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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKLPNGWVYCDADGSQFDSSLTPYLINAVLDIRLSFM 80
Cdd:cd23175   32 PIDTLLGGKVCVDDFNNQFYSLHLKAPWTVGITKFYGGWDKLLRKLPDGWVYCDADGSQFDSSLTPYLINAVLRIRLHFM 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  81 EEWDIGERMLMNLYTEIVFTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLSCGIDSDMIDSVCRMFANGD 160
Cdd:cd23175  112 EDWDIGEQMLRNLYTEIVYTPILTPDGTIVKKFKGNNSGQPSTVVDNTLMVMIAMYYALLKLGIDFEEIDERCVFFCNGD 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 340629666 161 DLLLAVNPDYEYILDLFSNHFSDLGLNFDFSSRTKDKSDLWFMS 204
Cdd:cd23175  192 DLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMS 235

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]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  339 QTEEQKKAAEEQRQKAAADAEAKRKAAAD----EEARKAREAEAERKRQADAAAKGKQDK 394
Cdd:TIGR02794 113 QAEEKQKQAEEAKAKQAAEAKAKAEAEAErkakEEAAKQAEEEAKAKAAAEAKKKAEEAK 172

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKLPNGWVYCDADGSQFDSSLTPYLINAVLDIRLSFM 80
Cdd:cd23175   32 PIDTLLGGKVCVDDFNNQFYSLHLKAPWTVGITKFYGGWDKLLRKLPDGWVYCDADGSQFDSSLTPYLINAVLRIRLHFM 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  81 EEWDIGERMLMNLYTEIVFTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLSCGIDSDMIDSVCRMFANGD 160
Cdd:cd23175  112 EDWDIGEQMLRNLYTEIVYTPILTPDGTIVKKFKGNNSGQPSTVVDNTLMVMIAMYYALLKLGIDFEEIDERCVFFCNGD 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 340629666 161 DLLLAVNPDYEYILDLFSNHFSDLGLNFDFSSRTKDKSDLWFMS 204
Cdd:cd23175  192 DLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMS 235

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666    1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKL--PNGWVYCDaDGSQFDSSLTPYLINAVLDIRLS 78
Cdd:pfam00680 176 PVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLarFGDYVYEL-DYSGFDSSVPPWLIRFAFEILRE 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   79 FME-EWDIGErmLMNLYTEIVFTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLS----CGIDSDMIDSVC 153
Cdd:pfam00680 255 LLGfPSNVKE--WRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKslenDGPRVCNLDKYF 332

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  154 RMFANGDDLLLAVNPDYEYILDLFSNHFSDLGLNFDFSSRT----KDKSDLWFMSTRGIKYNEMYIPKLEKERIVAILEW 229
Cdd:pfam00680 333 DFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKTfpvsRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEY 412

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 340629666  230 DRSK-QPQHRLEAICAsMIEAWGYPDLLHEIRKFYAWLL 267
Cdd:pfam00680 413 IRSKpVPSGQLENIRA-YASHHGYEFYRDLLYRFVEWLA 450

cell envelope integrity inner membrane protein TolA; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 340629666 339 QTEEQKKAAEEQRQKAAADAEAKRKAAADEEARKAREAEAERKRQADAAAKGKQDKD 395
Cdd:PRK09510 126 QAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAE 182

polarized growth protein Scy;

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  336 TPPQTEEQKKAAEEQRQKAAADAEAKRKAAADEEARKAREAEAERKR-QADAAAKGKQDK 394
Cdd:NF041483  362 TAAQLAKAARTAEEVLTKASEDAKATTRAAAEEAERIRREAEAEADRlRGEAADQAEQLK 421

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666 338 PQTEEQKKAAEEQ--RQKAAADAEAKRKAAADEEARKAREAEAERKRQAdAAAKGKQDKDVNVGTSGTIAVPKLKAMSSK 415
Cdd:COG3064   95 AEKAKAAKEAEAAaaAEKAAAAAEKEKAEEAKRKAEEEAKRKAEEERKA-AEAEAAAKAEAEAARAAAAAAAAAAAAAAR 173

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 340629666 416 MRLPMAKGKNILHVEFLLGYKPAQQDISNTRATRA 450
Cdd:COG3064  174 AAAGAAAALVAAAAAAVEAADTAAAAAAALAAAAA 208

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 340629666 341 EEQKKAAEEQRQKAAADAEAKRKAA----ADEEARKAREAEAERKRQADAAAK 389
Cdd:cd22249   12 EAQLKKLEEERRKEREEEEKASEELirklQEEEERQRKREREEQLKQDEELAK 64

