NCBI Conserved Domain Search

Conserved domains on [gi|19352424|ref|NP_598184|]

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Nonstructural polyprotein [Sleeping disease virus]

Protein Classification

Graphical summary

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List of domain hits

Name

Accession

Description

Interval

E-value

ps-ssRNAv_RdRp-like super family

cl40470

conserved catalytic core domain of RNA-dependent RNA polymerase (RdRp) from the positive-sense ...

2134-2593

0e+00

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.

The actual alignment was detected with superfamily member cd23250:

Pssm-ID: 477363 Cd Length: 458 Bit Score: 871.79 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2134 MVDGLNCNLDTVTFEPAKVRSLPKKSKYNQPLIQSQVPGPMASTLQSILMAATKRNCNVTQMRELPTMDSAAMNVEAFKK 2213
Cdd:cd23250    1 MVDGSECCLDTATFCPAKLRSYPKKHAYHQPQIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRELPTLDSAAFNVECFKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2214 FACKDTDlWTEFAEKPVRLSPGQIEEYVFHLQGAKANVMHSRVEAACPdLSEVAMDRFTLDMKRDVKVTPGTKHVEERPK 2293
Cdd:cd23250   81 FACNNEY-WEEFKEKPIRLTTENVTTYVTKLKGPKAAALFAKTHNLVP-LQEVPMDRFVMDMKRDVKVTPGTKHTEERPK 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2294 VQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLGDKVLETDISSFDKSQDQAMAVTAL 2373
Cdd:cd23250  159 VQVIQAADPLATAYLCGIHRELVRRLNAVLLPNIHTLFDMSAEDFDAIIAEHFQPGDKVLETDIASFDKSQDDAMALTAL 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2374 MLLEDLGVEEDLLTLIEASFGDITSVHLPTGTRFQFGSMMKSGLFLTLFVNTLLNITIAARVLREQLADTRCAAFIGDDN 2453
Cdd:cd23250  239 MILEDLGVDQELLDLIEAAFGEITSVHLPTGTRFKFGAMMKSGMFLTLFVNTVLNIVIASRVLRERLTNSRCAAFIGDDN 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2454 VITGVVSDDMMVARCASWLNMEVKIMEMEIGDRSPYFCGGFLLLDTVTGTVSRVSDPVKRLMKMGKPALNDPETDVDRCR 2533
Cdd:cd23250  319 IVHGVVSDKLMADRCATWLNMEVKIIDAVIGEKPPYFCGGFILYDSVTGTACRVADPLKRLFKLGKPLPADDEQDEDRRR 398

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2534 ALREEVESWYRVGIQWPLQVAAATRYGVNHLPLATMAMATLAQDLRSYLGARGEYVSLYA 2593
Cdd:cd23250  399 ALHDEVKRWFRVGITSELEVAVESRYEVNGLSNILLAMATLAQSVKNFKALRGPPIHLYG 458

Macro_X_Nsp3-like

cd21557

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...

1436-1563

1.78e-37

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The X-domain, also called Mac1, is the macrodomain found in riboviral non-structural protein 3 (Nsp3), including the Nsp3 of Severe Acute Respiratory Syndrome Coronavirus (SARS-CoV) as well as SARS-CoV-2, and other coronaviruses (alpha-, beta-, gamma-, and deltacoronavirus), among others. The SARS-CoV-2 Nsp3 Mac1 is highly conserved among all CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. It appears to counter host-mediated antiviral ADP-ribosylation, a post-translational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Assays show that the de-MARylating activity leads to a rapid loss of substrate, and that Mac1 could not hydrolyze poly-ADP-ribose; thus, Mac1 is a MAR-hydrolase (mono-ADP ribosylhydrolase). Mac1 was originally named ADP-ribose-1"-phosphatase (ADRP) based on data demonstrating that it could remove the phosphate group from ADP-ribose-1"-phosphate; however, activity was modest and was unclear why this would impact a virus infection. This family also includes the X-domain of Avian infectious bronchitis virus (IBV) strain Beaudette coronavirus that does not bind ADP-ribose; the triple glycine sequence found in the X-domains of SARS-CoV and human coronavirus 229E (HCoV229E), which are involved in ADP-ribose binding, is not conserved in the IBV X-domain. SARS-CoVs have two other macrodomains referred to as the SUD-N (N-terminal subdomain, or Mac2) and SUD-M (middle SUD subdomain, or Mac3) of the SARS-unique domain (SUD), which also do not bind ADP-ribose; these bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). SARS-CoV SUD-N and SUD-M are not included in this group.

Pssm-ID: 438957 Cd Length: 127 Bit Score: 138.07 E-value: 1.78e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1436 EEVLVNAANSNGRPGDGVCGALYGAFGDAFP--------NGAIGAGNAVLVRG--LEATIIHAAGADFREVDeetGARQL 1505
Cdd:cd21557    1 EDVVVNAANENLKHGGGVAGAIYKATGGAFQkesdyikkNGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 19352424 1506 RAAYRAAATLvtangITSAAIPLLSTHIFSngrNRLEQSFGALVEAFDTTECDVTIYC 1563
Cdd:cd21557   78 AAAYKAVNKE-----YGSVLTPLLSAGIFG---VPPEQSLNALLDAVDTTDADVTVYC 127

Vmethyltransf super family

cl46422

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...

30-388

7.62e-26

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA viruses, including Hordei-, Tobra-, Tobamo-, Bromo-, Clostero- and Caliciviruses. This methyltransferase is involved in mRNA capping. Capping of mRNA enhances its stability. This usually occurs in the nucleus. Therefore, many viruses that replicate in the cytoplasm encode their own. This is a specific guanine-7-methyltransferase domain involved in viral mRNA cap0 synthesis. Specificity for guanine 7 position is shown by NMR in and in vivo role in cap synthesis. Based on secondary structure prediction, the basic fold is believed to be similar to the common AdoMet-dependent methyltransferase fold. A curious feature of this methyltransferase domain is that it together with flanking sequences seems to have guanylyltransferase activity coupled to the methyltransferase activity. The domain is found throughout the so-called Alphavirus superfamily, (including alphaviruses and several other groups). It forms the defining, unique feature of this superfamily.

The actual alignment was detected with superfamily member pfam01660:

Pssm-ID: 480762 Cd Length: 308 Bit Score: 110.46 E-value: 7.62e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424     30 KTAFPGFEVVASNRSS--NDHAAARAFSHLATKWIERDIDGRQVIVaDIGSAPARRVGA-PDNVtyHSVCPRKCAEDPER 106
Cdd:pfam01660   10 QELLENLGIEFSPYSVtpHSHPAAKALENLLLEVLPSYLPNPSTVL-DIKGSKLRHLKRgNPNV--HCCNPILDPRDVAR 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    107 lasYARKLVraVEKGDGHLVSDRITDlkdVLENPDTSLETTSIclnddvsckvkadIAVYQDVY--AVDAPSTIYAQADK 184
Cdd:pfam01660   87 ---YPEAFS--LEKSLGNGEDLRPTN---TFEDCRVLAPTTSY-------------AFMHDSLHdwSPEELADLFLRKPK 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    185 GTRVVYWIGFEPFVFHTDAmAGSFPLYDANWSDSavlaaknlplcysglsedsikwrfrfrdkplvpsGEIHYSVGSTH- 263
Cdd:pfam01660  146 LERLYATLVFPPELLFGDK-ESLYPELYTFWYKG----------------------------------DRFHFYPDGHLg 190

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    264 --YVEDRDkLKSWHLPSTFHfvAPNKYTCRCDTVVSCGGYVVKKITICEGIVGRPaneelatsyhrdgVVVTKFSDTInH 341
Cdd:pfam01660  191 gsYTHPLN-LLSWLTTSKIH--LPGGFTYTVERLESRGAHHLFKITRGDGLTPKV-------------IVPDSRTFGP-F 253

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 19352424    342 EQVSFPvVTYIPAVICDQMTAMTADpVKYPDVVKLLVGLNQRIVVNG 388
Cdd:pfam01660  254 EAVLLP-KIFVPRVLNYIRGKPIPL-TVVNKLFSYLRSLKKRVVING 298

FtsJ

pfam01728

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...

1207-1365

1.35e-23

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.

Pssm-ID: 426399 Cd Length: 179 Bit Score: 99.97 E-value: 1.35e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1207 FKTRAAVKFAELTKRVSY----NSVLDLGAARGGVTDYCVKKG-KTVTCVSEQWDS--KPR---GAVVITADINGPLNNL 1276
Cdd:pfam01728    1 YRSRAAYKLLEIDEKFGLlkpgKTVLDLGAAPGGWSQVALQRGaGKVVGVDLGPMQlwKPRndpGVTFIQGDIRDPETLD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1277 -------GIFDLVFCDAAGPRRYHHYAQCEDHARRSTSACKHGVERTAKGGVFIVKAYGMADrrTERAVECTARYFKSVS 1349
Cdd:pfam01728   81 lleellgRKVDLVLSDGSPFISGNKVLDHLRSLDLVKAALEVALELLRKGGNFVCKVFQGED--FSELLYLLKLGFEKVG 158

                          170
                   ....*....|....*.
gi 19352424   1350 VEKPVSSRITNVEVFF 1365
Cdd:pfam01728  159 VFKPPASRPESSEEYL 174

Viral_helicase1 super family

cl26263

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...

748-986

9.71e-15

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated and NTPase activity. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis.

The actual alignment was detected with superfamily member pfam01443:

Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 75.88 E-value: 9.71e-15

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    748 IYGVPGAGKTAIITTEVTTrdlvASGKKENCEDIKRCVLerRGLKIAARTVDSLLYGAYRGAVDTLYVDEAYACHSGTLL 827
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRT----SRVIRPTAELRTEGKP--DLPNLNVRTVDTFLMALLKPTGKILILDEYTLLPPGYIL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    828 ALIAAVRPtGKVVLCGDPKQVGCVNQLQM--RMHYNHEISDRVlrkniSRRCTHTLTAIVsnLNYEGRMKTTNPCKKPVL 905
Cdd:pfam01443   77 LLAAISGA-KLVILFGDPLQIPYHSRAPSflIPHFPSSLSHRV-----GRRTTYLLPSLR--APILSAKGFEVVVERSGE 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    906 IDTTGSTKPDKEALVLTCfrgwVKDLKILYPHnELMTAAASQGLTREKVYAVRCRVTSNPLYEPTSEHITVLLTRTNDEL 985
Cdd:pfam01443  149 YKVDYDPNGVLVLVYLTF----TQALKESLGV-RVTTVHEVQGLTFDSVTLVLDTDTDLLIISDSPEHLYVALTRHRKSL 223


                   .
gi 19352424    986 V 986
Cdd:pfam01443  224 H 224

PHA03307 super family

cl33723

transcriptional regulator ICP4; Provisional

1732-1985

1.19e-07

transcriptional regulator ICP4; Provisional

The actual alignment was detected with superfamily member PHA03307:

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 57.87 E-value: 1.19e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1732 PLTNIQDVTKVECTVRAPAEEPRPvrylqerrPVQAAARQPRPAIVAASVAGTATsrRTPAPGSVQVRLLPPRdgtvsrs 1811
Cdd:PHA03307  137 MLRPVGSPGPPPAASPPAAGASPA--------AVASDAASSRQAALPLSSPEETA--RAPSSPPAEPPPSTPP------- 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1812 srtssqssvtsSAGPIMPVPRRAPVAPAASLAGSVhshSVRSAPAILRAASTGARSVRSVQSGLTGHRDDAVSVAGSVRQ 1891
Cdd:PHA03307  200 -----------AAASPRPPRRSSPISASASSPAPA---PGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITL 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1892 PS--------GPPSSVSTPAAPRGLTREQFGAVR----------ARARRDLELEGSEHGSQASFRSGSLVVGSTASSYSQ 1953
Cdd:PHA03307  266 PTriweasgwNGPSSRPGPASSSSSPRERSPSPSpsspgsgpapSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGP 345

                         250       260       270
                  ....*....|....*....|....*....|..
gi 19352424  1954 RPDDQDTGSEPSGRGAAVRTRRRGQRDGPGGY 1985
Cdd:PHA03307  346 SPSRSPSPSRPPPPADPSSPRKRPRPSRAPSS 377

Name

Accession

Description

Interval

E-value

Togaviridae_RdRp

cd23250

RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ...

