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Conserved domains on  [gi|392920122|ref|NP_505567|]
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RuvB-like 1 [Caenorhabditis elegans]

Protein Classification

RuvB-like helicase( domain architecture ID 15918217)

RuvB-like helicase is a DNA helicase that plays an essential role in various complexes involved in fundamental processes such as transcription regulation, DNA damage response and apoptosis (via the chromatin remodelling complexes SWR1, INO80 and TIP60), maturation of small nuclear ribonucleoproteins, cellular development, cancer metastasis, and regulation of mitosis

EC:  3.6.4.12
Gene Ontology:  GO:0005524|GO:0003678|GO:0006259
PubMed:  10787406

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 32-387 0e+00

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


:

Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 549.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122   32 RIAAHSHVKGLGIDtETQEAHYEAAGFVGQAPARTAASIVVDMIRLKCMAGRAVLIAGPPATGKTAIALAMSQELGDGVP 111
Cdd:pfam06068   1 RISAHSHIRGLGLD-EDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  112 FVPLVASEVFSNEVKKTEVLMRSFRRAIGLRVKETKDVYEGEVTELSPVEASDNSGMGKTISHLVLSLKTAKGSKQLKLD 191
Cdd:pfam06068  80 FTSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSGGKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  192 PSIYDSILKQRVEVGDVIYIEANSGIVKRVGRCDVYASEFDLEADEFVPMPKGDVRKSKDIVQNVSLHDLDIANARPQGr 271
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQG- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  272 qgdvsnIVSqLMTPKKTEVTDRLRSEINKVVNEYIESGVAELMPGVLFIDEVHMLDVECFTYLYRALESPMAPVVVFATN 351
Cdd:pfam06068 239 ------ILS-LFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATN 311

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 392920122  352 RGTTTVRGLGDKAPHGIPPEMLDRLMIIPTMKYNEE 387
Cdd:pfam06068 312 RGICTIRGTDIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 392-457 4.28e-18

TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


:

Pssm-ID: 436097 [Multi-domain]  Cd Length: 66  Bit Score: 78.07  E-value: 4.28e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392920122  392 ILVHRTEAENVQFEEKAFDLLSKVGAEKSLRYALQLIAPARLCAQTCGREVIEVEDVDRCTKLFMD 457
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
 
Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 32-387 0e+00

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 549.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122   32 RIAAHSHVKGLGIDtETQEAHYEAAGFVGQAPARTAASIVVDMIRLKCMAGRAVLIAGPPATGKTAIALAMSQELGDGVP 111
Cdd:pfam06068   1 RISAHSHIRGLGLD-EDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  112 FVPLVASEVFSNEVKKTEVLMRSFRRAIGLRVKETKDVYEGEVTELSPVEASDNSGMGKTISHLVLSLKTAKGSKQLKLD 191
Cdd:pfam06068  80 FTSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSGGKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  192 PSIYDSILKQRVEVGDVIYIEANSGIVKRVGRCDVYASEFDLEADEFVPMPKGDVRKSKDIVQNVSLHDLDIANARPQGr 271
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQG- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  272 qgdvsnIVSqLMTPKKTEVTDRLRSEINKVVNEYIESGVAELMPGVLFIDEVHMLDVECFTYLYRALESPMAPVVVFATN 351
Cdd:pfam06068 239 ------ILS-LFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATN 311

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 392920122  352 RGTTTVRGLGDKAPHGIPPEMLDRLMIIPTMKYNEE 387
Cdd:pfam06068 312 RGICTIRGTDIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
17-469 7.05e-163