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKLPNGWVYCDADGSQFDSSLTPYLINAVLDIRLSFM 80
Cdd:cd23175   32 PIDTLLGGKVCVDDFNNQFYSLHLKAPWTVGITKFYGGWDKLLRKLPDGWVYCDADGSQFDSSLTPYLINAVLRIRLHFM 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  81 EEWDIGERMLMNLYTEIVFTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLSCGIDSDMIDSVCRMFANGD 160
Cdd:cd23175  112 EDWDIGEQMLRNLYTEIVYTPILTPDGTIVKKFKGNNSGQPSTVVDNTLMVMIAMYYALLKLGIDFEEIDERCVFFCNGD 191

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 340629666 161 DLLLAVNPDYEYILDLFSNHFSDLGLNFDFSSRTKDKSDLWFMS 204
Cdd:cd23175  192 DLLIAVSPEHEHILDTFSSSFSELGLNYDFSSRTRDKEELWFMS 235

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666    1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKL--PNGWVYCDaDGSQFDSSLTPYLINAVLDIRLS 78
Cdd:pfam00680 176 PVEYLLLERAFFDPFNQAFMLNNGFHPIQVGINPFDRGWPRLLRRLarFGDYVYEL-DYSGFDSSVPPWLIRFAFEILRE 254

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   79 FME-EWDIGErmLMNLYTEIVFTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLS----CGIDSDMIDSVC 153
Cdd:pfam00680 255 LLGfPSNVKE--WRAILELLIYTPIALPNGTVFKKTGGLPSGSPFTSIINSIVNYLLILYALLKslenDGPRVCNLDKYF 332

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  154 RMFANGDDLLLAVNPDYEYILDLFSNHFSDLGLNFDFSSRT----KDKSDLWFMSTRGIKYNEMYIPKLEKERIVAILEW 229
Cdd:pfam00680 333 DFFTYGDDSLVAVSPDFDPVLDRLSPHLKELGLTITPAKKTfpvsRELEEVSFLKRTFRKTPGGYRPPLDRKRILAQLEY 412

                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 340629666  230 DRSK-QPQHRLEAICAsMIEAWGYPDLLHEIRKFYAWLL 267
Cdd:pfam00680 413 IRSKpVPSGQLENIRA-YASHHGYEFYRDLLYRFVEWLA 450

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKLP-NGWVYCDADGSQFDSSLTPYLINAVLDIRLSF 79
Cdd:cd23169   29 PLDYTIAFRKYFGDFIAAFQKNRIKLEHAVGINPDSVEWTRLYRRLLkKGPNIFAGDYSNFDGSLPPDVMEAAFDIINDW 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  80 MEEW--DIGERMLMNLYTEIVfTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLSCGIDSDMID--SVCRM 155
Cdd:cd23169  109 YDEYvdDEDERVRKVLFEELI-NTIHLVGNLVYQVHGGNPSGNPLTTIINSIVNLLYIRYAWLRITGLTSLSDfkKNVRL 187

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666 156 FANGDDLLLAVNPDYEYILD--LFSNHFSDLGLNFdfssRTKDKS----------DLWFMStRGIKYNE---MYIPKLEK 220
Cdd:cd23169  188 VTYGDDVIISVSDEVKDEFNfvTISEFLKELGITY----TDADKSgdivpyrpleEVTFLK-RGFRPHPtpgLVLAPLDL 262

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|....
gi 340629666 221 ERIVAILEWDRSKqpQHRLEAICASMIEA------WGypdllheiRKFYAWLLE 268
Cdd:cd23169  263 ESIEEQLNWTRKE--DDLLEATIENARAAlllafgHG--------PEYYNKFRQ 306

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  17 NQFYAHHLIGPWTVGITKFYGGWNQLLEKLPNGWVYCDADGSQFDSSLTPYLINAVLDIRLSFMEEWDIGERMLMNLYTe 96
Cdd:cd23192   45 DALKAVCPTGPIAVGINMDSEDVEVIFERLSGFRYHYCLDYSKWDSTQSPAVTAAAIDILADLSEETPLRDSVVETLSS- 123

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  97 ivfTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTMLSC----GIDSDMIDSVCRMFANGDDLLLAVNPDYEY 172
Cdd:cd23192  124 ---PPMGIFDDVIFVTKRGLPSGMPFTSVINSLNHWLLFSAAVLKAyelvGIYTGNVFDEADFFTYGDDGVYAMPPATAS 200

                        170
                 ....*....|....*
gi 340629666 173 ILDLFSNHFSDLGLN 187
Cdd:cd23192  201 VMDEIIENLKSYGLK 215

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]