2134-2593

0e+00

RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Togaviridae, order Martellivirales. Togaviridae is a family of small, enveloped viruses with [(+)ssRNA] genomes of 10-12 kb, and contains a single genus, Alphavirus. Alphavirus includes a large number of species that are mostly mosquito-borne and pathogenic in their vertebrate hosts. Many are important human and veterinary pathogens (e.g., chikungunya virus, eastern equine encephalitis virus). The genus Alphavirus mainly consists of mosquito-borne viruses although other hematophagous insects, including ticks, lice, and cliff swallow bugs, have been implicated in transmission. Vertebrate hosts include humans, non-human primates, equids, birds, amphibians, reptiles, rodents, and pigs. There are two aquatic alphaviruses, southern elephant seal virus and salmon pancreas disease virus, infecting sea mammals and fish respectively. Interestingly, Eilat virus (EILV) has been shown to only infect insect cells and is incapable of replicating in vertebrate cells. 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: 438100 Cd Length: 458 Bit Score: 871.79 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2134 MVDGLNCNLDTVTFEPAKVRSLPKKSKYNQPLIQSQVPGPMASTLQSILMAATKRNCNVTQMRELPTMDSAAMNVEAFKK 2213
Cdd:cd23250    1 MVDGSECCLDTATFCPAKLRSYPKKHAYHQPQIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRELPTLDSAAFNVECFKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2214 FACKDTDlWTEFAEKPVRLSPGQIEEYVFHLQGAKANVMHSRVEAACPdLSEVAMDRFTLDMKRDVKVTPGTKHVEERPK 2293
Cdd:cd23250   81 FACNNEY-WEEFKEKPIRLTTENVTTYVTKLKGPKAAALFAKTHNLVP-LQEVPMDRFVMDMKRDVKVTPGTKHTEERPK 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2294 VQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLGDKVLETDISSFDKSQDQAMAVTAL 2373
Cdd:cd23250  159 VQVIQAADPLATAYLCGIHRELVRRLNAVLLPNIHTLFDMSAEDFDAIIAEHFQPGDKVLETDIASFDKSQDDAMALTAL 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2374 MLLEDLGVEEDLLTLIEASFGDITSVHLPTGTRFQFGSMMKSGLFLTLFVNTLLNITIAARVLREQLADTRCAAFIGDDN 2453
Cdd:cd23250  239 MILEDLGVDQELLDLIEAAFGEITSVHLPTGTRFKFGAMMKSGMFLTLFVNTVLNIVIASRVLRERLTNSRCAAFIGDDN 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2454 VITGVVSDDMMVARCASWLNMEVKIMEMEIGDRSPYFCGGFLLLDTVTGTVSRVSDPVKRLMKMGKPALNDPETDVDRCR 2533
Cdd:cd23250  319 IVHGVVSDKLMADRCATWLNMEVKIIDAVIGEKPPYFCGGFILYDSVTGTACRVADPLKRLFKLGKPLPADDEQDEDRRR 398

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2534 ALREEVESWYRVGIQWPLQVAAATRYGVNHLPLATMAMATLAQDLRSYLGARGEYVSLYA 2593
Cdd:cd23250  399 ALHDEVKRWFRVGITSELEVAVESRYEVNGLSNILLAMATLAQSVKNFKALRGPPIHLYG 458

RdRP_2

pfam00978

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...

2134-2581

1.51e-108

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The family also contains the following proteins: 2A protein from bromoviruses putative RNA dependent RNA polymerase from tobamoviruses Non structural polyprotein from togaviruses

Pssm-ID: 395779 Cd Length: 440 Bit Score: 354.64 E-value: 1.51e-108

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2134 MVDGlNCNLDTVTFEPAKVRSLPKKS-KYNQPLIQSQVPGPMASTLQSILMAATKRNCNVTQMRELPTMDSAAMNV-EAF 2211
Cdd:pfam00978    1 TSDI-SLDLDDCRLDPSKSKPKPKDKePYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVaERF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2212 KKFACkDTDLWTefAEKPVRLSPGQIEEYVFHLQGAKANVMhsrVEAACPDLSEVAMDRFTLDMKRDVK--VTPGTKHve 2289
Cdd:pfam00978   80 KKSFL-DKEKLD--KLDPIINTTENVSRWLDKQSGKKAAQL---KLDDLVPLHEVDLDRYKHMIKSDVKpkLDLSPQS-- 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2290 ERPKVQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLGDkVLETDISSFDKSQDQAMA 2369
Cdd:pfam00978  152 ERPALQTITYHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHFEFLDASED-FLEIDFSKFDKSQGELHL 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2370 VTALMLLEDLGVEEDLLTLIEAsFGDITSVhlptgTRFQFGSMM------KSGLFLTLFVNTLLNITIAARVLReqLADT 2443
Cdd:pfam00978  231 LVQLEILKLLGLDPELADLWFK-FHRQSYI-----KDRKNGVGFsvdyqrKSGDANTYLGNTLVTMAMLASVYD--LEKI 302

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2444 RCAAFIGDDNVITGVVSDDMMVARCASWLNMEVKIMEMEIgdrsPYFCGGFLLldTVTGTVSRVSDPVKRLMKMGKP-AL 2522
Cdd:pfam00978  303 DCAAFSGDDSLIFSPKPIEDPASRFATLFNMEAKVFDPSV----PYFCSKFLL--EVDGGAFFVPDPLKLLQKLGKKkIP 376

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19352424   2523 NDPETDVDRCRALREEVES---WYRVGIQwpLQVAAATRYGVNH-LPLATMAMATLAQDLRSY 2581
Cdd:pfam00978  377 DDEQHLDEIFTSLCDLTKSfndDCVVLEL--LDLAVARYYKYAPeGYAALCALHKALSSFTLF 437

Macro_X_Nsp3-like

cd21557

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...

1436-1563

1.78e-37

Pssm-ID: 438957 Cd Length: 127 Bit Score: 138.07 E-value: 1.78e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1436 EEVLVNAANSNGRPGDGVCGALYGAFGDAFP--------NGAIGAGNAVLVRG--LEATIIHAAGADFREVDeetGARQL 1505
Cdd:cd21557    1 EDVVVNAANENLKHGGGVAGAIYKATGGAFQkesdyikkNGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 19352424 1506 RAAYRAAATLvtangITSAAIPLLSTHIFSngrNRLEQSFGALVEAFDTTECDVTIYC 1563
Cdd:cd21557   78 AAAYKAVNKE-----YGSVLTPLLSAGIFG---VPPEQSLNALLDAVDTTDADVTVYC 127

Vmethyltransf

pfam01660

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...

30-388

7.62e-26

Pssm-ID: 396298 Cd Length: 308 Bit Score: 110.46 E-value: 7.62e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424     30 KTAFPGFEVVASNRSS--NDHAAARAFSHLATKWIERDIDGRQVIVaDIGSAPARRVGA-PDNVtyHSVCPRKCAEDPER 106
Cdd:pfam01660   10 QELLENLGIEFSPYSVtpHSHPAAKALENLLLEVLPSYLPNPSTVL-DIKGSKLRHLKRgNPNV--HCCNPILDPRDVAR 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    107 lasYARKLVraVEKGDGHLVSDRITDlkdVLENPDTSLETTSIclnddvsckvkadIAVYQDVY--AVDAPSTIYAQADK 184
Cdd:pfam01660   87 ---YPEAFS--LEKSLGNGEDLRPTN---TFEDCRVLAPTTSY-------------AFMHDSLHdwSPEELADLFLRKPK 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    185 GTRVVYWIGFEPFVFHTDAmAGSFPLYDANWSDSavlaaknlplcysglsedsikwrfrfrdkplvpsGEIHYSVGSTH- 263
Cdd:pfam01660  146 LERLYATLVFPPELLFGDK-ESLYPELYTFWYKG----------------------------------DRFHFYPDGHLg 190

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    264 --YVEDRDkLKSWHLPSTFHfvAPNKYTCRCDTVVSCGGYVVKKITICEGIVGRPaneelatsyhrdgVVVTKFSDTInH 341
Cdd:pfam01660  191 gsYTHPLN-LLSWLTTSKIH--LPGGFTYTVERLESRGAHHLFKITRGDGLTPKV-------------IVPDSRTFGP-F 253

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 19352424    342 EQVSFPvVTYIPAVICDQMTAMTADpVKYPDVVKLLVGLNQRIVVNG 388
Cdd:pfam01660  254 EAVLLP-KIFVPRVLNYIRGKPIPL-TVVNKLFSYLRSLKKRVVING 298

FtsJ

pfam01728

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...

1207-1365

1.35e-23

Pssm-ID: 426399 Cd Length: 179 Bit Score: 99.97 E-value: 1.35e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1207 FKTRAAVKFAELTKRVSY----NSVLDLGAARGGVTDYCVKKG-KTVTCVSEQWDS--KPR---GAVVITADINGPLNNL 1276
Cdd:pfam01728    1 YRSRAAYKLLEIDEKFGLlkpgKTVLDLGAAPGGWSQVALQRGaGKVVGVDLGPMQlwKPRndpGVTFIQGDIRDPETLD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1277 -------GIFDLVFCDAAGPRRYHHYAQCEDHARRSTSACKHGVERTAKGGVFIVKAYGMADrrTERAVECTARYFKSVS 1349
Cdd:pfam01728   81 lleellgRKVDLVLSDGSPFISGNKVLDHLRSLDLVKAALEVALELLRKGGNFVCKVFQGED--FSELLYLLKLGFEKVG 158

                          170
                   ....*....|....*.
gi 19352424   1350 VEKPVSSRITNVEVFF 1365
Cdd:pfam01728  159 VFKPPASRPESSEEYL 174

A1pp

smart00506

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...

1424-1545

3.70e-20

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).

