455.76 E-value: 3.60e-159
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| Poty_coat | pfam00767 | Potyvirus coat protein; |
395-627 | 1.50e-102 | |||||
Potyvirus coat protein; Pssm-ID: 279151 Cd Length: 243 Bit Score: 311.46 E-value: 1.50e-102
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
1-267 | 7.08e-65 | |||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 220.36 E-value: 7.08e-65
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-389 | 8.74e-10 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 60.63 E-value: 8.74e-10
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| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
339-395 | 2.84e-09 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 59.43 E-value: 2.84e-09
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
339-395 | 9.45e-07 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 51.58 E-value: 9.45e-07
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
296-398 | 1.11e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.52 E-value: 1.11e-04
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| growth_prot_Scy | NF041483 | polarized growth protein Scy; |
336-394 | 2.05e-04 | |||||
polarized growth protein Scy; Pssm-ID: 469371 [Multi-domain] Cd Length: 1293 Bit Score: 44.82 E-value: 2.05e-04
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| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
341-383 | 3.39e-04 | |||||
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: 41.56 E-value: 3.39e-04
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
338-450 | 8.87e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 42.33 E-value: 8.87e-04
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
338-474 | 3.75e-03 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 40.41 E-value: 3.75e-03
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| UDM1_RNF168_RNF169-like | cd22249 | UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ... |
341-389 | 5.00e-03 | |||||
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. Pssm-ID: 409016 [Multi-domain] Cd Length: 66 Bit Score: 35.71 E-value: 5.00e-03
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| Name | Accession | Description | Interval | E-value | |||||
| ps-ssRNAv_Potyviridae_RdRp | cd23175 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of ... |
1-204 | 3.60e-159 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Potyviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Potyviridae, order: Patatavirales. Potyviridae, is the largest family of RNA plant viruses, members of which have (+)ssRNA genomes and flexuous filamentous particles. The family is divided into eight genera: Brambyvirus, Bymovirus, Ipomovirus, Macluravirus, Poacevirus, Potyvirus, Rymovirus, and Tritimovirus. Most genomes are monopartite but those of members of the genus Bymovirus are bipartite. Some members cause serious disease epidemics in cultivated plants. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438025 Cd Length: 236 Bit Score: 455.76 E-value: 3.60e-159
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| Poty_coat | pfam00767 | Potyvirus coat protein; |
395-627 | 1.50e-102 | |||||
Potyvirus coat protein; Pssm-ID: 279151 Cd Length: 243 Bit Score: 311.46 E-value: 1.50e-102
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| RdRP_1 | pfam00680 | Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase ... |
1-267 | 7.08e-65 | |||||
Viral RNA-dependent RNA polymerase; This family represents the RNA-directed RNA polymerase found in many positive strand RNA eukaryotic viruses. Structural studies indicate that these proteins form the "right hand" structure found in all oligonucleotide polymerases, containing thumb, finger and palm domains, and also the additional bridging finger and thumb domains unique to RNA-directed RNA polymerases. Pssm-ID: 425815 Cd Length: 450 Bit Score: 220.36 E-value: 7.08e-65
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| RNA_dep_RNAP | cd01699 | RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the ... |
1-229 | 5.74e-39 | |||||
RNA_dep_RNAP: RNA-dependent RNA polymerase (RdRp) is an essential protein encoded in the genomes of all RNA containing viruses with no DNA stage. RdRp catalyzes synthesis of the RNA strand complementary to a given RNA template. RdRps of many viruses are products of processing of polyproteins. Some RdRps consist of one polypeptide chain, and others are complexes of several subunits. The domain organization and the 3D structure of the catalytic center of a wide range of RdRps, including those with a low overall sequence homology, are conserved. The catalytic center is formed by several motifs containing a number of conserved amino acid residues. This subfamily represents the RNA-dependent RNA polymerases from all positive-strand RNA eukaryotic viruses with no DNA stage. Pssm-ID: 238843 [Multi-domain] Cd Length: 278 Bit Score: 144.73 E-value: 5.74e-39