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  339 QTEEQKKAAEEQRQKAA----ADAEAKRKAAAdeEARKAREAEAERKRQADAAAKGKQDK 394
Cdd:TIGR02794  99 AAEKAAKQAEQAAKQAEekqkQAEEAKAKQAA--EAKAKAEAEAERKAKEEAAKQAEEEA 156

cell envelope integrity inner membrane protein TolA; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 340629666 339 QTEEQKKAAEEQRQKAAADAEAKRKAAADEEARKAREAEAERKRQADAAAKGKQDKD 395
Cdd:PRK09510 126 QAALKQKQAEEAAAKAAAAAKAKAEAEAKRAAAAAKKAAAEAKKKAEAEAAKKAAAE 182

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  51 VYCDADGSQFDSSLTPYLINAvldirlsfmeewdigermlmnlyteivftpiatpdgsvikkfkGNNSGQPSTVVDNTLM 130
Cdd:cd23167    1 HVVESDYSGFDSSISPDLLKA-------------------------------------------GQPSGSPNTSADNSLI 37

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 340629666 131 VILAFNYTMLSCGIDSDMIDSVCrMFANGDDLLLAVN 167
Cdd:cd23167   38 NLLLARLALRKACGRAEFLNSVG-ILVYGDDSLVSVP 73

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  39 WNQLLEKLPNGWVYCdADGSQFDSSLTPYLINAVLDIRLSFMEEWDIGERMLMNLY--TEIVFTPIATPDGsvikkfkGN 116
Cdd:cd23193  124 WTRLFASLKQDNVYD-LDYSGFDASLSSQLFEAAVEVLAECHGDPELVLRYLEPIInsKHVVGDERYTVEG-------GM 195

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 340629666 117 NSGQPSTVVDNTLMVILAFNYTMLSCGIDSdmiDSVCRMFANGDDLLLAVNPD 169
Cdd:cd23193  196 PSGCPCTSILNSICNNLVVRYALLETGKFD---PDEYYILAYGDDVLVSTDEP 245

cell envelope integrity inner membrane protein TolA; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 340629666 333 DAGTPPQTEEQKKAAEEQRQKAAADAEAKRKAAADEEA-----RKAREAEAERKRQADAAAKGK 391
Cdd:PRK09510 182 EAKKKAEAEAAAKAAAEAKKKAEAEAKKKAAAEAKKKAaaeakAAAAKAAAEAKAAAEKAAAAK 245

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   1 PLETLLGGKVCVDDFNNQFY---------AHHLIGPwtVGITKFYGGWNQLLEKLPNGwVYCD-----ADGSQFD---SS 63
Cdd:cd23168   16 RARTILGVSIISTDVGRQLHqavlaaivnTRSANIV--IIGTKFYGGWHKMLRYLYPG-VIEDpvlmgWDYPKCDrsvPN 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  64 LTPYLINAVL----DIRLSFMEEWdigeRMLMNLYTEIVFTPIATpDGSVIKKFKGNNSGQPSTVVDNTLMVILAFNYTM 139
Cdd:cd23168   93 MLRYLANLLLaslyDNCCNLSEIV----HLLINECAQVLYDYVVY-GGNLYRKPGGVSSGDSTTAISNSIYNYFQTFIAN 167

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666 140 LSCGIDSdmidsvcrmfangDDLLLAVNPD-YEYILDLFSNHFsdLGLN------FDFSSRTKDKSDLwFMSTRGIKYNE 212
Cdd:cd23168  168 VRLAILS-------------DDGVACINPDlIDLGDVASVSFF--LASYyytnnkKKYSSTCWVEPHE-FCSPHEFKSDD 231

                        250
                 ....*....|.
gi 340629666 213 MYIPKLEKERI 223
Cdd:cd23168  232 KYQDRVERVYL 242

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  39 WNQL---LEKLPNGwvyCDADGSQFDSSLTPYLINAVLDIrLSFMEEWDIGER---MLMNLYTEIVFTPIATPDgSVIKK 112
Cdd:cd23198   73 WNRLyhyLNRHPNA---VDFDVSNWDGHLPAELFYAVLDI-IKTVLGLKPNSPnakVIYSILTEVMNCHIQFED-IIYQK 147

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666 113 FKGNNSGQPSTVVDNTLMVILAFNYTMLSCGIDSDMIDSVCRMFAN------GDDLLLAVNpdyEYILDLFSNH-----F 181
Cdd:cd23198  148 LRGLISGFPGTAEVNTLAHWLLIYYIYLYLAQNTIYDMTITAFLRNvsaifyGDDIIITIS---DEILHWFNGKtiqrmY 224