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 467.91  E-value: 7.05e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  17 LAPIEEVKPtPKQIKRIAAHSHVKGLGIDtETQEAHYEAAGFVGQAPARTAASIVVDMIRLKCMAGRAVLIAGPPATGKT 96
Cdd:COG1224    1 MSEIREIEK-VKEFERISAHSHIRGLGLD-ENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKT 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  97 AIALAMSQELGDGVPFVPLVASEVFSNEVKKTEVLMRSFRRAIGLRVKETKDVYEGEVTELS--------------PVEA 162
Cdd:COG1224   79 ALAVAIARELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKiryarhpynpyvkvPREA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 163 sdnsgmgktishlVLSLKTAKGSKQLKLDPSIYDSILKQRVEVGDVIYIEANSGIVKRVGRCDVYASE-FDLEADEFVPM 241
Cdd:COG1224  159 -------------TITLATKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAKGEGAKtYDIETKRIVEV 225

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 242 PKGDVRKSKDIVQNVSLHDLDIANARpqgRQGDVSNIVSqlMTPKKtEVTDRLRSEINKVVNEYIESGVAELMPGVLFID 321
Cdd:COG1224  226 PSGPVKKEKEIVRTLTLHDLDLYLAA---QRAAFSALFG--FFEER-EIPSEVRKQVDELVKKWIEEGKAELVPGVLFID 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 322 EVHMLDVECFTYLYRALESPMAPVVVFATNRGTTTVRGLGDKAPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTEAEN 401
Cdd:COG1224  300 DAHMLDIEAFSFLTRAMESELAPIIILATNRGITKIRGTDIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEED 379

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392920122 402 VQFEEKAFDLLSKVGAEKSLRYALQLIAPARLCAQTCGREVIEVEDVDRCTKLFMDRGES---LKKAEEEM 469
Cdd:COG1224  380 IELSDDALEELTKIGVERSLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESveyVKEYEELF 450
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 392-457 4.28e-18

TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 436097 [Multi-domain]  Cd Length: 66  Bit Score: 78.07  E-value: 4.28e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392920122  392 ILVHRTEAENVQFEEKAFDLLSKVGAEKSLRYALQLIAPARLCAQTCGREVIEVEDVDRCTKLFMD 457
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 317-431 2.62e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 52.90  E-value: 2.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPmAPVVVFATnrGTTTVrglgdkapHGIPPEMLDRLMIIPTMKYNEEDIRKILVHR 396
Cdd:PRK14953 122 VYIIDEAHMLTKEAFNALLKTLEEP-PPRTIFIL--CTTEY--------DKIPPTILSRCQRFIFSKPTKEQIKEYLKRI 190

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 392920122 397 TEAENVQFEEKAFDLLSKVgAEKSLRYALQLIAPA 431
Cdd:PRK14953 191 CNEEKIEYEEKALDLLAQA-SEGGMRDAASLLDQA 224
dnaX_nterm TIGR02397
DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ ...
 320-429 1.37e-06

DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274111 [Multi-domain]  Cd Length: 355  Bit Score: 50.26  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  320 IDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTE 398
Cdd:TIGR02397 123 IDEVHMLSKSAFNALLKTLEEPPEHVVfILATTE------------PHKIPATILSRCQRFDFKRIPLEDIVERLKKILD 190

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 392920122  399 AENVQFEEKAFDLLSKVgAEKSLRYAL----QLIA 429
Cdd:TIGR02397 191 KEGIKIEDEALELIARA-ADGSLRDALslldQLIS 224
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 76-138 3.12e-06

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 46.89  E-value: 3.12e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392920122  76 RLKCMAGRAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:cd19481   20 RYGLGLPKGILLYGPPGTGKTLLAKALAGEL--GLPLIVVKLSSLLSKYVGESEKNLRKiFERA 81
 
Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 32-387 0e+00

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 549.60  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122   32 RIAAHSHVKGLGIDtETQEAHYEAAGFVGQAPARTAASIVVDMIRLKCMAGRAVLIAGPPATGKTAIALAMSQELGDGVP 111
Cdd:pfam06068   1 RISAHSHIRGLGLD-EDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTP 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  112 FVPLVASEVFSNEVKKTEVLMRSFRRAIGLRVKETKDVYEGEVTELSPVEASDNSGMGKTISHLVLSLKTAKGSKQLKLD 191
Cdd:pfam06068  80 FTSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSGGKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  192 PSIYDSILKQRVEVGDVIYIEANSGIVKRVGRCDVYASEFDLEADEFVPMPKGDVRKSKDIVQNVSLHDLDIANARPQGr 271
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARPQG- 238