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| ps-ssRNAv-Picornavirales | cd23169 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ... |
1-268 | 5.29e-24 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRp of Picornavirales, an order of (+)ssRNA viruses. The order Picornavirales comprises viruses that historically are referred to as picorna-like viruses and which are classified into eight virus families: Caliciviridae, Dicistroviridae, Iflaviridae, Marnaviridae, Picornaviridae, Polycipiviridae, Secoviridae, and Solinviviridae. All known genomes of Picornavirales members encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The picornavirus genome is replicated via a negative-sense (-) RNA intermediate by the viral RdRp, named 3Dpol, which uses VPg (the product of 3B) as a primer to initiate the replication process. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438019 Cd Length: 309 Bit Score: 103.06 E-value: 5.29e-24
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| ps-ssRNAv_Astroviridae_RdRp | cd23172 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of ... |
14-181 | 7.56e-14 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Astroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Astroviridae, order, Stellavirales. Astrovirus has a non-segmented, (+)ssRNA genome within a non-enveloped icosahedral capsid. The family Astroviridae comprises two genera, Mamastrovirus, which infect mammals, and Avastrovirus, which infect birds. Astroviruses have been isolated from stools from a wide variety of mammals and birds. Human astroviruses have been shown to be an important cause of gastroenteritis in young children. Duck astrovirus causes an often-fatal hepatitis in ducklings. Astroviruses infecting turkeys, guinea fowl and chickens affect multiple organs, including the kidney and thymus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438022 Cd Length: 243 Bit Score: 71.73 E-value: 7.56e-14
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| Caliciviridae_RdRp | cd23192 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of ... |
17-187 | 2.83e-13 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Caliciviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Caliciviridae, order Picornavirales. Member viruses have a viral (+)ssRNA genome, which is not segmented. The family Caliciviridae, includes eleven genera: seven genera of which infect mammals (Lagovirus, Norovirus, Nebovirus, Recovirus, Sapovirus, Valovirus, and Vesivirus), two genera of which infect birds (Bavovirus, Nacovirus), and two genera of which infect fish (Minovirus and Salovirus). Each genus includes 1-2 species. Human noroviruses are a leading cause of acute gastroenteritis in humans. Furthermore, unclassified caliciviruses have been detected in geese, yellowfin seabream, greater green snake, arctic lamprey, frogs and various Australian birds, highlighting the wide host range of viruses in the family Caliciviridae. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438042 Cd Length: 310 Bit Score: 71.14 E-value: 2.83e-13
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-389 | 8.74e-10 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 60.63 E-value: 8.74e-10
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-394 | 9.91e-10 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 60.63 E-value: 9.91e-10
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| Dicistroviridae_RdRp | cd23194 | RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense ... |
30-249 | 2.03e-09 | |||||
RNA-dependent RNA polymerase (RdRp) in the family Dicistroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the RdRp of RNA viruses belonging to the family Dicistroviridae, order Picornavirales. Dicistroviridae is a family of small non-enveloped viruses with a (+)ssRNA genome of approximately 8-10 kilobases. The family contains 3 genera: Aparavirus, Cripavirus, and Triatovirus. All members infect arthropod hosts with some having devastating economic consequences, such as acute bee paralysis virus, Kashmir bee virus, and Israeli acute paralysis virus in domesticated honeybees, and taura syndrome virus and mud crab virus in the seafood industry. On the contrary, host specificity and other desirable traits make several members of this group amenable to development as biopesticides for insect control, such as Solenopsis invicta virus 1 against fire ants, and triatoma virus against triatomine bugs that vector Chagas disease. Members in the family Dicistroviridae have similarity to viruses in the Picornavirales members (Iflaviridae, Picornaviridae, Marnaviridae and Secoviridae). The genomes of viruses of these taxa encode proteins with helicase, 3C-like protease, and RdRp domains, as well as capsid proteins with related structures, although the genome organizations can differ among viruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438044 [Multi-domain] Cd Length: 315 Bit Score: 59.44 E-value: 2.03e-09
