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Conserved domains on  [gi|9790083|ref|NP_062659|]
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ruvB-like 1 [Mus musculus]

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 ...
 14-369 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: 620.87  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083     14 RIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPF 93
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083     94 CPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGyGKTISHVIIGLKTAKGTKQLKLD 173
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSG-GKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    174 PSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPqgg 253
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARP--- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    254 QDILSMmgqlMKPKKTEITDKLRGEINKVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNR 333
Cdd:pfam06068 237 QGILSL----FSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNR 312

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 9790083    334 GNCVIRGTeDITSPHGIPLDLLDRVMIIRTMLYTPQ 369
Cdd:pfam06068 313 GICTIRGT-DIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 374-439 1.86e-27

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: 104.26  E-value: 1.86e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9790083    374 IIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYD 439
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 ...
 14-369 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: 620.87  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083     14 RIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPF 93
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083     94 CPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGyGKTISHVIIGLKTAKGTKQLKLD 173
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSG-GKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    174 PSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPqgg 253
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARP--- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    254 QDILSMmgqlMKPKKTEITDKLRGEINKVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNR 333
Cdd:pfam06068 237 QGILSL----FSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNR 312

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 9790083    334 GNCVIRGTeDITSPHGIPLDLLDRVMIIRTMLYTPQ 369
Cdd:pfam06068 313 GICTIRGT-DIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
3-456 0e+00

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 529.16  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    3 IEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALA 82
Cdd:COG1224   4 IREIEKVKEFERISAHSHIRGLGLDENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTALAVA 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   83 IAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLK 162
Cdd:COG1224  84 IARELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKIRYARHPYNPYVKVPREATITLA 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083  163 TAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATE-FDLEAEEYVPLPKGDVHKKKEIIQDVTLH 241
Cdd:COG1224 164 TKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAKGEGAKtYDIETKRIVEVPSGPVKKEKEIVRTLTLH 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083  242 DLDVANARPQGGQDILSMMGQlmkpkKTEITDKLRGEINKVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALES 321
Cdd:COG1224 244 DLDLYLAAQRAAFSALFGFFE-----EREIPSEVRKQVDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRAMES 318

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083  322 SIAPIVIFASNRGNCVIRGTeDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKT 401
Cdd:COG1224 319 ELAPIIILATNRGITKIRGT-DIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIGVER 397

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|....*
gi 9790083  402 TLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK 456
Cdd:COG1224 398 SLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESVEYVKEYEELFLK 452
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 374-439 1.86e-27

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: 104.26  E-value: 1.86e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9790083    374 IIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYD 439
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 40-100 4.39e-09

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: 55.70  E-value: 4.39e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9790083   40 VGQENAREACGVIVELIKS----KKMAGR---AVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSE 100
Cdd:cd19501   7 AGCEEAKEELKEVVEFLKNpekfTKLGAKipkGVLLVGPPGTGKTLLAKAVAGEAG--VPFFSISGSD 72
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
40-90 3.86e-08

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 54.75  E-value: 3.86e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9790083    40 VGQENAREACGViveLIKSKKMAGRA---VLLAGPPGTGKTALALAIAQELGSK 90
Cdd:PRK00080  28 IGQEKVKENLKI---FIEAAKKRGEAldhVLLYGPPGLGKTTLANIIANEMGVN 78
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 40-91 7.06e-06

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 47.68  E-value: 7.06e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 9790083     40 VGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKV 91
Cdd:TIGR00635   7 IGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNL 58
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 63-90 1.90e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.59  E-value: 1.90e-04
                           10        20
                   ....*....|....*....|....*...
gi 9790083      63 GRAVLLAGPPGTGKTALALAIAQELGSK 90
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPP 29
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 62-97 5.37e-04

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 41.30  E-value: 5.37e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 9790083    62 AGRAVLLAGPPGTGKTALALAIAQEL---GSKVPFCPMV 97
Cdd:NF038214  89 RAENVLLLGPPGTGKTHLAIALGYAAcrqGYRVRFTTAA 127
 
Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 14-369 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: 620.87  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083     14 RIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVPF 93
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083     94 CPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGyGKTISHVIIGLKTAKGTKQLKLD 173
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSG-GKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    174 PSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATEFDLEAEEYVPLPKGDVHKKKEIIQDVTLHDLDVANARPqgg 253
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARP--- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    254 QDILSMmgqlMKPKKTEITDKLRGEINKVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALESSIAPIVIFASNR 333
Cdd:pfam06068 237 QGILSL----FSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNR 312

                         330       340       350
                  ....*....|....*....|....*....|....*.
gi 9790083    334 GNCVIRGTeDITSPHGIPLDLLDRVMIIRTMLYTPQ 369
Cdd:pfam06068 313 GICTIRGT-DIISPHGIPLDLLDRLLIITTEPYTRE 347
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
3-456 0e+00

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 529.16  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    3 IEEVKSTTKTQRIASHSHVKGLGLDESGLAKQAASGLVGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALA 82
Cdd:COG1224   4 IREIEKVKEFERISAHSHIRGLGLDENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTALAVA 83

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   83 IAQELGSKVPFCPMVGSEVYSTEIKKTEVLMENFRRAIGLRIKETKEVYEGEVTELTPCETENPMGGYGKTISHVIIGLK 162
Cdd:COG1224  84 IARELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKIRYARHPYNPYVKVPREATITLA 163

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083  163 TAKGTKQLKLDPSIFESLQKERVEAGDVIYIEANSGAVKRQGRCDTYATE-FDLEAEEYVPLPKGDVHKKKEIIQDVTLH 241
Cdd:COG1224 164 TKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAKGEGAKtYDIETKRIVEVPSGPVKKEKEIVRTLTLH 243

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083  242 DLDVANARPQGGQDILSMMGQlmkpkKTEITDKLRGEINKVVNKYIDQGVAELVPGVLFVDEVHMLDIECFTYLHRALES 321
Cdd:COG1224 244 DLDLYLAAQRAAFSALFGFFE-----EREIPSEVRKQVDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRAMES 318

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083  322 SIAPIVIFASNRGNCVIRGTeDITSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKIRAQTEGINISEEALNHLGEIGTKT 401
Cdd:COG1224 319 ELAPIIILATNRGITKIRGT-DIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIGVER 397

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|....*
gi 9790083  402 TLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYDAKSSAKILADQQDKYMK 456
Cdd:COG1224 398 SLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESVEYVKEYEELFLK 452
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 374-439 1.86e-27

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: 104.26  E-value: 1.86e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 9790083    374 IIKIRAQTEGINISEEALNHLGEIGTKTTLRYSVQLLTPANLLAKINGKDSIEKEHVEEISELFYD 439
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
39-93 1.33e-09

Predicted ATPase, AAA+ superfamily [General function prediction only];


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 58.36  E-value: 1.33e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9790083   39 LVGQENAREACGVIVE-------LIKSKKMAGRAVLLAGPPGTGKTALALAIAQELgsKVPF 93
Cdd:COG1223   4 VVGQEEAKKKLKLIIKelrrrenLRKFGLWPPRKILFYGPPGTGKTMLAEALAGEL--KLPL 63
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 40-100 4.39e-09

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: 55.70  E-value: 4.39e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 9790083   40 VGQENAREACGVIVELIKS----KKMAGR---AVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSE 100
Cdd:cd19501   7 AGCEEAKEELKEVVEFLKNpekfTKLGAKipkGVLLVGPPGTGKTLLAKAVAGEAG--VPFFSISGSD 72
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 54-119 5.98e-09

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: 54.98  E-value: 5.98e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083   54 ELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEVYSTEIKKTEVLMEN-FRRA 119
Cdd:cd19481  17 RLRRYGLGLPKGILLYGPPGTGKTLLAKALAGELG--LPLIVVKLSSLLSKYVGESEKNLRKiFERA 81
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 66-119 7.10e-09