Pssm-ID: 214701 Cd Length: 133 Bit Score: 88.52 E-value: 3.70e-20

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    1424 YRVLNKNIITAEEEVLVNAANSNGRPGDGVCGALYGAFG-----DAFPN---GAIGAGNAVLVRGLEAT---IIHAAGAD 1492
Cdd:smart00506    2 LKVVKGDITKPRADAIVNAANSDGAHGGGVAGAIARAAGkalskEEVRKlagGECPVGTAVVTEGGNLPakyVIHAVGPR 81

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 19352424    1493 FREvDEETGARQLRAAYRAAATLVTANGITSAAIPLLSTHIFSNGRNRLEQSF 1545
Cdd:smart00506   82 ASG-HSKEGFELLENAYRNCLELAIELGITSVALPLIGTGIYGVPKDRSAQAL 133

YmdB

COG2110

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...

1430-1578

1.92e-17

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];

Pssm-ID: 441713 Cd Length: 168 Bit Score: 82.15 E-value: 1.92e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1430 NIITAEEEVLVNAANSNGRPGDGVCGALYGAFG--------DAFPNGAIGAGNAVLVRG--LEAT-IIHAAGADFREVDE 1498
Cdd:COG2110    7 DITELDVDAIVNAANSSLLGGGGVAGAIHRAAGpelleecrRLCKQGGCPTGEAVITPAgnLPAKyVIHTVGPVWRGGGP 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1499 ETgARQLRAAYRAAATLVTANGITSAAIPLLSTHIF----SNGRNRLEQSFGALVEAFDTTEcDVTIYCLANNMAARIQQ 1574
Cdd:COG2110   87 SE-EELLASCYRNSLELAEELGIRSIAFPAIGTGVGgfpwEEAAPIAVETLRDFLEEHPSLE-EVRFVLFDEEDYEAYRR 164


                 ....
gi 19352424 1575 LIDD 1578
Cdd:COG2110  165 ALAR 168

Macro

pfam01661

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...

1440-1534

5.54e-16

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent: in certain cases it is believed to bind non-covalently; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site.

Pssm-ID: 460286 Cd Length: 116 Bit Score: 76.06 E-value: 5.54e-16

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1440 VNAANSNGRPGDGVCGALYGAFGDAF-------PNGAIGAGNAVLVRG--LEAT-IIHAAGADFREVDEETGARQLRAAY 1509
Cdd:pfam01661    1 VNAANSRLLGGGGVAGAIHRAAGPELleecrelKKGGCPTGEAVVTPGgnLPAKyVIHTVGPTWRHGGSHGEEELLESCY 80

                           90       100
                   ....*....|....*....|....*
gi 19352424   1510 RAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:pfam01661   81 RNALALAEELGIKSIAFPAISTGIY 105

Viral_helicase1

pfam01443

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...

748-986

9.71e-15

Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 75.88 E-value: 9.71e-15

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    748 IYGVPGAGKTAIITTEVTTrdlvASGKKENCEDIKRCVLerRGLKIAARTVDSLLYGAYRGAVDTLYVDEAYACHSGTLL 827
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRT----SRVIRPTAELRTEGKP--DLPNLNVRTVDTFLMALLKPTGKILILDEYTLLPPGYIL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    828 ALIAAVRPtGKVVLCGDPKQVGCVNQLQM--RMHYNHEISDRVlrkniSRRCTHTLTAIVsnLNYEGRMKTTNPCKKPVL 905
Cdd:pfam01443   77 LLAAISGA-KLVILFGDPLQIPYHSRAPSflIPHFPSSLSHRV-----GRRTTYLLPSLR--APILSAKGFEVVVERSGE 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    906 IDTTGSTKPDKEALVLTCfrgwVKDLKILYPHnELMTAAASQGLTREKVYAVRCRVTSNPLYEPTSEHITVLLTRTNDEL 985
Cdd:pfam01443  149 YKVDYDPNGVLVLVYLTF----TQALKESLGV-RVTTVHEVQGLTFDSVTLVLDTDTDLLIISDSPEHLYVALTRHRKSL 223


                   .
gi 19352424    986 V 986
Cdd:pfam01443  224 H 224

PRK00431

ADP-ribose-binding protein;

1425-1534

1.64e-08

ADP-ribose-binding protein;

Pssm-ID: 234759 Cd Length: 177 Bit Score: 56.39 E-value: 1.64e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1425 RVLNKNIITAEEEVLVNAANSNGRPGDGVCGALYGAFGDA---------FPNGAIGAGNAVLVRG--LEAT-IIHAAGAD 1492
Cdd:PRK00431    6 EVVQGDITELEVDAIVNAANSSLLGGGGVDGAIHRAAGPEileecrelrQQQGPCPTGEAVITSAgrLPAKyVIHTVGPV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 19352424  1493 FREVDEETgARQLRAAYRAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:PRK00431   86 WRGGEDNE-AELLASAYRNSLRLAAELGLRSIAFPAISTGVY 126

PHA03307

transcriptional regulator ICP4; Provisional

1732-1985

1.19e-07

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 57.87 E-value: 1.19e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1732 PLTNIQDVTKVECTVRAPAEEPRPvrylqerrPVQAAARQPRPAIVAASVAGTATsrRTPAPGSVQVRLLPPRdgtvsrs 1811
Cdd:PHA03307  137 MLRPVGSPGPPPAASPPAAGASPA--------AVASDAASSRQAALPLSSPEETA--RAPSSPPAEPPPSTPP------- 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1812 srtssqssvtsSAGPIMPVPRRAPVAPAASLAGSVhshSVRSAPAILRAASTGARSVRSVQSGLTGHRDDAVSVAGSVRQ 1891
Cdd:PHA03307  200 -----------AAASPRPPRRSSPISASASSPAPA---PGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITL 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1892 PS--------GPPSSVSTPAAPRGLTREQFGAVR----------ARARRDLELEGSEHGSQASFRSGSLVVGSTASSYSQ 1953
Cdd:PHA03307  266 PTriweasgwNGPSSRPGPASSSSSPRERSPSPSpsspgsgpapSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGP 345

                         250       260       270
                  ....*....|....*....|....*....|..
gi 19352424  1954 RPDDQDTGSEPSGRGAAVRTRRRGQRDGPGGY 1985
Cdd:PHA03307  346 SPSRSPSPSRPPPPADPSSPRKRPRPSRAPSS 377

DEXXQc_Upf1-like

cd17934

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...

748-847

8.73e-05

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, HELZ, Mov10L1, Aquarius, IGHMBP2 (SMUBP2), coronavirus Nsp13, and similar proteins. They belong to the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 438708 [Multi-domain] Cd Length: 121 Bit Score: 44.15 E-value: 8.73e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  748 IYGVPGAGKTAIITTEVTTRDLVASGKKencedikrcVLerrglkIAART---VDsllygayrgAVDTLYVDEAYACHSG 824
Cdd:cd17934    4 IQGPPGTGKTTTIAAIVLQLLKGLRGKR---------VL------VTAQSnvaVD---------NVDVVIIDEASQITEP 59

                         90       100
                 ....*....|....*....|...
gi 19352424  825 TLLALIAAVRptgKVVLCGDPKQ 847
Cdd:cd17934   60 ELLIALIRAK---KVVLVGDPKQ 79

DNA2

COG1112

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];

811-896

8.44e-04

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];

Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 44.73 E-value: 8.44e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  811 DTLYVDEAYAChsgTLLALIAAVRPTGKVVLCGDPKQ---VGCVNQLQMRMHYNHEIS--DRVLRK--------NISRRC 877
Cdd:COG1112  557 DLVIIDEASQA---TLAEALGALARAKRVVLVGDPKQlppVVFGEEAEEVAEEGLDESllDRLLARlpergvmlREHYRM 633

                         90
                 ....*....|....*....
gi 19352424  878 THTLTAIVSNLNYEGRMKT 896
Cdd:COG1112  634 HPEIIAFSNRLFYDGKLVP 652

RlmE

COG0293

23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...

1210-1364

1.32e-03

23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]; 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification

Pssm-ID: 440062 [Multi-domain] Cd Length: 208 Bit Score: 42.37 E-value: 1.32e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1210 RAAVKFAELTKR----VSYNSVLDLGAARGGVTDYCVKK----GKTVTCVSEQWDSKPrGAVVITADINGP--------- 1272
Cdd:COG0293   33 RAAYKLLEIDEKdkliKPGMRVVDLGAAPGGWSQVAAKRvggkGRVIALDLLPMEPIP-GVEFIQGDFREDevldqllea 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1273 LNNLGiFDLVFCDAA----GprryhHYAQceDHARR---STSACKHGVERTAKGGVFIVKAY-GMADRRTERAVEctaRY 1344
Cdd:COG0293  112 LGGRK-VDLVLSDMApntsG-----HKSV--DHARSmylVELALDFARKVLKPGGAFVVKVFqGEGFDELLKELK---KL 180

                        170       180
                 ....*....|....*....|
gi 19352424 1345 FKSVSVEKPVSSRITNVEVF 1364
Cdd:COG0293  181 FKKVKHRKPKASRARSSEVY 200

Name

Accession

Description

Interval

E-value

Togaviridae_RdRp

cd23250

RNA-dependent RNA polymerase (RdRp) in the family Togaviridae of positive-sense ...

2134-2593

0e+00

Pssm-ID: 438100 Cd Length: 458 Bit Score: 871.79 E-value: 0e+00

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2134 MVDGLNCNLDTVTFEPAKVRSLPKKSKYNQPLIQSQVPGPMASTLQSILMAATKRNCNVTQMRELPTMDSAAMNVEAFKK 2213
Cdd:cd23250    1 MVDGSECCLDTATFCPAKLRSYPKKHAYHQPQIRSAVPSPFQNTLQNVLAAATKRNCNVTQMRELPTLDSAAFNVECFKK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2214 FACKDTDlWTEFAEKPVRLSPGQIEEYVFHLQGAKANVMHSRVEAACPdLSEVAMDRFTLDMKRDVKVTPGTKHVEERPK 2293
Cdd:cd23250   81 FACNNEY-WEEFKEKPIRLTTENVTTYVTKLKGPKAAALFAKTHNLVP-LQEVPMDRFVMDMKRDVKVTPGTKHTEERPK 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2294 VQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLGDKVLETDISSFDKSQDQAMAVTAL 2373
Cdd:cd23250  159 VQVIQAADPLATAYLCGIHRELVRRLNAVLLPNIHTLFDMSAEDFDAIIAEHFQPGDKVLETDIASFDKSQDDAMALTAL 238

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2374 MLLEDLGVEEDLLTLIEASFGDITSVHLPTGTRFQFGSMMKSGLFLTLFVNTLLNITIAARVLREQLADTRCAAFIGDDN 2453
Cdd:cd23250  239 MILEDLGVDQELLDLIEAAFGEITSVHLPTGTRFKFGAMMKSGMFLTLFVNTVLNIVIASRVLRERLTNSRCAAFIGDDN 318

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2454 VITGVVSDDMMVARCASWLNMEVKIMEMEIGDRSPYFCGGFLLLDTVTGTVSRVSDPVKRLMKMGKPALNDPETDVDRCR 2533
Cdd:cd23250  319 IVHGVVSDKLMADRCATWLNMEVKIIDAVIGEKPPYFCGGFILYDSVTGTACRVADPLKRLFKLGKPLPADDEQDEDRRR 398

                        410       420       430       440       450       460
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2534 ALREEVESWYRVGIQWPLQVAAATRYGVNHLPLATMAMATLAQDLRSYLGARGEYVSLYA 2593
Cdd:cd23250  399 ALHDEVKRWFRVGITSELEVAVESRYEVNGLSNILLAMATLAQSVKNFKALRGPPIHLYG 458

RdRP_2

pfam00978

RNA dependent RNA polymerase; This family may represent an RNA dependent RNA polymerase. The ...