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  272 qgdvsnIVSqLMTPKKTEVTDRLRSEINKVVNEYIESGVAELMPGVLFIDEVHMLDVECFTYLYRALESPMAPVVVFATN 351
Cdd:pfam06068 239 ------ILS-LFSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATN 311

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 392920122  352 RGTTTVRGLGDKAPHGIPPEMLDRLMIIPTMKYNEE 387
Cdd:pfam06068 312 RGICTIRGTDIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
17-469 7.05e-163

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 467.91  E-value: 7.05e-163
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  17 LAPIEEVKPtPKQIKRIAAHSHVKGLGIDtETQEAHYEAAGFVGQAPARTAASIVVDMIRLKCMAGRAVLIAGPPATGKT 96
Cdd:COG1224    1 MSEIREIEK-VKEFERISAHSHIRGLGLD-ENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKT 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  97 AIALAMSQELGDGVPFVPLVASEVFSNEVKKTEVLMRSFRRAIGLRVKETKDVYEGEVTELS--------------PVEA 162
Cdd:COG1224   79 ALAVAIARELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKiryarhpynpyvkvPREA 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 163 sdnsgmgktishlVLSLKTAKGSKQLKLDPSIYDSILKQRVEVGDVIYIEANSGIVKRVGRCDVYASE-FDLEADEFVPM 241
Cdd:COG1224  159 -------------TITLATKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAKGEGAKtYDIETKRIVEV 225

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 242 PKGDVRKSKDIVQNVSLHDLDIANARpqgRQGDVSNIVSqlMTPKKtEVTDRLRSEINKVVNEYIESGVAELMPGVLFID 321
Cdd:COG1224  226 PSGPVKKEKEIVRTLTLHDLDLYLAA---QRAAFSALFG--FFEER-EIPSEVRKQVDELVKKWIEEGKAELVPGVLFID 299

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 322 EVHMLDVECFTYLYRALESPMAPVVVFATNRGTTTVRGLGDKAPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTEAEN 401
Cdd:COG1224  300 DAHMLDIEAFSFLTRAMESELAPIIILATNRGITKIRGTDIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEED 379

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392920122 402 VQFEEKAFDLLSKVGAEKSLRYALQLIAPARLCAQTCGREVIEVEDVDRCTKLFMDRGES---LKKAEEEM 469
Cdd:COG1224  380 IELSDDALEELTKIGVERSLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESveyVKEYEELF 450
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 392-457 4.28e-18

TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 436097 [Multi-domain]  Cd Length: 66  Bit Score: 78.07  E-value: 4.28e-18
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 392920122  392 ILVHRTEAENVQFEEKAFDLLSKVGAEKSLRYALQLIAPARLCAQTCGREVIEVEDVDRCTKLFMD 457
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
320-427 3.21e-08

DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 55.20  E-value: 3.21e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 320 IDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTE 398
Cdd:COG2812  120 IDEAHMLTTEAFNALLKTLEEPPPHVVfILATTE------------PQKLLPTILSRCQRFDFRRLPPEEIAEHLAKIAE 187

                         90       100
                 ....*....|....*....|....*....
gi 392920122 399 AENVQFEEKAFDLLSKVgAEKSLRYALQL 427
Cdd:COG2812  188 REGIEIEPEALALIARA-ADGSMRDALSL 215
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 317-431 2.62e-07