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 340629666 182 SDLGlnFDFSSRTKDK--------SDLWFMSTrgiKYNEM----YIPKLEKERIVAILEWDRSKQ 234
Cdd:cd23198  225 EEHG--YPVTSAAKDTeipeskplSDCQFLKS---SWNPIlpgyYIRKMDIEVVYDLVYWVRAKE 284

cell envelope integrity inner membrane protein TolA; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 340629666 341 EEQKKAAEEQRQKAAADA------EAKRKAAAD------EEARKAREAEAERKRQADAAAKGKQD 393
Cdd:PRK09510 150 EAEAKRAAAAAKKAAAEAkkkaeaEAAKKAAAEakkkaeAEAAAKAAAEAKKKAEAEAKKKAAAE 214

cell envelope integrity inner membrane protein TolA; Provisional

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 340629666 339 QTEEQKKAAEEQRQKAAADAEAKRKAAADEEARKAREAEAERKRQADAAAKGKQDKD--VNVGTSG 402
Cdd:PRK09510 204 EAEAKKKAAAEAKKKAAAEAKAAAAKAAAEAKAAAEKAAAAKAAEKAAAAKAAAEVDdlFGGLDSG 269

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 340629666 341 EEQKKAAEEQRQKAAADAEAKRKAAADEEARKAREAEAER------KRQADAAAK 389
Cdd:COG3064    4 ALEEKAAEAAAQERLEQAEAEKRAAAEAEQKAKEEAEEERlaeleaKRQAEEEAR 58

MAEBL; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 340629666  339 QTEEQKKAAEEQRQKAAA--DAEAKRKAaadEEARKAREA-EAERKRQADAAAKGKQDK 394
Cdd:PTZ00121 1491 KAEEAKKKADEAKKAAEAkkKADEAKKA---EEAKKADEAkKAEEAKKADEAKKAEEKK 1546

MAEBL; Provisional

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 340629666  339 QTEEQKKAAEEQRQKAAADA---EAKRKAaadEEARKAREA--EAERKRQADAAAKGKQDK 394
Cdd:PTZ00121 1399 KAEEDKKKADELKKAAAAKKkadEAKKKA---EEKKKADEAkkKAEEAKKADEAKKKAEEA 1456

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666   1 PLETLLGGKVCVDDFNNQFYAHHLIGPWTVGITKFYGGWNQLLEKLPNGWVYCDADGSQFDSSLTPYLINAVLDIRLSFM 80
Cdd:cd23200   29 PVDLILFSGALYGPYKEAYTKAGLKCYHAVGIDPKSVGWQQLATYMTKHPNYFDADYKNYDKYLHRQVFKAVRKIQRSVI 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  81 E-----EWDIGERMLmnlyTEIVFTPIATPDGSVIKKFKGNNSGQPSTVVDNTLMVIL--AFNYTMLSCGIDSDMIDSVC 153
Cdd:cd23200  109 QqvcpdKWDKARAVE----ELDAIDTYVVDYQTVYKTNRGNKSGSYTTTIDNCLANDIygLYAWVKTTGLRSLWDYRQNV 184

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666 154 RMFANGDDLLLAVNPDY--EYILDLFSNHFSDLGLNFDFSSRTKDK------SDLWFMSTRGIKYNEMYIPKLEKERIVA 225
Cdd:cd23200  185 SSVAFGDDIIKSVSDEYkdKYNYCTYRDVLNATGHIMTPGSKDGEEkpftsfENLQFLKRGFKLENGMVLAPLLQRSIEG 264

                        250       260       270
                 ....*....|....*....|....*....|
gi 340629666 226 ILEWD--RSKQPQHRLEAICASMIEA--WG 251
Cdd:cd23200  265 PFVWTdiREDQITVWVNLVQEQLIEAalWG 294

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 340629666 338 PQTEEQKKAAEEQrQKAAADAEAKRKAA-ADEEARKAREAEAERKRQADAAAKGKQDK 394
Cdd:COG3064   85 AAAEAEKKAAAEK-AKAAKEAEAAAAAEkAAAAAEKEKAEEAKRKAEEEAKRKAEEER 141

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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 340629666  36 YGGWNQLLEKLPngWVYCDADGSQFDSSLTPYLINAVLDIRLSFMEEwdigERMLMNLYTEIVFTPIATPDGSVIKKfKG 115
Cdd:cd23216  112 YTHFDSLMDQVK--WNVLALDFKKFDGSLSPQVMEEAVDILASFHDM----PQMVVDIHKHTIYSTNVVSDETWFVE-GG 184

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 340629666 116 NNSGQPSTVVDNTLMVILAFNYTMLSCGIDSDMIdsvcRMFANGDDLLLAVN 167
Cdd:cd23216  185 MCSGSPCTTVLNTICNLLVNTTILLSEGIQPDNF----YIAAYGDDTIISVD 232