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| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
339-395 | 2.84e-09 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 59.43 E-value: 2.84e-09
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| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
341-395 | 8.19e-09 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 57.89 E-value: 8.19e-09
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| ps-ssRNAv_RdRp-like | cd23167 | conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ... |
51-167 | 8.80e-09 | |||||
conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense single-stranded RNA [(+)ssRNA] viruses and closely related viruses; This family contains the catalytic core domain of RdRp of RNA viruses which belong to Group IV of the Baltimore classification system, and are a group of related viruses that have positive-sense (+), single-stranded (ss) genomes made of ribonucleic acid (RNA). RdRp (also known as RNA replicase) catalyzes the replication of RNA from an RNA template; specifically, it catalyzes the synthesis of the RNA strand complementary to a given RNA template. The Baltimore Classification is divided into 7 classes, 3 of which include RNA viruses: Group IV (+) RNA viruses, Group III double-stranded (ds) RNA viruses, and Group V negative-sense (-) RNA viruses. Baltimore groups of viruses differ with respect to the nature of their genome (i.e., the nucleic acid form that is packaged into virions) and correspond to distinct strategies of genome replication and expression. (+) viral RNA is similar to mRNA and thus can be immediately translated by the host cell. (+)ssRNA viruses can also produce (+) copies of the genome from (-) strands of an intermediate dsRNA genome. This acts as both a transcription and a replication process since the replicated RNA is also mRNA. RdRps belong to the expansive class of polymerases containing so-called palm catalytic domains along with the accessory fingers and thumb domains. All RdRps also have six conserved structural motifs (A-F), located in its majority in the palm subdomain (A-E motifs) and the F motif is located on the finger subdomain. All these motifs have been shown to be implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. In addition to Group IV viruses, this model also includes Picobirnaviruses (PBVs), members of the family Picobirnaviridae of dsRNA viruses (Baltimore classification Group III), which are bi-segmented dsRNA viruses. The phylogenetic tree of the RdRps of RNA viruses (realm Riboviria) showed that picobirnaviruses are embedded in the branch of diverse (+)RNA viruses; sometimes they are collectively referred to as the picornavirus supergroup. RdRps of members of the family Permutatetraviridae, a distinct group of RNA viruses that encompass a circular permutation within the RdRp palm domain, are not included in this model. Pssm-ID: 438017 [Multi-domain] Cd Length: 73 Bit Score: 52.34 E-value: 8.80e-09
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
341-394 | 1.17e-08 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 57.16 E-value: 1.17e-08
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| ps-ssRNA_Picornaviridae | cd23193 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of ... |
39-169 | 1.80e-08 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Picornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Picornaviridae, order Picornavirales. The Picornaviridae family consists of small, icosahedral viruses with (+)ssRNA genomes. Characteristic features of all members of the family Picornaviridae are three capsid proteins with beta-barrel folding, polyprotein processing by virus-encoded cysteine proteinase(s), and replication by an RdRp with a YGDD sequence motif. The family Picornaviridae comprises 68 genera containing 158 species, but many viruses are presently awaiting classification. The established genera of the family include: Aphthovirus, Avisivirus, Crohivirus, Enterovirus, Teschovirus, Cardiovirus, Erbovirus, Kobuvirus, Hepatovirus, Parechovirus, Aquamavirus, Avihepatovirus, Avisivirus, Cosavirus, Dicipivirus, Fipivirus, Gallivirus, Hunnivirus, Kunsagivirus, Limnipivirus, Megrivirus, Mischivirus, Mosavirus, Oscivirus, Pasivirus, Passerivirus, Rabovirus, Rosavirus, Sakobuvirus, Salivirus, Sapelovirus, Senecavirus, Sicinivirus, and Tremovirus. The Picornaviridae contains many important human and animal pathogens including enteroviruses (such as poliovirus, enterovirus, coxsackievirus, and rhinovirus), cardioviruses (such as encephalomyocarditis virus and Theiler's virus), hepatitis A virus and foot-and-mouth disease virus. Infection with various picornaviruses may cause encephalitis, febrile rash illnesses (hand-foot-and-mouth disease), aseptic meningitis, hepatitis, conjunctivitis, herpangina, myositis and myocarditis, and the common cold. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438043 Cd Length: 345 Bit Score: 56.79 E-value: 1.80e-08