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 52.90  E-value: 2.62e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPmAPVVVFATnrGTTTVrglgdkapHGIPPEMLDRLMIIPTMKYNEEDIRKILVHR 396
Cdd:PRK14953 122 VYIIDEAHMLTKEAFNALLKTLEEP-PPRTIFIL--CTTEY--------DKIPPTILSRCQRFIFSKPTKEQIKEYLKRI 190

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 392920122 397 TEAENVQFEEKAFDLLSKVgAEKSLRYALQLIAPA 431
Cdd:PRK14953 191 CNEEKIEYEEKALDLLAQA-SEGGMRDAASLLDQA 224
dnaX_nterm TIGR02397
DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ ...
 320-429 1.37e-06

DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274111 [Multi-domain]  Cd Length: 355  Bit Score: 50.26  E-value: 1.37e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  320 IDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTE 398
Cdd:TIGR02397 123 IDEVHMLSKSAFNALLKTLEEPPEHVVfILATTE------------PHKIPATILSRCQRFDFKRIPLEDIVERLKKILD 190

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 392920122  399 AENVQFEEKAFDLLSKVgAEKSLRYAL----QLIA 429
Cdd:TIGR02397 191 KEGIKIEDEALELIARA-ADGSLRDALslldQLIS 224
PRK07133 PRK07133
DNA polymerase III subunits gamma and tau; Validated
 320-427 1.38e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235943 [Multi-domain]  Cd Length: 725  Bit Score: 50.97  E-value: 1.38e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 320 IDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTE 398
Cdd:PRK07133 124 IDEVHMLSKSAFNALLKTLEEPPKHVIfILATTE------------VHKIPLTILSRVQRFNFRRISEDEIVSRLEFILE 191

                         90       100
                 ....*....|....*....|....*....
gi 392920122 399 AENVQFEEKAFDLLSKVgAEKSLRYALQL 427
Cdd:PRK07133 192 KENISYEKNALKLIAKL-SSGSLRDALSI 219
PRK14961 PRK14961
DNA polymerase III subunits gamma and tau; Provisional
 317-431 1.65e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184925 [Multi-domain]  Cd Length: 363  Bit Score: 50.19  E-value: 1.65e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPV-VVFAtnrgTTTVrglgdkapHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14961 122 VYLIDEVHMLSRHSFNALLKTLEEPPQHIkFILA----TTDV--------EKIPKTILSRCLQFKLKIISEEKIFNFLKY 189

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 392920122 396 RTEAENVQFEEKAFDLLSKvGAEKSLRYALQLIAPA 431
Cdd:PRK14961 190 ILIKESIDTDEYALKLIAY-HAHGSMRDALNLLEHA 224
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 76-138 3.12e-06

proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410889 [Multi-domain]  Cd Length: 158  Bit Score: 46.89  E-value: 3.12e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392920122  76 RLKCMAGRAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:cd19481   20 RYGLGLPKGILLYGPPGTGKTLLAKALAGEL--GLPLIVVKLSSLLSKYVGESEKNLRKiFERA 81
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 317-425 4.24e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 48.99  E-value: 4.24e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14962 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVfVLATTN------------LEKVPPTIISRCQVIEFRNISDELIIKRLQE 187

                         90       100       110
                 ....*....|....*....|....*....|
gi 392920122 396 RTEAENVQFEEKAFDLLSKvGAEKSLRYAL 425
Cdd:PRK14962 188 VAEAEGIEIDREALSFIAK-RASGGLRDAL 216
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 317-431 7.03e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 48.55  E-value: 7.03e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPV-VVFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK08691 122 VYIIDEVHMLSKSAFNAMLKTLEEPPEHVkFILATTD------------PHKVPVTVLSRCLQFVLRNMTAQQVADHLAH 189