2134-2581

1.51e-108

Pssm-ID: 395779 Cd Length: 440 Bit Score: 354.64 E-value: 1.51e-108

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2134 MVDGlNCNLDTVTFEPAKVRSLPKKS-KYNQPLIQSQVPGPMASTLQSILMAATKRNCNVTQMRELPTMDSAAMNV-EAF 2211
Cdd:pfam00978    1 TSDI-SLDLDDCRLDPSKSKPKPKDKePYLVPVLRTAAPSPRQNTLKEVLLALKKRNFNVPELQESVDLDDTAERVaERF 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2212 KKFACkDTDLWTefAEKPVRLSPGQIEEYVFHLQGAKANVMhsrVEAACPDLSEVAMDRFTLDMKRDVK--VTPGTKHve 2289
Cdd:pfam00978   80 KKSFL-DKEKLD--KLDPIINTTENVSRWLDKQSGKKAAQL---KLDDLVPLHEVDLDRYKHMIKSDVKpkLDLSPQS-- 151

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2290 ERPKVQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLGDkVLETDISSFDKSQDQAMA 2369
Cdd:pfam00978  152 ERPALQTITYHDKGVTAYFSPIFRELFERLLYVLKPKIVFPTGMTSSLIAEHFEFLDASED-FLEIDFSKFDKSQGELHL 230

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2370 VTALMLLEDLGVEEDLLTLIEAsFGDITSVhlptgTRFQFGSMM------KSGLFLTLFVNTLLNITIAARVLReqLADT 2443
Cdd:pfam00978  231 LVQLEILKLLGLDPELADLWFK-FHRQSYI-----KDRKNGVGFsvdyqrKSGDANTYLGNTLVTMAMLASVYD--LEKI 302

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   2444 RCAAFIGDDNVITGVVSDDMMVARCASWLNMEVKIMEMEIgdrsPYFCGGFLLldTVTGTVSRVSDPVKRLMKMGKP-AL 2522
Cdd:pfam00978  303 DCAAFSGDDSLIFSPKPIEDPASRFATLFNMEAKVFDPSV----PYFCSKFLL--EVDGGAFFVPDPLKLLQKLGKKkIP 376

                          410       420       430       440       450       460
                   ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 19352424   2523 NDPETDVDRCRALREEVES---WYRVGIQwpLQVAAATRYGVNH-LPLATMAMATLAQDLRSY 2581
Cdd:pfam00978  377 DDEQHLDEIFTSLCDLTKSfndDCVVLEL--LDLAVARYYKYAPeGYAALCALHKALSSFTLF 437

ps-ssRNAv_Martellivirales_RdRp

cd23208

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of ...

2269-2455

8.20e-57

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Martellivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Martellivirales, class Alsuviricetes. The order Martellivirales consists of seven families: Bromoviridae, Closteroviridae, Endornaviridae, Kitaviridae, Mayoviridae, Togaviridae, and Virgaviridae. 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: 438058 [Multi-domain] Cd Length: 190 Bit Score: 195.66 E-value: 8.20e-57

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2269 DRFTLDMKRDVKVTPGTKHVEERPKVQVIQAADPMATAYLCAIHRELVRRLKAVL--KPSIHVLFDMSSEDFDAIVGHGM 2346
Cdd:cd23208    1 DKYEMMIKSDVKPKLDLTAQQEYPKLQTIVYHDKNITAIFCPIFKELFERLLSCLkkKVVIYTGMMTSAELNDFISALHL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2347 KLGDKVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTLIEASFGDiTSVHLPTGTRFQFGS-MMKSGLFLTLFVNT 2425
Cdd:cd23208   81 ESGYYVLEIDFSKFDKSQGALHLLTELLILRRLGVDEPLLVLWEFAHTQ-STTRDINNGISFETAyQRKSGDAFTYFGNT 159

                        170       180       190
                 ....*....|....*....|....*....|
gi 19352424 2426 LLNITIAARVLreQLADTRCAAFIGDDNVI 2455
Cdd:cd23208  160 LVTMAALLDVL--DLEKIVCIAFGGDDSLI 187

Macro_X_Nsp3-like

cd21557

X-domain (or Mac1 domain) of viral non-structural protein 3 and related macrodomains; The ...

1436-1563

1.78e-37

Pssm-ID: 438957 Cd Length: 127 Bit Score: 138.07 E-value: 1.78e-37

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1436 EEVLVNAANSNGRPGDGVCGALYGAFGDAFP--------NGAIGAGNAVLVRG--LEATIIHAAGADFREVDeetGARQL 1505
Cdd:cd21557    1 EDVVVNAANENLKHGGGVAGAIYKATGGAFQkesdyikkNGPLKVGTAVLLPGhgLAKNIIHVVGPRKRKGQ---DDQLL 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 19352424 1506 RAAYRAAATLvtangITSAAIPLLSTHIFSngrNRLEQSFGALVEAFDTTECDVTIYC 1563
Cdd:cd21557   78 AAAYKAVNKE-----YGSVLTPLLSAGIFG---VPPEQSLNALLDAVDTTDADVTVYC 127

Kitaviridae_RdRp

cd23254

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of ...

2270-2518

1.88e-27

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Kitaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Kitaviridae, order Martellivirales. The family Kitaviridae is composed of five recognized species among the three genera: Blueberry necrotic ring blotch virus and Tea plant necrotic ring blotch virus (genus Blunervirus); Citrus leprosis virus C and Citrus leprosis virus C2 (genus Cilevirus); and Hibiscus green spot virus 2 (genus Higrevirus). Although related, there are considerable physical and genetic distinctions between members of the different genera. For example, cile- and higreviruses are associated with a bacilliform virion, whereas a spherical virion has been observed for the lone blunervirus for which microscopy has been reported. Moreover, the replication-associated polyproteins are encoded by a single genomic RNA for cile- and higreviruses, but are split between two genomic RNAs for blunerviruses. 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: 438104 Cd Length: 267 Bit Score: 114.17 E-value: 1.88e-27

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2270 RFTLDMKRDVKVTPGTKHVEERPKVQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIV-----GH 2344
Cdd:cd23254    2 VYSFMIKRNPKPNLTVDAAYKYPALQTIAYHDKDINAIFCPIFRELKKRLLAVLKPNFVIFTDMSPEDFEELLnrrfpPE 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2345 GMKLGDKVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTL-----IEASFGDITSvHLPTGTRFQfgsmMKSGLFL 2419
Cdd:cd23254   82 VLSKLLHKLEIDISKYDKSQGELALLFECKLMRRFGVPEELVELwfnahVLTTLYDRTN-KLKALVEYQ----RKSGDAS 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2420 TLFVNTLLNITIAARVLReqLADTRCAAFIGDDNVITG-VVSDDMMVARCASWLNMEVKIMEMEigdrSPYFCGGFLLld 2498
Cdd:cd23254  157 TFFGNTLFLMAVLADLFD--LSDLELALFSGDDSLLFGrNLLDYDDSQHFALKFNLESKFLNYK----YPYFCSKFLL-- 228

                        250       260
                 ....*....|....*....|
gi 19352424 2499 TVTGTVSRVSDPVKRLMKMG 2518
Cdd:cd23254  229 PVGGRWYFVPDPVKLLTKLG 248

Vmethyltransf

pfam01660

Viral methyltransferase; This RNA methyltransferase domain is found in a wide range of ssRNA ...

30-388

7.62e-26

Pssm-ID: 396298 Cd Length: 308 Bit Score: 110.46 E-value: 7.62e-26

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424     30 KTAFPGFEVVASNRSS--NDHAAARAFSHLATKWIERDIDGRQVIVaDIGSAPARRVGA-PDNVtyHSVCPRKCAEDPER 106
Cdd:pfam01660   10 QELLENLGIEFSPYSVtpHSHPAAKALENLLLEVLPSYLPNPSTVL-DIKGSKLRHLKRgNPNV--HCCNPILDPRDVAR 86

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    107 lasYARKLVraVEKGDGHLVSDRITDlkdVLENPDTSLETTSIclnddvsckvkadIAVYQDVY--AVDAPSTIYAQADK 184
Cdd:pfam01660   87 ---YPEAFS--LEKSLGNGEDLRPTN---TFEDCRVLAPTTSY-------------AFMHDSLHdwSPEELADLFLRKPK 145

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    185 GTRVVYWIGFEPFVFHTDAmAGSFPLYDANWSDSavlaaknlplcysglsedsikwrfrfrdkplvpsGEIHYSVGSTH- 263
Cdd:pfam01660  146 LERLYATLVFPPELLFGDK-ESLYPELYTFWYKG----------------------------------DRFHFYPDGHLg 190

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    264 --YVEDRDkLKSWHLPSTFHfvAPNKYTCRCDTVVSCGGYVVKKITICEGIVGRPaneelatsyhrdgVVVTKFSDTInH 341
Cdd:pfam01660  191 gsYTHPLN-LLSWLTTSKIH--LPGGFTYTVERLESRGAHHLFKITRGDGLTPKV-------------IVPDSRTFGP-F 253

                          330       340       350       360
                   ....*....|....*....|....*....|....*....|....*..
gi 19352424    342 EQVSFPvVTYIPAVICDQMTAMTADpVKYPDVVKLLVGLNQRIVVNG 388
Cdd:pfam01660  254 EAVLLP-KIFVPRVLNYIRGKPIPL-TVVNKLFSYLRSLKKRVVING 298

Closteroviridae_RdRp

cd23253

RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense ...