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| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-393 | 2.57e-08 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 56.01 E-value: 2.57e-08
|
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| ps-ssRNAv_Nidovirales_RdRp | cd23168 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of ... |
1-223 | 2.78e-08 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Nidovirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This family contains the catalytic core domain of RdRP of Nidovirales, an order of enveloped, (+)ssRNA viruses which infect vertebrates and invertebrates. Host organisms include mammals, birds, reptiles, amphibians, fish, arthropods, mollusks, and helminths. The order Nidovirales currently comprises 88 formally recognized virus species of (+)ssRNA viruses which are classified into nine virus families: Abyssoviridae, Arteriviridae, Coronaviridae, Euroniviridae, Medioniviridae, Mesoniviridae, Mononiviridae, Roniviridae, and Tobaniviridae. Based on the genome size, the members of the order Nidovirales can be divided into two groups, large and small nidoviruses. The genomes of the large nidoviruses are well over 25 kb in length with size differences in the 5 kb range. Planarian secretory cell nidovirus (PSCNV), only member of the Mononiviridae family, has the largest known non-segmented RNA genome of 41.1 kb; its host is the planarian flatworm. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438018 [Multi-domain] Cd Length: 310 Bit Score: 55.83 E-value: 2.78e-08
|
|||||||||
| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
333-391 | 2.79e-08 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 56.35 E-value: 2.79e-08
|
|||||||||
| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
339-396 | 4.86e-08 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 55.58 E-value: 4.86e-08
|
|||||||||
| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
341-394 | 4.68e-07 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 52.16 E-value: 4.68e-07
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
339-395 | 9.45e-07 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 51.58 E-value: 9.45e-07
|
|||||||||
| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
341-393 | 1.52e-06 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 50.96 E-value: 1.52e-06
|
|||||||||
| Polycipiviridae_RdRp | cd23198 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of ... |
39-234 | 2.29e-06 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Polycipiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Polycipiviridae (polycistronic picorna-like viruses), order Picornavirales. Polycipiviridae is a family of picorna-like viruses with non-segmented, linear, (+)ssRNA genomes of approximately 10-12 kb. Their genomes are polycistronic, with four (or more) consecutive 5'-proximal open reading frames (ORFs) encoding structural (and possibly other) proteins and a long 3' ORF encoding the replication polyprotein. Members of species within the family are typically found in ants, with Apple picorna-like virus 1 and the unnamed Polycipiviridae virus in fruit bat stool as exceptions. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438048 Cd Length: 317 Bit Score: 50.10 E-value: 2.29e-06
|
|||||||||
| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-393 | 2.74e-06 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 49.84 E-value: 2.74e-06
|
|||||||||
| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
339-402 | 3.01e-06 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 49.80 E-value: 3.01e-06
|
|||||||||
| Fipivirus_RdRp | cd23229 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of ... |
39-180 | 4.75e-06 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the genus Fipivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the catalytic core domain of the RdRp of RNA viruses belonging to the Fipivirus genus within the family Picornaviridae, order Picornavirales. The Fipivirus contains viruses with (+)ssRNA genomes that produce nonenveloped virions. This genus contains five species: Fipivirus A (Wuhan sharpbelly picornavirus 2), Fipivirus B (Wuhan sharpbelly picornavirus 3), Fipivirus C (Wenling crossorhombus picornavirus), Fipivirus D (Wenling jack mackerels picornavirus) and Fipivirus E (Wenling banjofish picornavirus 1). All contain viruses from fish. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438079 Cd Length: 394 Bit Score: 49.42 E-value: 4.75e-06
|
|||||||||
| Nora-virus_RdRp | cd23200 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like ... |