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 392920122 396 RTEAENVQFEEKAFDLLSKvGAEKSLRYALQLIAPA 431
Cdd:PRK08691 190 VLDSEKIAYEPPALQLLGR-AAAGSMRDALSLLDQA 224
PRK05563 PRK05563
DNA polymerase III subunits gamma and tau; Validated
 320-429 1.51e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235505 [Multi-domain]  Cd Length: 559  Bit Score: 47.56  E-value: 1.51e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 320 IDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRlmiipTMKYN-----EEDIRKIL 393
Cdd:PRK05563 125 IDEVHMLSTGAFNALLKTLEEPPAHVIfILATTE------------PHKIPATILSR-----CQRFDfkrisVEDIVERL 187

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 392920122 394 VHRTEAENVQFEEKAFDLLSKVgAEKSLRYAL----QLIA 429
Cdd:PRK05563 188 KYILDKEGIEYEDEALRLIARA-AEGGMRDALsildQAIS 226
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 83-179 1.76e-05

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 44.97  E-value: 1.76e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  83 RAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTE-VLMRSFRRAiglrvKETKD--VYEGEVTELSP 159
Cdd:cd19503   35 RGVLLHGPPGTGKTLLARAVANEA--GANFLSISGPSIVSKYLGESEkNLREIFEEA-----RSHAPsiIFIDEIDALAP 107

                         90       100
                 ....*....|....*....|
gi 392920122 160 VEASDNSGMGKTISHLVLSL 179
Cdd:cd19503  108 KREEDQREVERRVVAQLLTL 127
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 317-448 2.32e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 46.70  E-value: 2.32e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPmAPVVVFATnrGTTTVRglgdkaphGIPPEMLDR-----LMIIPTMKyneedIRK 391
Cdd:PRK14964 119 VYIIDEVHMLSNSAFNALLKTLEEP-APHVKFIL--ATTEVK--------KIPVTIISRcqrfdLQKIPTDK-----LVE 182

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392920122 392 ILVHRTEAENVQFEEKAFDLLSKvGAEKSLRYALQLIAPARLCAqtcgREVIEVEDV 448
Cdd:PRK14964 183 HLVDIAKKENIEHDEESLKLIAE-NSSGSMRNALFLLEQAAIYS----NNKISEKSV 234
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 85-138 2.78e-05

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 43.74  E-value: 2.78e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 392920122   85 VLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKEL--GAPFIEISGSELVSKYVGESEKRLRElFEAA 53
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 317-427 2.96e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 46.02  E-value: 2.96e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMA-PVVVFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14970 111 IYIIDEVHMLSSAAFNAFLKTLEEPPAhAIFILATTE------------KHKIIPTILSRCQIFDFKRITIKDIKEHLAG 178

                         90       100       110
                 ....*....|....*....|....*....|..
gi 392920122 396 RTEAENVQFEEKAFDLLSKvGAEKSLRYALQL 427
Cdd:PRK14970 179 IAVKEGIKFEDDALHIIAQ-KADGALRDALSI 209
PRK14958 PRK14958
DNA polymerase III subunits gamma and tau; Provisional
 317-428 6.58e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184922 [Multi-domain]  Cd Length: 509  Bit Score: 45.49  E-value: 6.58e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPVVVFatnrgtttvrgLGDKAPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHR 396
Cdd:PRK14958 122 VYLIDEVHMLSGHSFNALLKTLEEPPSHVKFI-----------LATTDHHKLPVTVLSRCLQFHLAQLPPLQIAAHCQHL 190

                         90       100       110
                 ....*....|....*....|....*....|..
gi 392920122 397 TEAENVQFEEKAFDLLSKvGAEKSLRYALQLI 428
Cdd:PRK14958 191 LKEENVEFENAALDLLAR-AANGSVRDALSLL 221
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 59-149 6.64e-05

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 42.90  E-value: 6.64e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  59 VGQAPARTAASIVVDMIRLKCmagraVLIAGPPATGKTAIALAMSQELG-DGVPFVPLVASEVFSNEVKKTEVLMRSFRR 137
Cdd:cd00009    1 VGQEEAIEALREALELPPPKN-----LLLYGPPGTGKTTLARAIANELFrPGAPFLYLNASDLLEGLVVAELFGHFLVRL 75