2270-2520

4.53e-25

RNA-dependent RNA polymerase (RdRp) in the family Closteroviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Closteroviridae, order Martellivirales. Viruses in the family Closteroviridae have a mono-, bi- or tripartite (+)ssRNA genome of 13-19 kb, and non-enveloped, filamentous particles 650-2200 nm long and 12 nm in diameter. They infect plants, mainly dicots, many of which are fruit crops. Members of the family are classified into four genera: Ampelovirus, Closterovirus, Crinivirus and Velarivirus. Their genetic diversity is primarily influenced by strong negative selection and recombination. Closteroviridae viruses are mostly phloem-restricted and induce specific cytoplasmic aggregates of virus particles intermingled with membranous vesicles derived from the endoplasmic reticulum and possibly mitochondria. Their transmission is by aphids, whiteflies, pseudococcid mealybugs or soft scale insects in a semi-persistent manner. 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: 438103 Cd Length: 266 Bit Score: 107.26 E-value: 4.53e-25

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2270 RFTLDMKRDVKVTPGTKHVEERPKVQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIhVLFD-MSSEDFDAIVGHgmKL 2348
Cdd:cd23253    2 SFKLMVKGDMKPKLDSSSLSKYPPGQNIVYHERAINAFFSPIFLEVFDRIKYCLSDKI-ILYSgMNLEELASLIRS--KL 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2349 GD-----KVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTLIEASFGDITSVHLPTGTRFQFGSMMKSGLFLTLFV 2423
Cdd:cd23253   79 GDpldeyKTVEIDFSKFDKSQGVLFKVYEELVYKFFGFSEELYDNWKCSEYFSCRATSDSGVSLELGAQRRTGSPNTWLG 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2424 NTLLNITIAARVLReqLADTRCAAFIGDDNVI---------TGVVSDDMmvarcaswlNMEVKIMEmeigDRSPYFCGGF 2494
Cdd:cd23253  159 NTLVTLGILSSSYD--LDDIDLLLVSGDDSLIfskkplpnkANEINLDF---------GFEAKFIE----NSVPYFCSKF 223

                        250       260
                 ....*....|....*....|....*.
gi 19352424 2495 LLldTVTGTVSRVSDPVKRLMKMGKP 2520
Cdd:cd23253  224 II--EDRGKIKVVPDPVKLFEKLSVP 247

FtsJ

pfam01728

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...

1207-1365

1.35e-23

Pssm-ID: 426399 Cd Length: 179 Bit Score: 99.97 E-value: 1.35e-23

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1207 FKTRAAVKFAELTKRVSY----NSVLDLGAARGGVTDYCVKKG-KTVTCVSEQWDS--KPR---GAVVITADINGPLNNL 1276
Cdd:pfam01728    1 YRSRAAYKLLEIDEKFGLlkpgKTVLDLGAAPGGWSQVALQRGaGKVVGVDLGPMQlwKPRndpGVTFIQGDIRDPETLD 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1277 -------GIFDLVFCDAAGPRRYHHYAQCEDHARRSTSACKHGVERTAKGGVFIVKAYGMADrrTERAVECTARYFKSVS 1349
Cdd:pfam01728   81 lleellgRKVDLVLSDGSPFISGNKVLDHLRSLDLVKAALEVALELLRKGGNFVCKVFQGED--FSELLYLLKLGFEKVG 158

                          170
                   ....*....|....*.
gi 19352424   1350 VEKPVSSRITNVEVFF 1365
Cdd:pfam01728  159 VFKPPASRPESSEEYL 174

A1pp

smart00506

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by ...

1424-1545

3.70e-20

Appr-1"-p processing enzyme; Function determined by Martzen et al. Extended family detected by reciprocal PSI-BLAST searches (unpublished results, and Pehrson _ Fuji).

Pssm-ID: 214701 Cd Length: 133 Bit Score: 88.52 E-value: 3.70e-20

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    1424 YRVLNKNIITAEEEVLVNAANSNGRPGDGVCGALYGAFG-----DAFPN---GAIGAGNAVLVRGLEAT---IIHAAGAD 1492
Cdd:smart00506    2 LKVVKGDITKPRADAIVNAANSDGAHGGGVAGAIARAAGkalskEEVRKlagGECPVGTAVVTEGGNLPakyVIHAVGPR 81

                            90       100       110       120       130
                    ....*....|....*....|....*....|....*....|....*....|...
gi 19352424    1493 FREvDEETGARQLRAAYRAAATLVTANGITSAAIPLLSTHIFSNGRNRLEQSF 1545
Cdd:smart00506   82 ASG-HSKEGFELLENAYRNCLELAIELGITSVALPLIGTGIYGVPKDRSAQAL 133

Virgaviridae_RdRp

cd23251

RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense ...

2128-2519

2.70e-18

RNA-dependent RNA polymerase (RdRp) in the family Virgaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Virgaviridae, order Martellivirales. The Virgaviridae is a family of plant viruses with rod-shaped virions, a (+)ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein similar to those of the alpha-like supergroup. Plants serve as natural hosts. The name of the family is derived from the Latin word virga (rod), as all viruses in this family are rod-shaped. There are currently 59 species in this family, divided among seven genera: Goravirus, Furovirus, Hordeivirus, Pecluvirus, Pomovirus, Tobamovirus, and Tobravirus. 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: 438101 Cd Length: 427 Bit Score: 90.37 E-value: 2.70e-18

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2128 YDAYLDMVDGLNCNLDTVTFEPAKVRSLPKKSKYNQPLIQSQVPGPMASTLQSILMAATKRNCNVTQMRELPTMDSAAMN 2207
Cdd:cd23251   11 FDGYTVATSDINLNVEDCTLDPSKSVKVWQEKEGLKPVLRTAMPEKRQNGLLESLLALIKRNMAAPKLQGAVNEFETIER 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2208 V--EAFKKFackdtdlwteFAEKPVRLSPGQIEEYV--------FHLQGAKANVMHSrveaacpdLSEVAMDRFTLDMKR 2277
Cdd:cd23251   91 VikKAKDVF----------FDEDLIDRSPLSTRESFlrwwdkqsTTARAQLLADDRV--------LDEIDVCTYNFMIKN 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2278 DVK----VTPGTkhveERPKVQVIQAADPMATAYLCAIHRELVRRLKAVLKPsiHVLFD--MSSEDFDAIVGH-GMKLGD 2350
Cdd:cd23251  153 DVKpkldLSPQS----EYAALQTVVYPDKIVNALFGPIFKEINERILSALDP--HVVFNtrMTAEELNETVEFlDPDEEY 226

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2351 KVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTLIEASfgditsvHLPTGTR-FQFGSM------MKSGLFLTLFV 2423
Cdd:cd23251  227 DALEIDFSKFDKSKTSLHIRAVIELYKLFGLDGMLAFLWEKS-------QCQTTVKdRQNGIKayllyqQKSGNCDTYGS 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2424 NTLlnitIAARVLREQLADTRC--AAFIGDDNVI---TGVVSDDMMvARCASWLNMEVKIMEMeigdRSPYFCGGFLLld 2498
Cdd:cd23251  300 NTW----SAALALLSMLPLEKAifMIFGGDDSLIlfpKGLVIPDPC-RRLASLWNFECKLFKF----KYGYFCGKFLL-- 368

                        410       420
                 ....*....|....*....|..
gi 19352424 2499 tVTGTVSRVS-DPVKRLMKMGK 2519
Cdd:cd23251  369 -KHGDGYIFYpDPLKLITKLGR 389

YmdB

COG2110

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ...

1430-1578

1.92e-17

O-acetyl-ADP-ribose deacetylase (regulator of RNase III), contains Macro domain [Translation, ribosomal structure and biogenesis];

Pssm-ID: 441713 Cd Length: 168 Bit Score: 82.15 E-value: 1.92e-17

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1430 NIITAEEEVLVNAANSNGRPGDGVCGALYGAFG--------DAFPNGAIGAGNAVLVRG--LEAT-IIHAAGADFREVDE 1498
Cdd:COG2110    7 DITELDVDAIVNAANSSLLGGGGVAGAIHRAAGpelleecrRLCKQGGCPTGEAVITPAgnLPAKyVIHTVGPVWRGGGP 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1499 ETgARQLRAAYRAAATLVTANGITSAAIPLLSTHIF----SNGRNRLEQSFGALVEAFDTTEcDVTIYCLANNMAARIQQ 1574
Cdd:COG2110   87 SE-EELLASCYRNSLELAEELGIRSIAFPAIGTGVGgfpwEEAAPIAVETLRDFLEEHPSLE-EVRFVLFDEEDYEAYRR 164


                 ....
gi 19352424 1575 LIDD 1578
Cdd:COG2110  165 ALAR 168

Macro

pfam01661

Macro domain; The Macro or A1pp domain is a module of about 180 amino acids which can bind ...

1440-1534

5.54e-16

Pssm-ID: 460286 Cd Length: 116 Bit Score: 76.06 E-value: 5.54e-16

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424   1440 VNAANSNGRPGDGVCGALYGAFGDAF-------PNGAIGAGNAVLVRG--LEAT-IIHAAGADFREVDEETGARQLRAAY 1509
Cdd:pfam01661    1 VNAANSRLLGGGGVAGAIHRAAGPELleecrelKKGGCPTGEAVVTPGgnLPAKyVIHTVGPTWRHGGSHGEEELLESCY 80

                           90       100
                   ....*....|....*....|....*
gi 19352424   1510 RAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:pfam01661   81 RNALALAEELGIKSIAFPAISTGIY 105

Viral_helicase1

pfam01443

Viral (Superfamily 1) RNA helicase; Helicase activity for this family has been demonstrated ...

748-986

9.71e-15

Pssm-ID: 366646 [Multi-domain] Cd Length: 227 Bit Score: 75.88 E-value: 9.71e-15

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    748 IYGVPGAGKTAIITTEVTTrdlvASGKKENCEDIKRCVLerRGLKIAARTVDSLLYGAYRGAVDTLYVDEAYACHSGTLL 827
Cdd:pfam01443    3 VHGVPGCGKSTLIRKLLRT----SRVIRPTAELRTEGKP--DLPNLNVRTVDTFLMALLKPTGKILILDEYTLLPPGYIL 76

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    828 ALIAAVRPtGKVVLCGDPKQVGCVNQLQM--RMHYNHEISDRVlrkniSRRCTHTLTAIVsnLNYEGRMKTTNPCKKPVL 905
Cdd:pfam01443   77 LLAAISGA-KLVILFGDPLQIPYHSRAPSflIPHFPSSLSHRV-----GRRTTYLLPSLR--APILSAKGFEVVVERSGE 148

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    906 IDTTGSTKPDKEALVLTCfrgwVKDLKILYPHnELMTAAASQGLTREKVYAVRCRVTSNPLYEPTSEHITVLLTRTNDEL 985
Cdd:pfam01443  149 YKVDYDPNGVLVLVYLTF----TQALKESLGV-RVTTVHEVQGLTFDSVTLVLDTDTDLLIISDSPEHLYVALTRHRKSL 223


                   .
gi 19352424    986 V 986
Cdd:pfam01443  224 H 224

Mayoviridae_RdRp

cd23256

RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense ...