1-251 | 1.61e-05 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in a novel picorna-like Drosophila virus, Nora virus; This group contains the catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the unclassified Nora virus, a new picorna-like virus family. Nora virus has a (+)ssRNA genome followed by a poly(A) tail. Unlike other picorna-like viruses, the genome has four open reading frames (ORFs). One ORF encodes a picornavirus-like cassette of proteins for virus replication, including an iflavirus-like RdRp and a helicase that is related to those of mammalian picornaviruses. The three other ORFs are not closely related to any previously described viruses. Nora virus is present as a persistent infection in several tested laboratory stocks and wild-caught flies. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438050 Cd Length: 306 Bit Score: 47.22 E-value: 1.61e-05
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
341-389 | 1.68e-05 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 47.73 E-value: 1.68e-05
|
|||||||||
| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
342-391 | 1.92e-05 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 47.15 E-value: 1.92e-05
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 1.99e-05 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 48.21 E-value: 1.99e-05
|
|||||||||
| tolA | PRK09510 | cell envelope integrity inner membrane protein TolA; Provisional |
339-395 | 2.18e-05 | |||||
cell envelope integrity inner membrane protein TolA; Provisional Pssm-ID: 236545 [Multi-domain] Cd Length: 387 Bit Score: 47.11 E-value: 2.18e-05
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 2.66e-05 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 47.44 E-value: 2.66e-05
|
|||||||||
| PRK07735 | PRK07735 | NADH-quinone oxidoreductase subunit C; |
331-391 | 3.29e-05 | |||||
NADH-quinone oxidoreductase subunit C; Pssm-ID: 236081 [Multi-domain] Cd Length: 430 Bit Score: 46.51 E-value: 3.29e-05
|
|||||||||
| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
334-394 | 4.28e-05 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 45.99 E-value: 4.28e-05
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
338-394 | 7.11e-05 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 45.80 E-value: 7.11e-05
|
|||||||||
| Aalivirus_RdRp | cd23216 | RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded ... |
36-167 | 1.10e-04 | |||||
RNA-dependent RNA polymerase (RdRp) in the genus Aalivirus of positive-sense single-stranded RNA [(+)ssRNA] viruses, within the family Picornaviridae; This group contains the RdRp of RNA viruses belonging to the Aalivirus genus within the family Picornaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. Aalivirus is a new picornavirus found in ducks in China. It is most closely related to duck hepatitis A virus (genus Avihepatovirus) and to avisivirus A1 (genus Avisivirus). The name "aalivirus" is derived from Avihepatovirus/Avisivirus-like virus. RdRps are multi-domain proteins that play a pivotal role in enterovirus replication. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438066 Cd Length: 337 Bit Score: 44.66 E-value: 1.10e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
296-398 | 1.11e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.52 E-value: 1.11e-04
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
331-411 | 1.14e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 45.03 E-value: 1.14e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 1.34e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 45.52 E-value: 1.34e-04
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
339-396 | 1.55e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 44.65 E-value: 1.55e-04
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
339-395 | 1.56e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 44.65 E-value: 1.56e-04
|
|||||||||
| growth_prot_Scy | NF041483 | polarized growth protein Scy; |
336-394 | 2.05e-04 | |||||
polarized growth protein Scy; Pssm-ID: 469371 [Multi-domain] Cd Length: 1293 Bit Score: 44.82 E-value: 2.05e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-396 | 2.78e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 44.36 E-value: 2.78e-04
|
|||||||||
| tolA_full | TIGR02794 | TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the ... |
339-389 | 3.14e-04 | |||||
TolA protein; TolA couples the inner membrane complex of itself with TolQ and TolR to the outer membrane complex of TolB and OprL (also called Pal). Most of the length of the protein consists of low-complexity sequence that may differ in both length and composition from one species to another, complicating efforts to discriminate TolA (the most divergent gene in the tol-pal system) from paralogs such as TonB. Selection of members of the seed alignment and criteria for setting scoring cutoffs are based largely conserved operon struction. //The Tol-Pal complex is required for maintaining outer membrane integrity. Also involved in transport (uptake) of colicins and filamentous DNA, and implicated in pathogenesis. Transport is energized by the proton motive force. TolA is an inner membrane protein that interacts with periplasmic TolB and with outer membrane porins ompC, phoE and lamB. [Transport and binding proteins, Other, Cellular processes, Pathogenesis] Pssm-ID: 274303 [Multi-domain] Cd Length: 346 Bit Score: 43.30 E-value: 3.14e-04