                         90
                 ....*....|..
gi 392920122 138 AIGLRVKETKDV 149
Cdd:cd00009   76 LFELAEKAKPGV 87
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 317-446 7.86e-05

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 45.07  E-value: 7.86e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPV-VVFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14957 122 VYLIDEVHMLSKQSFNALLKTLEEPPEYVkFILATTD------------YHKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 392920122 396 RTEAENVQFEEKAFDLLSkVGAEKSLRYALQLIAPArlcAQTCGREVIEVE 446
Cdd:PRK14957 190 ILAKENINSDEQSLEYIA-YHAKGSLRDALSLLDQA---ISFCGGELKQAQ 236
PRK06305 PRK06305
DNA polymerase III subunits gamma and tau; Validated
 320-427 8.78e-05

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180523 [Multi-domain]  Cd Length: 451  Bit Score: 44.76  E-value: 8.78e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 320 IDEVHMLDVECFTYLYRALESPMAPV-VVFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHRTE 398
Cdd:PRK06305 127 IDEVHMLTKEAFNSLLKTLEEPPQHVkFFLATTE------------IHKIPGTILSRCQKMHLKRIPEETIIDKLALIAK 194

                         90       100
                 ....*....|....*....|....*....
gi 392920122 399 AENVQFEEKAFDLLSKvGAEKSLRYALQL 427
Cdd:PRK06305 195 QEGIETSREALLPIAR-AAQGSLRDAESL 222
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 83-141 1.44e-04

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 42.39  E-value: 1.44e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122  83 RAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRAIGL 141
Cdd:cd19518   35 RGVLLHGPPGCGKTMLANAIAGEL--KVPFLKISATEIVSGVSGESEEKIRElFDQAISN 92
PRK14969 PRK14969
DNA polymerase III subunits gamma and tau; Provisional
 317-431 1.54e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237873 [Multi-domain]  Cd Length: 527  Bit Score: 43.97  E-value: 1.54e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPV-VVFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14969 122 VYIIDEVHMLSKSAFNAMLKTLEEPPEHVkFILATTD------------PQKIPVTVLSRCLQFNLKQMPPPLIVSHLQH 189

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 392920122 396 RTEAENVQFEEKAFDLLSKvGAEKSLRYALQLIAPA 431
Cdd:PRK14969 190 ILEQENIPFDATALQLLAR-AAAGSMRDALSLLDQA 224
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 82-138 1.93e-04

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 43.75  E-value: 1.93e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 392920122  82 GRAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:COG0464  191 PRGLLLYGPPGTGKTLLARALAGEL--GLPLIEVDLSDLVSKYVGETEKNLREvFDKA 246
PRK14951 PRK14951
DNA polymerase III subunits gamma and tau; Provisional
 317-427 2.73e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237865 [Multi-domain]  Cd Length: 618  Bit Score: 43.55  E-value: 2.73e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPV-VVFATNRgtttvrglgdkaPHGIPPEMLDRlmiipTMKYN-----EEDIR 390
Cdd:PRK14951 127 VFMIDEVHMLTNTAFNAMLKTLEEPPEYLkFVLATTD------------PQKVPVTVLSR-----CLQFNlrpmaPETVL 189

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 392920122 391 KILVHRTEAENVQFEEKAFDLLSKvGAEKSLRYALQL 427
Cdd:PRK14951 190 EHLTQVLAAENVPAEPQALRLLAR-AARGSMRDALSL 225
PRK06645 PRK06645
DNA polymerase III subunits gamma and tau; Validated
 317-436 4.42e-04

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 180643 [Multi-domain]  Cd Length: 507  Bit Score: 42.54  E-value: 4.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPVV-VFAtnrgTTTVRglgdkaphGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK06645 131 IFIIDEVHMLSKGAFNALLKTLEEPPPHIIfIFA----TTEVQ--------KIPATIISRCQRYDLRRLSFEEIFKLLEY 198