2233-2560

3.04e-12

RNA-dependent RNA polymerase (RdRp) in the family Mayoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Mayoviridae, order Martellivirales. The Mayoviridae family consists of two genera, Idaeovirus and Pteridovirus. The genus Idaeovirus contains Raspberry bushy dwarf virus (RBDV), named after the host with which it was first associated (red raspberry, Rubus idaeu) and the disease which is characterized by bushiness (stunting and proliferation of canes); RBDV has recently been found causing an infection in grapevines. RBDV occurs in all tissues of the plant, including seed and pollen, and is transmitted in association with pollen, both vertically to the seed and horizontally to the pollinated plant; this is the only known method of natural spread of RBDV. 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: 438106 Cd Length: 329 Bit Score: 70.54 E-value: 3.04e-12

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2233 SPGQIEEYVfhlqgakaNVMHSRV-EAACPDLSevAMDRFTLDMKRDVKVTPGTKHVEERPKVQVIQAADPMATAYLCAI 2311
Cdd:cd23256    6 SADQIQLYQ--------NKVGNKVnDPVVLALT--SLNKYSHMIKRDRKPVLTTAVQSEYTKAATITYHDKDITQVATPI 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2312 HRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLG-DKVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTLIE 2390
Cdd:cd23256   76 FRQFKTRLLACKKSNLCIPLDHDHDISGWLTNRHLGSEnGTFTEIDFSKFDKSQGELHQLIQDLILLRFGCDPEFVSLWS 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2391 ASFGDITSVHLPTGTRFQFGSMMKSGLFLTLFVNTLLNITIAARVL-REQLADTRCAAFIGDDNVITGVVSDDMMVARCA 2469
Cdd:cd23256  156 TAHRSSSIKDQNVGISFKTDFQRRTGDAFTFLGNSLVTAVMLAYVLsFEDEKKIRYMLVGGDDSLICSYGPISVPLEPLS 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2470 SWLNMEVKIMEmeigDRSPYFCGGFLLldTVTGTVSRVSDPVKRLMKMGKPALNDPETDVDRCR-ALREEVESWYRVGIQ 2548
Cdd:cd23256  236 TIFNMSCKLIQ----PSCPYFASRYII--RVGDEILCVPDPYKLLVKMGRKDIPDNEASLEEVRtGLADSAKPLFDDEVK 309

                        330
                 ....*....|..
gi 19352424 2549 WPLQVAAATRYG 2560
Cdd:cd23256  310 QKLSILVQIRYN 321

Bromoviridae_RdRp

cd23252

RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense ...

2253-2518

1.05e-09

RNA-dependent RNA polymerase (RdRp) in the family Bromoviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the RdRp of RNA viruses belonging to the family Bromoviridae, order Martellivirales. The Bromoviridae family of plant viruses contains tri-segmented, (+)ssRNA viruses with a total genome size of about 8 kb. There are six genera in this family: Alfamovirus, Anulavirus, Bromovirus, Cucumovirus, Ilarvirus, and Oleavirus. Bromoviridae virions are variable in morphology (spherical or bacilliform) and are transmitted mechanically, in/on the pollen and non-persistently by insect vectors. Members of the family cause major disease epidemics in fruit, vegetable and fodder crops such as tomato, cucurbits, bananas, and alfalfa. 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: 438102 Cd Length: 332 Bit Score: 62.63 E-value: 1.05e-09

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2253 HSRVEAACPD------LSEVAMDRFTLDMKRDVK-VTPGTKHVEeRP--------KVQVIQAADPMataYLCAIHReLVR 2317
Cdd:cd23252   65 LDRVSNAVANrflttvIDVDRLDKYMHMIKSDLKpVEDDSLHVE-RPvpatityhKKGIVMQFSPL---FLAAFER-LLR 139

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2318 RLKA-VLKPS--IHVLFDMSSEDFDAIVghgmklgdKVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLltlIEASFG 2394
Cdd:cd23252  140 CLRSkIVIPSgkIHQLFMIDPSVLNASK--------HFKEIDFSKFDKSQGELHHEIQEHILNALGCPAPF---TKWWFD 208

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2395 DITSVHL---PTGTRFQFGSMMKSGLFLTLFVNTLLNITIAARVLREQLADTRCAAFIGDDNVITGV---VSDDMMVarC 2468
Cdd:cd23252  209 FHRRSYIsdrRAGVGFSVDFQRRTGDAFTYLGNTLVTLAELAYVYDLDDPNFDFVVASGDDSLIGSVeplPRDDEDL--F 286

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|.
gi 19352424 2469 ASWLNMEVKIMemeigDRSPYFCGGFLLLD-TVTGTVSRVSDPVKRLMKMG 2518
Cdd:cd23252  287 TTLFNFEAKFP-----HNQPFICSKFLLSDeFGDENVFSVPDPLKLLQRLG 332

Macro_Af1521_BAL-like

cd02907

macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse ...

1432-1534

1.36e-08

macrodomain, Af1521-like family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. The macrodomains in this family show similarity to Af1521, a protein from Archaeoglobus fulgidus containing a stand-alone macrodomain. Af1521 binds ADP-ribose and exhibits phosphatase activity toward ADP-ribose-1"-monophosphate (Appr-1"-p). Also included in this family are the N-terminal (or first) macrodomains of BAL (B-aggressive lymphoma) proteins which contain multiple macrodomains, such as the first macrodomain of mono-ADP-ribosyltransferase PARP14 (PARP-14, also known as ADP-ribosyltransferase diphtheria toxin-like 8, ATRD8, B aggressive lymphoma protein 2, or BAL2). Most BAL proteins also contain a C-terminal PARP active site and are also named as PARPs. Human BAL1 (or PARP-9) was originally identified as a risk-related gene in diffuse large B-cell lymphoma that promotes malignant B-cell migration. Some BAL family proteins exhibit PARP activity. Poly (ADP-ribosyl)ation is an immediate DNA-damage-dependent post-translational modification of histones and other nuclear proteins. BAL proteins may also function as transcriptional repressors.

Pssm-ID: 394877 [Multi-domain] Cd Length: 158 Bit Score: 56.34 E-value: 1.36e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1432 ITAEE-EVLVNAANSNGRPGDGVCGALYGAFGDAFP---------NGAIGAGNAVLVR--GLEAT-IIHAAGADFREVDE 1498
Cdd:cd02907   11 ITKEKvDAIVNAANERLKHGGGVAGAISKAGGPEIQeecdkyikkNGKLRVGEVVVTSagKLPCKyVIHAVGPRWSGGSK 90

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 19352424 1499 ETGARQLRAAYRAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:cd02907   91 EECEDLLYKAVLNSLEEAEELKATSIAIPAISSGIF 126

PRK00431

ADP-ribose-binding protein;

1425-1534

1.64e-08

ADP-ribose-binding protein;

Pssm-ID: 234759 Cd Length: 177 Bit Score: 56.39 E-value: 1.64e-08

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1425 RVLNKNIITAEEEVLVNAANSNGRPGDGVCGALYGAFGDA---------FPNGAIGAGNAVLVRG--LEAT-IIHAAGAD 1492
Cdd:PRK00431    6 EVVQGDITELEVDAIVNAANSSLLGGGGVDGAIHRAAGPEileecrelrQQQGPCPTGEAVITSAgrLPAKyVIHTVGPV 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 19352424  1493 FREVDEETgARQLRAAYRAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:PRK00431   86 WRGGEDNE-AELLASAYRNSLRLAAELGLRSIAFPAISTGVY 126

Macro_OAADPr_deacetylase

cd02908

macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of ...

1432-1534

2.20e-08

macrodomain, O-acetyl-ADP-ribose (OAADPr) family; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. This family includes eukaryotic macrodomain proteins such as human MacroD1 and MacroD2, and bacterial proteins such as Escherichia coli YmdB; these have been shown to be O-acetyl-ADP-ribose (OAADPr) deacetylases that efficiently catalyze the hydrolysis of OAADPr to produce ADP-ribose and free acetate. OAADPr is a sirtuin reaction product generated from the NAD+-dependent protein deacetylation reactions and has been implicated as a signaling molecule. By acting on mono-ADP-ribosylated substrates, OAADPr deacetylases may reverse cellular ADP-ribosylation.

Pssm-ID: 438955 Cd Length: 166 Bit Score: 55.98 E-value: 2.20e-08

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1432 ITAEE-EVLVNAANSNGRPGDGVCGALYGAFGdafP---------NGAIGAGNAVLVRG--LEAT-IIHAAGADFREVDE 1498
Cdd:cd02908    9 ITKLEvDAIVNAANSSLLGGGGVDGAIHRAAG---PelleecrklGGVCPTGEAKITPGynLPAKyVIHTVGPIGEGGVE 85

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 19352424 1499 ETgARQLRAAYRAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:cd02908   86 EE-PELLASCYRSSLELALENGLKSIAFPCISTGIY 120

PHA03307

transcriptional regulator ICP4; Provisional

1732-1985

1.19e-07

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 57.87 E-value: 1.19e-07

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1732 PLTNIQDVTKVECTVRAPAEEPRPvrylqerrPVQAAARQPRPAIVAASVAGTATsrRTPAPGSVQVRLLPPRdgtvsrs 1811
Cdd:PHA03307  137 MLRPVGSPGPPPAASPPAAGASPA--------AVASDAASSRQAALPLSSPEETA--RAPSSPPAEPPPSTPP------- 199

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1812 srtssqssvtsSAGPIMPVPRRAPVAPAASLAGSVhshSVRSAPAILRAASTGARSVRSVQSGLTGHRDDAVSVAGSVRQ 1891
Cdd:PHA03307  200 -----------AAASPRPPRRSSPISASASSPAPA---PGRSAADDAGASSSDSSSSESSGCGWGPENECPLPRPAPITL 265

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1892 PS--------GPPSSVSTPAAPRGLTREQFGAVR----------ARARRDLELEGSEHGSQASFRSGSLVVGSTASSYSQ 1953
Cdd:PHA03307  266 PTriweasgwNGPSSRPGPASSSSSPRERSPSPSpsspgsgpapSSPRASSSSSSSRESSSSSTSSSSESSRGAAVSPGP 345

                         250       260       270
                  ....*....|....*....|....*....|..
gi 19352424  1954 RPDDQDTGSEPSGRGAAVRTRRRGQRDGPGGY 1985
Cdd:PHA03307  346 SPSRSPSPSRPPPPADPSSPRKRPRPSRAPSS 377

Macro_Ttha0132-like

cd03330

Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein ...

1425-1531

3.88e-07

Macrodomain, uncharacterized family similar to Thermus thermophilus hypothetical protein Ttha0132; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response. This family is composed of uncharacterized proteins containing a stand-alone macrodomain, similar to Thermus thermophilus hypothetical protein Ttha0132.

Pssm-ID: 394879 Cd Length: 147 Bit Score: 51.67 E-value: 3.88e-07

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1425 RVLNKNIITAEEEVLVNAANSNGRPGDGVCGALYGAFG-----DAFPNGAIGAGNAVLVRG--LEA-TIIHAAGAdfrEV 1496
Cdd:cd03330    3 IVVQGDITEQDADAIVNAANRRLLMGSGVAGAIKRKGGeeierEAMRKGPIRVGEAVETGAgkLPAkYVIHAAVM---GM 79

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 19352424 1497 DEETGARQLRAAYRAAATLVTANGITSAAIPLLST 1531
Cdd:cd03330   80 PGRSSEESIRDATRNALAKAEELGLESVAFPAIGT 114

ps-ssRNAv-Picornavirales

cd23169

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Picornavirales of ...