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: 53.75  E-value: 7.10e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 9790083     66 VLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEVYSTEIKKTEVLMEN-FRRA 119
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG--APFIEISGSELVSKYVGESEKRLRElFEAA 53
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 40-88 1.13e-08

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: 54.04  E-value: 1.13e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 9790083     40 VGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELG 88
Cdd:pfam05496  10 IGQEKVKENLKIFIEAAKQRGEALDHVLLYGPPGLGKTTLANIIANEMG 58
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
40-90 3.86e-08

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 54.75  E-value: 3.86e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 9790083    40 VGQENAREACGViveLIKSKKMAGRA---VLLAGPPGTGKTALALAIAQELGSK 90
Cdd:PRK00080  28 IGQEKVKENLKI---FIEAAKKRGEAldhVLLYGPPGLGKTTLANIIANEMGVN 78
PRK04195 PRK04195
replication factor C large subunit; Provisional
 37-91 5.07e-08

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 54.93  E-value: 5.07e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083    37 SGLVGQENAREAcgvIVELIKS--KKMAGRAVLLAGPPGTGKTALALAIAQELGSKV 91
Cdd:PRK04195  14 SDVVGNEKAKEQ---LREWIESwlKGKPKKALLLYGPPGVGKTSLAHALANDYGWEV 67
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 40-123 6.71e-08

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: 51.76  E-value: 6.71e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   40 VGQENAREAcgvIVELIKSKKmaGRAVLLAGPPGTGKTALALAIAQELG-SKVPFCPMVGSEVYSTEIKKTEVLMENFRR 118
Cdd:cd00009   1 VGQEEAIEA---LREALELPP--PKNLLLYGPPGTGKTTLARAIANELFrPGAPFLYLNASDLLEGLVVAELFGHFLVRL 75


                ....*
gi 9790083  119 AIGLR 123
Cdd:cd00009  76 LFELA 80
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 46-101 9.78e-08

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 53.47  E-value: 9.78e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 9790083   46 REAcgVIVELIKSKKMA------GRAVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEV 101
Cdd:COG1222  91 REA--VELPLKNPELFRkygiepPKGVLLYGPPGTGKTLLAKAVAGELG--APFIRVRGSEL 148
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 64-119 1.61e-07

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: 50.75  E-value: 1.61e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEVYSTEIKKTE-VLMENFRRA 119
Cdd:cd19503  35 RGVLLHGPPGTGKTLLARAVANEAG--ANFLSISGPSIVSKYLGESEkNLREIFEEA 89
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 39-120 2.02e-07

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: 52.99  E-value: 2.02e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   39 LVGQENAREACGVIVELIKSKKMA--------GRAVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEVYSTEIKKTE 110
Cdd:COG0464 159 LGGLEEVKEELRELVALPLKRPELreeyglppPRGLLLYGPPGTGKTLLARALAGELG--LPLIEVDLSDLVSKYVGETE 236

                        90
                ....*....|
gi 9790083  111 vlmENFRRAI 120
Cdd:COG0464 237 ---KNLREVF 243
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 40-89 4.65e-07

Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair];


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 51.62  E-value: 4.65e-07
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|...
gi 9790083   40 VGQENAREACGViveLIKSKKMAGRA---VLLAGPPGTGKTALALAIAQELGS 89
Cdd:COG2255  31 IGQEKVKENLKI---FIEAAKKRGEAldhVLLYGPPGLGKTTLAHIIANEMGV 80
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
42-88 4.77e-07

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 51.13  E-value: 4.77e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 9790083   42 QENAREAcgvIVELIKSKKMAgRAVLLAGPPGTGKTALALAIAQELG 88
Cdd:COG0470   1 QEEAWEQ---LLAAAESGRLP-HALLLHGPPGIGKTTLALALARDLL 43
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
41-100 7.14e-07

ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 51.58  E-value: 7.14e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083   41 GQENAREACGVIVELIKS----KKMAGRA---VLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSE 100
Cdd:COG0465 146 GVDEAKEELQEIVDFLKDpekfTRLGAKIpkgVLLVGPPGTGKTLLAKAVAGE--AGVPFFSISGSD 210
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
33-100 9.03e-07