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 392920122 396 RTEAENVQFEEKAFDLLSkVGAEKSLRYALQLIAPARLCAQ 436
Cdd:PRK06645 199 ITKQENLKTDIEALRIIA-YKSEGSARDAVSILDQAASMSA 238
PRK14955 PRK14955
DNA polymerase III subunits gamma and tau; Provisional
 317-424 5.08e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184919 [Multi-domain]  Cd Length: 397  Bit Score: 42.19  E-value: 5.08e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMA-PVVVFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14955 130 VYIIDEVHMLSIAAFNAFLKTLEEPPPhAIFIFATTE------------LHKIPATIASRCQRFNFKRIPLEEIQQQLQG 197

                         90       100
                 ....*....|....*....|....*....
gi 392920122 396 RTEAENVQFEEKAFDLLSKvGAEKSLRYA 424
Cdd:PRK14955 198 ICEAEGISVDADALQLIGR-KAQGSMRDA 225
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 317-448 7.65e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 42.04  E-value: 7.65e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPV-VVFATNRgtttvrglgdkaPHGIPPEMLDRLmiiptmkyNEEDIRKI--- 392
Cdd:PRK14965 122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVkFIFATTE------------PHKVPITILSRC--------QRFDFRRIplq 181

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 392920122 393 -----LVHRTEAENVQFEEKAFDLLSKVGaEKSLRYALQLIAPARLCaqtCGREVIEvEDV 448
Cdd:PRK14965 182 kivdrLRYIADQEGISISDAALALVARKG-DGSMRDSLSTLDQVLAF---CGDAVGD-DDV 237
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 83-138 1.02e-03

second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase domains; This subfamily includes the second of two ATPase domains of the molecular chaperone CDC48 in yeast and p97 or VCP in metazoans, Peroxisomal biogenesis factor 1 (PEX1) and -6 (PEX6), Valosin-containing protein-like ATPase (VAT), and nuclear VCP-like protein (NVL). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 39.57  E-value: 1.02e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 392920122  83 RAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:cd19511   28 KGVLLYGPPGCGKTLLAKALASEA--GLNFISVKGPELFSKYVGESERAVREiFQKA 82
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 58-107 1.09e-03

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 39.79  E-value: 1.09e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 392920122   58 FVGQAPARTAASIVVDMIRLKCMAGRAVLIAGPPATGKTAIALAMSQELG 107
Cdd:pfam05496   9 YIGQEKVKENLKIFIEAAKQRGEALDHVLLYGPPGLGKTTLANIIANEMG 58
ftsH CHL00176
cell division protein; Validated
 85-119 1.64e-03

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 40.80  E-value: 1.64e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 392920122  85 VLIAGPPATGKTAIALAMSQELgdGVPFVPLVASE 119
Cdd:CHL00176 219 VLLVGPPGTGKTLLAKAIAGEA--EVPFFSISGSE 251
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 81-138 2.62e-03

ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 39.99  E-value: 2.62e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 392920122  81 AGRAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:COG1222  111 PPKGVLLYGPPGTGKTLLAKAVAGEL--GAPFIRVRGSELVSKYIGEGARNVREvFELA 167
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 83-138 3.32e-03

AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two members each from three archaeal species. It also includes yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein). These proteins in eukaryotes are involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus.


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 39.89  E-value: 3.32e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 392920122   83 RAVLIAGPPATGKTAIALAMSQElgDGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:TIGR01243 488 KGVLLFGPPGTGKTLLAKAVATE--SGANFIAVRGPEILSKWVGESEKAIREiFRKA 542
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 76-138 3.68e-03