2280-2463

1.60e-06

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: 52.60 E-value: 1.60e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2280 KVTPGtkhveerpKVQVIQAAdPMATAYLCaihRELVRRLKAVLKPSIHVLF-----DMSSEDFDAIVGHGMKLGDKVLE 2354
Cdd:cd23169   16 KVKAG--------KTRLFSAS-PLDYTIAF---RKYFGDFIAAFQKNRIKLEhavgiNPDSVEWTRLYRRLLKKGPNIFA 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2355 TDISSFDKSQDQAMAVTALMLLEDL-----GVEEDLL--TLIEASfgdITSVHLPTGTRFQFGSMMKSGLFLTLFVNTLL 2427
Cdd:cd23169   84 GDYSNFDGSLPPDVMEAAFDIINDWydeyvDDEDERVrkVLFEEL---INTIHLVGNLVYQVHGGNPSGNPLTTIINSIV 160

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*
gi 19352424 2428 NI---------TIAARVLREQLADTRCAAFiGDDNVITgvVSDDM 2463
Cdd:cd23169  161 NLlyiryawlrITGLTSLSDFKKNVRLVTY-GDDVIIS--VSDEV 202

PHA03247

large tegument protein UL36; Provisional

1732-1905

2.25e-06

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 53.79 E-value: 2.25e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1732 PLTNIQDVTKVEctvRAPAEEPRPVRYLQERRPVQAAARQPRPAIVAASVAgTATSRRTPAPGSVQVRLLPPrdgtvsrs 1811
Cdd:PHA03247 2694 SLTSLADPPPPP---PTPEPAPHALVSATPLPPGPAAARQASPALPAAPAP-PAVPAGPATPGGPARPARPP-------- 2761

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1812 sRTSSQSSVTSSAGPIMPVPRRAPVAPAASLAGSVHSHSVRSAPAILRAASTGARSvrsvqsgltghrddAVSVAGSVRQ 1891
Cdd:PHA03247 2762 -TTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAA--------------ALPPAASPAG 2826

                         170
                  ....*....|....
gi 19352424  1892 PSGPPSSvSTPAAP 1905
Cdd:PHA03247 2827 PLPPPTS-AQPTAP 2839

Endornaviridae_RdRp

cd23255

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of ...

2305-2455

4.27e-06

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the family Endornaviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the family Endornaviridae, order Martellivirales. The family Endornaviridae includes viruses with linear (+)ssRNA genomes that range from 9.7 to 17.6 kb. The family consists of two genera, Alphaendornavirus and Betaendornavirus. Alphaendornavirus includes species whose members infect plants, fungi and oomycetes, while the genus Betaendornavirus includes species whose members infect ascomycete fungi. Plant endornaviruses are transmitted only through the gametes. A conserved RNA-dependent RNA polymerase domain located in the C-terminal region of the polyprotein is a feature common to all endornaviruses. 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: 438105 Cd Length: 237 Bit Score: 50.61 E-value: 4.27e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2305 TAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGhGMKLGDKVLETDISSFDKSQDQAMAVTALMLLEDLGVEED 2384
Cdd:cd23255   69 CAIFSPIFNEAKKRLKSLLKPKVVYADGLTPDELSARLR-LVKNVKYFFEDDLSKQDRQTDKPIIDVEMELYKLLGVDPN 147

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19352424 2385 LLTLIEasfgditSVHL-----PTGTRFQFGSMMKSGLFLTLFVNTLLNITIAARVLREQLADTRCAAFIGDDNVI 2455
Cdd:cd23255  148 VIELWR-------EVHEnwrfkGKGVRGVGDAMRLTGQATTALGNVITNLLVHSRLVKRNGSNLKLMLVLGDDNLI 216

Gammaflexiviridae_RdRp

cd23249

RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense ...

2293-2492

7.96e-06

RNA-dependent RNA polymerase (RdRp) in the family Gammaflexiviridae of positive-sense single-stranded RNA [(+)ssRNA] viruses, in the order Tymovirales; This group contains the RdRp of RNA viruses belonging to the family Gammaflexiviridae, order Tymovirales. Virions within the Gammaflexiviridae family are flexuous filaments of 720 nm modal length and about 13 nm in diameter. Members of the Tymovirales order are mainly plant pathogens that are characterized by similarities in their replication-associated polyproteins, which account for the majority of their genomic coding capacity. They are considered to form a group, phylogenetically, referred to as flexiviruses, with filamentous virions. 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: 438099 Cd Length: 354 Bit Score: 50.67 E-value: 7.96e-06

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2293 KVQVIQAADPMAtaylcaihRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKLGDKVLETDISSFDKSQDQAMAVTA 2372
Cdd:cd23249  102 RAQVLLAWGPLA--------RYLDRRIRALLPPHIYIHSGRTNEDFERFVAAHWDFTRESTEGDYTAFDASQDADFLNFE 173

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2373 LMLLEDLGVEEDlltLIEASFGDITSVHLPTGTrfqFGSMMKSGLFLTLFVNTLLNITIAArvLREQLADTRCAAFIGDD 2452
Cdd:cd23249  174 TLLMRALGVPLD---LIEAYLEMKASITSHLGP---LAIMRFSGEVWTYLFNTLGNMAYTA--AKYEVPPPVPRVYGGDD 245

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 19352424 2453 NVITGVVSddmmVARCASWLNMEVKIMEMEIGDRSPYFCG 2492
Cdd:cd23249  246 KSINSRIT----VRPGWSQLVGQFNLVEKPVVTYEPTFCG 281

Macro_SF

cd02749

macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular ...

1438-1534

3.17e-05

macrodomain superfamily; Macrodomains are found in a variety of proteins with diverse cellular functions, as a stand-alone domain or in combination with other domains like in histone macroH2A and some PARPs (poly ADP-ribose polymerases). Macrodomains can recognize ADP-ribose (ADPr) in both its free and protein-linked forms, in related ligands, such as O-acyl-ADP-ribose (OAADPr), and even in ligands unrelated to ADPr. Macrodomains include the yeast macrodomain Poa1 which is a phosphatase of ADP-ribose-1"-phosphate, a by-product of tRNA splicing. Some macrodomains have ADPr-unrelated binding partners such as the coronavirus SUD-N (N-terminal subdomain) and SUD-M (middle subdomain) of the SARS-unique domain (SUD) which bind G-quadruplexes (unusual nucleic-acid structures formed by consecutive guanosine nucleotides). Macrodomains regulate a wide variety of cellular and organismal processes, including DNA damage repair, signal transduction, and immune response.

Pssm-ID: 394871 Cd Length: 121 Bit Score: 45.47 E-value: 3.17e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1438 VLVNAANSNGRPGDGVCGALYGAFGDAF--------PNGAIGAGNAVLVRG---LEATIIHAAGADFREVDEETGArqLR 1506
Cdd:cd02749    2 AIVNPANNDLYLGGGVAKAISKKAGGDLqeeceerkKNGYLKVGEVAVTKGgnlPARYIIHVVGPVASSKKKTYEP--LK 79

                         90       100
                 ....*....|....*....|....*...
gi 19352424 1507 AAYRAAATLVTANGITSAAIPLLSTHIF 1534
Cdd:cd02749   80 KCVKNCLSLADEKGLKSVAFPAIGTGIA 107

DEXXQc_Upf1-like

cd17934

DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...

748-847

8.73e-05

Pssm-ID: 438708 [Multi-domain] Cd Length: 121 Bit Score: 44.15 E-value: 8.73e-05

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  748 IYGVPGAGKTAIITTEVTTRDLVASGKKencedikrcVLerrglkIAART---VDsllygayrgAVDTLYVDEAYACHSG 824
Cdd:cd17934    4 IQGPPGTGKTTTIAAIVLQLLKGLRGKR---------VL------VTAQSnvaVD---------NVDVVIIDEASQITEP 59

                         90       100
                 ....*....|....*....|...
gi 19352424  825 TLLALIAAVRptgKVVLCGDPKQ 847
Cdd:cd17934   60 ELLIALIRAK---KVVLVGDPKQ 79

AAA_30

pfam13604

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...

750-851

2.49e-04

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. There is a Walker A and Walker B.

Pssm-ID: 433343 [Multi-domain] Cd Length: 191 Bit Score: 44.48 E-value: 2.49e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424    750 GVPGAGKTAIITT-----EVTTRDLVA---SGKKENcedikrcVLeRRGLKIAARTVDSLLY----GAYRGAVDTLYVDE 817
Cdd:pfam13604   25 GPAGTGKTTALKAlreawEAAGYRVIGlapTGRAAK-------VL-GEELGIPADTIAKLLHrlggRAGLDPGTLLIVDE 96

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 19352424    818 AYACHSGTLLALIAAVRPTG-KVVLCGDPKQVGCV 851
Cdd:pfam13604   97 AGMVGTRQMARLLKLAEDAGaRVILVGDPRQLPSV 131

DEXSc_RecD-like

cd17933

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1. ...

750-847

3.91e-04

DEXS-box helicase domain of RecD and similar proteins; RecD is a member of the RecBCD (EC 3.1.11.5, Exonuclease V) complex. It is the alpha chain of the complex and functions as a 3'-5' helicase. The RecBCD enzyme is both a helicase that unwinds, or separates the strands of DNA, and a nuclease that makes single-stranded nicks in DNA. RecD is a member of the DEAD-like helicase superfamily, a diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.

Pssm-ID: 350691 [Multi-domain] Cd Length: 155 Bit Score: 43.31 E-value: 3.91e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  750 GVPGAGKTAiittevTTRDLVASGKKENcediKRCVLE----------RRGLKIAARTVDSLLY------GAYRGA---- 809
Cdd:cd17933   19 GGAGTGKTT------TLKALLAALEAEG----KRVVLAaptgkaakrlSESTGIEASTIHRLLGinpgggGFYYNEenpl 88

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 19352424  810 -VDTLYVDEAYACHSGTLLALIAAVRPTGKVVLCGDPKQ 847
Cdd:cd17933   89 dADLLIVDEASMVDTRLMAALLSAIPAGARLILVGDPDQ 127

PRK07003

DNA polymerase III subunit gamma/tau;

1736-1923

5.03e-04

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 45.61 E-value: 5.03e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1736 IQDVTKVECTVRAPAEEPRPVRYLQERRPVQAAArQPRPAIVAASVAgTATSRRTPAPGSVQVrlLPPRDGTVSRSSRTS 1815
Cdd:PRK07003  439 GDDAADGDAPVPAKANARASADSRCDERDAQPPA-DSGSASAPASDA-PPDAAFEPAPRAAAP--SAATPAAVPDARAPA 514

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1816 SQSSVTSSAGPIMPVPRRAPVAPAASlAGSVHSHSVRSAPAILRAASTGARSVRSVQSGLTGhRDDAVSVAGSVRQPSGP 1895
Cdd:PRK07003  515 AASREDAPAAAAPPAPEARPPTPAAA-APAARAGGAAAALDVLRNAGMRVSSDRGARAAAAA-KPAAAPAAAPKPAAPRV 592

                         170       180
                  ....*....|....*....|....*....
gi 19352424  1896 PSSVSTPAAP-RGLTREQFGAVRARARRD 1923
Cdd:PRK07003  593 AVQVPTPRARaATGDAPPNGAARAEQAAE 621

PRK07003

DNA polymerase III subunit gamma/tau;

1748-1921

8.35e-04

DNA polymerase III subunit gamma/tau;