|
|||||||||
| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
341-383 | 3.39e-04 | |||||
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: 41.56 E-value: 3.39e-04
|
|||||||||
| PRK12472 | PRK12472 | hypothetical protein; Provisional |
339-387 | 3.55e-04 | |||||
hypothetical protein; Provisional Pssm-ID: 237110 [Multi-domain] Cd Length: 508 Bit Score: 43.71 E-value: 3.55e-04
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
339-396 | 3.74e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 43.49 E-value: 3.74e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 5.26e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.21 E-value: 5.26e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
341-394 | 5.39e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 43.21 E-value: 5.39e-04
|
|||||||||
| ps-ssRNAv_Flaviviridae_RdRp | cd23178 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of ... |
35-164 | 6.39e-04 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Flaviviridae of positive-sense single-stranded RNA (+ssRNA) viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Flaviviridae, order Amarillovirales. Flaviviridae, is a family of small, enveloped viruses with RNA genomes of 9-13 kb. Most infect mammals and birds. Many flaviviruses are host-specific and pathogenic, such as hepatitis C virus in the genus Hepacivirus. The majority of known members in the genus Flavivirus are arthropod borne, and many are important human and veterinary pathogens (e.g., yellow fever virus, dengue virus). Virions are typically spherical in shape with a lipid envelope. Virions have a single, small, basic capsid (C) protein and two (genera Flavivirus, Hepacivirus and Pegivirus) or three (genus Pestivirus) envelope proteins. They contain a single, long ORF flanked by 5'- and 3'-terminal non-coding regions, which form specific secondary structures required for genome replication and translation. Translational initiation of genomic RNA is cap dependent in the case of members of the genus Flavivirus. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438028 Cd Length: 284 Bit Score: 42.12 E-value: 6.39e-04
|
|||||||||
| PRK07735 | PRK07735 | NADH-quinone oxidoreductase subunit C; |
331-424 | 6.41e-04 | |||||
NADH-quinone oxidoreductase subunit C; Pssm-ID: 236081 [Multi-domain] Cd Length: 430 Bit Score: 42.66 E-value: 6.41e-04
|
|||||||||
| MAP7 | pfam05672 | MAP7 (E-MAP-115) family; The organization of microtubules varies with the cell type and is ... |
341-394 | 6.46e-04 | |||||
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: 40.79 E-value: 6.46e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-424 | 6.96e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 42.82 E-value: 6.96e-04
|
|||||||||
| ERM_helical | pfam20492 | Ezrin/radixin/moesin, alpha-helical domain; The ERM family consists of three closely-related ... |
341-392 | 7.03e-04 | |||||
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: 39.90 E-value: 7.03e-04
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
339-395 | 7.21e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 42.72 E-value: 7.21e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 7.45e-04 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 42.82 E-value: 7.45e-04
|
|||||||||
| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
338-450 | 8.87e-04 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 42.33 E-value: 8.87e-04
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 1.06e-03 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 42.44 E-value: 1.06e-03
|
|||||||||
| PRK07735 | PRK07735 | NADH-quinone oxidoreductase subunit C; |
334-424 | 1.24e-03 | |||||
NADH-quinone oxidoreductase subunit C; Pssm-ID: 236081 [Multi-domain] Cd Length: 430 Bit Score: 41.50 E-value: 1.24e-03
|
|||||||||
| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 1.38e-03 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 42.05 E-value: 1.38e-03
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| Marnaviridae_RdRp | cd23195 | catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of ... |
56-210 | 1.65e-03 | |||||
catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Marnaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Picornavirales; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Marnaviridae, order Picornavirales. Member viruses have a (+)ssRNA genome. They are mono- or dicistronic, have a polyadenylate tail and have conserved motifs for RNA helicase, RdRp, and structural protein domains. The first RNA virus isolated and characterized that infects a marine protist was Heterosigma akashiwo RNA virus (HaRNAV) in the genus Marnavirus, that infects the toxic bloom-forming Raphidophyte alga, Heterosigma akashiwo. Recently, it has undergone a major taxonomic revision and now includes 20 species within 7 genera, which include Bacillarnavirus, Kusarnavirus, Labyrnavirus, Locarnavirus, Marnavirus, Salisharnavirus, and Sogarnavirus. RdRps catalyze RNA template-dependent formation of phosphodiester bonds between ribonucleotides in the presence of divalent metal ions. The initiation of synthesis occurs at the 3'-end of the template in a VPg-dependent manner, and proceeds in the direction of 5'-3'. The active sites of RdRps are highly conserved in different species of picornaviruses. The RdRp domain displays a right hand with three functional subdomains, called fingers, palm, and thumb. All RdRps contain conserved polymerase motifs (A-G), located in the palm (A-E motifs) and finger (F-G) subdomains. All these motifs have been implicated in RdRp fidelity such as processes of correct incorporation and reorganization of nucleotides. Pssm-ID: 438045 Cd Length: 310 Bit Score: 40.89 E-value: 1.65e-03
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| PTZ00121 | PTZ00121 | MAEBL; Provisional |
339-394 | 1.71e-03 | |||||
MAEBL; Provisional Pssm-ID: 173412 [Multi-domain] Cd Length: 2084 Bit Score: 41.67 E-value: 1.71e-03
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| Caldesmon | pfam02029 | Caldesmon; |
341-389 | 1.74e-03 | |||||
Caldesmon; Pssm-ID: 460421 [Multi-domain] Cd Length: 495 Bit Score: 41.39 E-value: 1.74e-03
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| TolA | COG3064 | Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; |
338-474 | 3.75e-03 | |||||
Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis]; Pssm-ID: 442298 [Multi-domain] Cd Length: 485 Bit Score: 40.41 E-value: 3.75e-03
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| YqiK | COG2268 | Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; |
339-392 | 4.30e-03 | |||||
Uncharacterized membrane protein YqiK, contains Band7/PHB/SPFH domain [Function unknown]; Pssm-ID: 441869 [Multi-domain] Cd Length: 439 Bit Score: 39.86 E-value: 4.30e-03
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| PRK07735 | PRK07735 | NADH-quinone oxidoreductase subunit C; |
339-424 | 4.59e-03 | |||||
NADH-quinone oxidoreductase subunit C; Pssm-ID: 236081 [Multi-domain] Cd Length: 430 Bit Score: 39.96 E-value: 4.59e-03
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| UDM1_RNF168_RNF169-like | cd22249 | UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, ... |
341-389 | 5.00e-03 | |||||
UDM1 (ubiquitin-dependent DSB recruitment module 1) found in RING finger proteins RNF168, RNF169 and similar proteins; This model represents the UDM1 (ubiquitin-dependent double-strand break [DSB] recruitment module 1) found in RING finger proteins, RNF168 and RNF169. RNF168 is an E3 ubiquitin-protein ligase that promotes non-canonical K27 ubiquitination to signal DNA damage. It functions, together with RNF8, as a DNA damage response (DDR) factor that promotes a series of ubiquitylation events on substrates such as H2A and H2AX. With H2AK13/15 ubiquitylation, it facilitates recruitment of repair factors p53-binding protein 1 (53BP1) or the RAP80-BRCA1 complex to sites of double-strand breaks (DSBs), and inhibits homologous recombination (HR) in cells deficient in the tumor suppressor BRCA1. RNF168 also promotes H2A neddylation, which antagonizes ubiquitylation of H2A and regulates DNA damage repair. In addition, RNF168 forms a functional complex with RAD6A or RAD6B during the DNA damage response. RNF169 is an uncharacterized E3 ubiquitin-protein ligase paralogous to RNF168. It functions as a negative regulator of the DNA damage signaling cascade. RNF169 recognizes polyubiquitin structures but does not itself contribute to double-strand break (DSB)-induced chromatin ubiquitylation. It contributes to the regulation of DSB repair pathway utilization via functionally competing with recruiting repair factors, 53BP1 and RAP80-BRCA1, for association with RNF168-modified chromatin, independent of its catalytic activity, limiting the magnitude of the RNF8/RNF168-dependent signaling response to DSBs. The UDM1 domain comprises LRM1 (LR motif 1), UMI (ubiquitin-interacting motif [UIM]- and MIU-related UBD) and MIU1 (motif interacting with ubiquitin 1). Mutations of Ub-interacting residues in UDM1 have little effect on the accumulation of RNF168 to DSB sites, suggesting that it may not be the main site of binding ubiquitylated and polyubiquitylated targets. Pssm-ID: 409016 [Multi-domain] Cd Length: 66 Bit Score: 35.71 E-value: 5.00e-03
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| PRK00247 | PRK00247 | putative inner membrane protein translocase component YidC; Validated |
339-392 | 9.35e-03 | |||||
putative inner membrane protein translocase component YidC; Validated Pssm-ID: 178945 [Multi-domain] Cd Length: 429 Bit Score: 38.68 E-value: 9.35e-03
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