second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ATPase domains; The Valosin-containing protein-like ATPase of Thermoplasma acidophilum (VAT), is an archaeal homolog of the ubiquitous Cdc48/p97. It is a protein unfoldase that functions in concert with the 20S proteasome by unfolding proteasome substrates and passing them on for degradation. VAT forms a homohexamer, each monomer contains two tandem ATPase domains, referred to as D1 and D2, and an N-terminal domain. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 38.25  E-value: 3.68e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 392920122  76 RLKCMAGRAVLIAGPPATGKTAIALAMSQElgDGVPFVPLVASEVFSNEVKKTEVLMRS-FRRA 138
Cdd:cd19529   21 RLGIRPPKGILLYGPPGTGKTLLAKAVATE--SNANFISVKGPELLSKWVGESEKAIREiFRKA 82
PRK14963 PRK14963
DNA polymerase III subunits gamma and tau; Provisional
 317-428 4.95e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184927 [Multi-domain]  Cd Length: 504  Bit Score: 39.44  E-value: 4.95e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPVV-VFATNRgtttvrglgdkaPHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK14963 119 VYILDEAHMMSKSAFNALLKTLEEPPEHVIfILATTE------------PEKMPPTILSRTQHFRFRRLTEEEIAGKLRR 186

                         90       100       110
                 ....*....|....*....|....*....|...
gi 392920122 396 RTEAENVQFEEKAFDLLSKVgAEKSLRYALQLI 428
Cdd:PRK14963 187 LLEAEGREAEPEALQLVARL-ADGAMRDAESLL 218
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 83-119 5.28e-03

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 37.98  E-value: 5.28e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 392920122  83 RAVLIAGPPATGKTAIALAMSQELgdGVPFVPLVASE 119
Cdd:cd19501   38 KGVLLVGPPGTGKTLLAKAVAGEA--GVPFFSISGSD 72
PRK07003 PRK07003
DNA polymerase III subunit gamma/tau;
317-427 6.94e-03

DNA polymerase III subunit gamma/tau;


Pssm-ID: 235906 [Multi-domain]  Cd Length: 830  Bit Score: 39.06  E-value: 6.94e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPmAPVVVFAtnrgtttvrgLGDKAPHGIPPEMLDRLMIIPTMKYNEEDIRKILVHR 396
Cdd:PRK07003 122 VYMIDEVHMLTNHAFNAMLKTLEEP-PPHVKFI----------LATTDPQKIPVTVLSRCLQFNLKQMPAGHIVSHLERI 190

                         90       100       110
                 ....*....|....*....|....*....|.
gi 392920122 397 TEAENVQFEEKAFDLLSKvGAEKSLRYALQL 427
Cdd:PRK07003 191 LGEERIAFEPQALRLLAR-AAQGSMRDALSL 220
PRK05896 PRK05896
DNA polymerase III subunits gamma and tau; Validated
 317-428 7.73e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235638 [Multi-domain]  Cd Length: 605  Bit Score: 38.67  E-value: 7.73e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 392920122 317 VLFIDEVHMLDVECFTYLYRALESPMAPVV-VFATNRGtttvrglgdkapHGIPPEMLDRLMIIPTMKYNEEDIRKILVH 395
Cdd:PRK05896 122 VYIIDEAHMLSTSAWNALLKTLEEPPKHVVfIFATTEF------------QKIPLTIISRCQRYNFKKLNNSELQELLKS 189

                         90       100       110
                 ....*....|....*....|....*....|...
gi 392920122 396 RTEAENVQFEEKAFDLLSKVgAEKSLRYALQLI 428
Cdd:PRK05896 190 IAKKEKIKIEDNAIDKIADL-ADGSLRDGLSIL 221
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 50-116 8.96e-03

type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 38.67  E-value: 8.96e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 392920122   50 EAHYEAAGFVG-----QAPARTAASIVVDMIRLK---CMAGRA--VLIAGPPATGKTAIALAMSQEL-GDGVPFVPLV 116
Cdd:TIGR03922 270 EAEAELAEQIGlervkRQVAALKSSTAMALARAErglPVAQTSnhMLFAGPPGTGKTTIARVVAKIYcGLGVLRKPLV 347
 
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

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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