Pssm-ID: 235906 [Multi-domain] Cd Length: 830 Bit Score: 44.84 E-value: 8.35e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1748 APAEEPRPVRYLQERRP--VQAAARQPRPAIVAASVAGTATSRRTPAPGSVQ----VRLLPPRDGTVSRSSRTSSQSSVT 1821
Cdd:PRK07003  372 VPARVAGAVPAPGARAAaaVGASAVPAVTAVTGAAGAALAPKAAAAAAATRAeappAAPAPPATADRGDDAADGDAPVPA 451

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1822 SSAGPIMPVPRRAPVAPAASLAGSVHSHSVRSAPAILR--AASTGARSVRSVQSGLTGHRDDAVSVAGSVRQPSGPPSSV 1899
Cdd:PRK07003  452 KANARASADSRCDERDAQPPADSGSASAPASDAPPDAAfePAPRAAAPSAATPAAVPDARAPAAASREDAPAAAAPPAPE 531

                         170       180
                  ....*....|....*....|..
gi 19352424  1900 STPAAPrgltreqfGAVRARAR 1921
Cdd:PRK07003  532 ARPPTP--------AAAAPAAR 545

DNA2

COG1112

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];

811-896

8.44e-04

Superfamily I DNA and/or RNA helicase [Replication, recombination and repair];

Pssm-ID: 440729 [Multi-domain] Cd Length: 819 Bit Score: 44.73 E-value: 8.44e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  811 DTLYVDEAYAChsgTLLALIAAVRPTGKVVLCGDPKQ---VGCVNQLQMRMHYNHEIS--DRVLRK--------NISRRC 877
Cdd:COG1112  557 DLVIIDEASQA---TLAEALGALARAKRVVLVGDPKQlppVVFGEEAEEVAEEGLDESllDRLLARlpergvmlREHYRM 633

                         90
                 ....*....|....*....
gi 19352424  878 THTLTAIVSNLNYEGRMKT 896
Cdd:COG1112  634 HPEIIAFSNRLFYDGKLVP 652

ps-ssRNAv_Alsuviricetes_RdRp

cd23182

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of ...

2275-2458

9.82e-04

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the class Alsuviricetes of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the class Alsuviricetes, phylum: Kitrinoviricota. Alsuviricetes is a class of [(+)ssRNA] viruses which infect eukaryotes. The name of the group is a syllabic abbreviation of "alpha supergroup" with the suffix -viricetes indicating a virus class. The class Alsuviricetes includes three orders: Hepelivirales, Martellivirales, and Tymovirales. 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: 438032 [Multi-domain] Cd Length: 187 Bit Score: 42.59 E-value: 9.82e-04

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2275 MKRDVKVTPGTKHVEERPkVQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKL-GDKVL 2353
Cdd:cd23182    7 IKTQQKVSPKTPFNTGKA-GQTIAAHSKSINFVLGPWIRYLEERLRDGSRTHRYSNGLMDEEEAMLSQWKINHVpHATFV 85

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2354 ETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTLIEASFGDITSVHLPTGTRFQFGSMMKSGLFLTLFVNTLLNitiAA 2433
Cdd:cd23182   86 SNDYTAFDKSHNGESLLLEAAIMRRIGTPAAAPNLFIELHGKRTLRAKVLGGSGELDGMRDSGAAWTYCRNTDYN---LA 162

                        170       180
                 ....*....|....*....|....*
gi 19352424 2434 RVLREQLADTRCAAFIGDDNVITGV 2458
Cdd:cd23182  163 VMLSLYRLKVKPAAFSGDDSLLCGS 187

RlmE

COG0293

23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...

1210-1364

1.32e-03

Pssm-ID: 440062 [Multi-domain] Cd Length: 208 Bit Score: 42.37 E-value: 1.32e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1210 RAAVKFAELTKR----VSYNSVLDLGAARGGVTDYCVKK----GKTVTCVSEQWDSKPrGAVVITADINGP--------- 1272
Cdd:COG0293   33 RAAYKLLEIDEKdkliKPGMRVVDLGAAPGGWSQVAAKRvggkGRVIALDLLPMEPIP-GVEFIQGDFREDevldqllea 111

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 1273 LNNLGiFDLVFCDAA----GprryhHYAQceDHARR---STSACKHGVERTAKGGVFIVKAY-GMADRRTERAVEctaRY 1344
Cdd:COG0293  112 LGGRK-VDLVLSDMApntsG-----HKSV--DHARSmylVELALDFARKVLKPGGAFVVKVFqGEGFDELLKELK---KL 180

                        170       180
                 ....*....|....*....|
gi 19352424 1345 FKSVSVEKPVSSRITNVEVF 1364
Cdd:COG0293  181 FKKVKHRKPKASRARSSEVY 200

PHA03247

large tegument protein UL36; Provisional

1748-1906

2.63e-03

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 43.39 E-value: 2.63e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1748 APAEEPRPVRYLQERRPVQAAA--RQPRPAIVAASVAGTATSRRTPAPGSVQvRLLPPRDGTVSRSSRTSSQSSVTSSAG 1825
Cdd:PHA03247 2657 APGRVSRPRRARRLGRAAQASSppQRPRRRAARPTVGSLTSLADPPPPPPTP-EPAPHALVSATPLPPGPAAARQASPAL 2735

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1826 PIMPVPRRAPVAPAASlaGSVHSHSVRSAPAILRAASTGARSVRSVQSGLTGHRDDAVSVAGSVRQPSGPPSSVSTPAAP 1905
Cdd:PHA03247 2736 PAAPAPPAVPAGPATP--GGPARPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLA 2813


                  .
gi 19352424  1906 R 1906
Cdd:PHA03247 2814 P 2814

ps-ssRNAv_Hepelivirales_RdRp

cd23209

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of ...

2270-2455

4.14e-03

catalytic core domain of RNA-dependent RNA polymerase (RdRp) in the order Hepelivirales of positive-sense single-stranded RNA [(+)ssRNA] viruses; This group contains the catalytic core domain of RdRp of RNA viruses belonging to the order Hepelivirales, class Alsuviricetes. This Hepelivirales order consists of four families: Alphatetraviridae, Benyviridae, Hepeviridae, and Matonaviridae. 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: 438059 [Multi-domain] Cd Length: 183 Bit Score: 40.55 E-value: 4.14e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2270 RFTLDMKRDVKVTPGtKHVEERPKVQVIQAADPMATAYLCAIHRELVRRLKAVLKPSIHVLFDMSSEDFDAIVGHGMKlg 2349
Cdd:cd23209    2 KITFFQKDCRKFTDC-EPVAHGKAGQGISAWSKELCFVFGPWFRALEKILRRALKPNVLYANGHEAEPFVDKINQAHS-- 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424 2350 DKVLETDISSFDKSQDQAMAVTALMLLEDLGVEEDLLTLIEASFGDITsVHLPTGtRFQFGSMMKSGLFLTLFVNTLLNI 2429
Cdd:cd23209   79 AVFIENDFTEFDSTQNLFSLLVELEILEACGMPPALAELYRALRAKWT-LQAREG-SLEGTCKKTSGEPGTLLHNTIWNM 156

                        170       180
                 ....*....|....*....|....*.
gi 19352424 2430 TIAARVLREQlaDTRCAAFIGDDNVI 2455
Cdd:cd23209  157 AVMMHMVRGG--VRKAAAFKGDDSVV 180

PRK07764

DNA polymerase III subunits gamma and tau; Validated

1736-1905

4.21e-03

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 42.67 E-value: 4.21e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1736 IQDVTKVECTVRAPAEEPRPVRYLQERRPVQAAAR---QPRPAIVAASVAGTATSRRTPAPGSVQVRLLPPRDGTVSRSS 1812
Cdd:PRK07764  574 LAEELGGDWQVEAVVGPAPGAAGGEGPPAPASSGPpeeAARPAAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHH 653

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1813 RTSSQSSVTSSAGPIMPVPRR--APVAPAASLAGSVHSHSVRSAPAILRAASTGARSVRSVQSGLTGHRDDAvsvAGSVR 1890
Cdd:PRK07764  654 PKHVAVPDASDGGDGWPAKAGgaAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAA---QGASA 730

                         170
                  ....*....|....*
gi 19352424  1891 QPSGPPSSVSTPAAP 1905
Cdd:PRK07764  731 PSPAADDPVPLPPEP 745

PHA03307

transcriptional regulator ICP4; Provisional

1741-1964

4.76e-03

transcriptional regulator ICP4; Provisional

Pssm-ID: 223039 [Multi-domain] Cd Length: 1352 Bit Score: 42.47 E-value: 4.76e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1741 KVECTVRAPAEEPRPVRYLQERRPVQAAARQPRPAIVAASVAGTATSRR----------------------------TPA 1792
Cdd:PHA03307  178 SPEETARAPSSPPAEPPPSTPPAAASPRPPRRSSPISASASSPAPAPGRsaaddagasssdssssessgcgwgpeneCPL 257

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1793 PGSVQVRLLPPRDGTVSRSSRTSSQSSVTSSAGPIMPVPRRAPVAPAASLAGSVHSHSVRSAPAilRAASTGARSVRS-V 1871
Cdd:PHA03307  258 PRPAPITLPTRIWEASGWNGPSSRPGPASSSSSPRERSPSPSPSSPGSGPAPSSPRASSSSSSS--RESSSSSTSSSSeS 335

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  1872 QSGLTGHRDDAVSVAGSVRQPSGPPSSVSTPAAPRGLTREQFGAV------RARARRDLEleGSEHGSQASFRSGS---- 1941
Cdd:PHA03307  336 SRGAAVSPGPSPSRSPSPSRPPPPADPSSPRKRPRPSRAPSSPAAsagrptRRRARAAVA--GRARRRDATGRFPAgrpr 413

                         250       260
                  ....*....|....*....|....*.
gi 19352424  1942 ---LVVGSTASSYSQRPDDQDTGSEP 1964
Cdd:PHA03307  414 pspLDAGAASGAFYARYPLLTPSGEP 439

RecD

COG0507

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...

750-847

4.81e-03

ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) [Replication, recombination and repair];

Pssm-ID: 440273 [Multi-domain] Cd Length: 514 Bit Score: 42.27 E-value: 4.81e-03

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19352424  750 GVPGAGKTAIITTevttrdLVAsgkkencedikrcVLERRGLKIA-------------------ARTVDSLLYGAYR--- 807
Cdd:COG0507  147 GGAGTGKTTTLRA------LLA-------------ALEALGLRVAlaaptgkaakrlsestgieARTIHRLLGLRPDsgr 207

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 19352424  808 ---------GAVDTLYVDEAYACHSGTLLALIAAVRPTG-KVVLCGDPKQ 847
Cdd:COG0507  208 frhnrdnplTPADLLVVDEASMVDTRLMAALLEALPRAGaRLILVGDPDQ 257

Blast search parameters

Data Source:	Precalculated data, version = cdd.v.3.21
Preset Options:	Database: CDSEARCH/cdd Low complexity filter: no Composition Based Adjustment: yes E-value threshold: 0.01