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 51.19  E-value: 9.03e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9790083    33 KQAASGLVGQENAREACGVIVELIKS----KKMAGR---AVLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSE 100
Cdd:PRK10733 148 KTTFADVAGCDEAKEEVAELVEYLREpsrfQKLGGKipkGVLMVGPPGTGKTLLAKAIAGE--AKVPFFTISGSD 220
ftsH CHL00176
cell division protein; Validated
 22-100 1.28e-06

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 50.82  E-value: 1.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    22 KGLGLDESGLAKQAASGLV-----GQENAREACGVIVELIK--SKKMAGRA-----VLLAGPPGTGKTALALAIAQElgS 89
Cdd:CHL00176 163 MNFGKSKARFQMEADTGITfrdiaGIEEAKEEFEEVVSFLKkpERFTAVGAkipkgVLLVGPPGTGKTLLAKAIAGE--A 240

                         90
                 ....*....|.
gi 9790083    90 KVPFCPMVGSE 100
Cdd:CHL00176 241 EVPFFSISGSE 251
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 64-119 1.39e-06

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: 48.05  E-value: 1.39e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSEVYSTEIKKTE-VLMENFRRA 119
Cdd:cd19511  28 KGVLLYGPPGCGKTLLAKALASE--AGLNFISVKGPELFSKYVGESErAVREIFQKA 82
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 31-88 1.62e-06

MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 49.40  E-value: 1.62e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 9790083   31 LAKQAASGLVGQENAREAcgVIVELikskkMAGRAVLLAGPPGTGKTALALAIAQELG 88
Cdd:COG0714   6 LRAEIGKVYVGQEELIEL--VLIAL-----LAGGHLLLEGVPGVGKTTLAKALARALG 56
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 39-89 3.06e-06

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). 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: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 46.96  E-value: 3.06e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 9790083   39 LVGQENAREACGVIV-------ELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGS 89
Cdd:cd19509   1 IAGLDDAKEALKEAVilpslrpDLFPGLRGPPRGILLYGPPGTGKTLLARAVASESGS 58
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 66-100 3.89e-06

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 48.68  E-value: 3.89e-06
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 9790083    66 VLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSE 100
Cdd:PRK03992 168 VLLYGPPGTGKTLLAKAVAHE--TNATFIRVVGSE 200
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 40-91 7.06e-06

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 47.68  E-value: 7.06e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 9790083     40 VGQENAREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKV 91
Cdd:TIGR00635   7 IGQEKVKEQLQLFIEAAKMRQEALDHLLLYGPPGLGKTTLAHIIANEMGVNL 58
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 64-119 9.03e-06

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: 45.56  E-value: 9.03e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELGSKvpFCPMVGSEVYSTEIKKTE-VLMENFRRA 119
Cdd:cd19529  28 KGILLYGPPGTGKTLLAKAVATESNAN--FISVKGPELLSKWVGESEkAIREIFRKA 82
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 37-115 1.01e-05

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. 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: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 45.62  E-value: 1.01e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   37 SGLVGQENAREAC--GVIV-----ELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKvpFCPMVGSEVYSTEIKKT 109
Cdd:cd19521   7 EDVAGLEGAKEALkeAVILpvkfpHLFTGNRKPWSGILLYGPPGTGKSYLAKAVATEANST--FFSVSSSDLVSKWMGES 84


                ....*.
gi 9790083  110 EVLMEN 115
Cdd:cd19521  85 EKLVKQ 90
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 52-92 1.48e-05

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 47.07  E-value: 1.48e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 9790083   52 IVELIKSKKMagraVLLAGPPGTGKTALALAIAQELGSKVP 92
Cdd:COG1401 214 FLAALKTKKN----VILAGPPGTGKTYLARRLAEALGGEDN 250
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 64-103 1.81e-05

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: 45.09  E-value: 1.81e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELgsKVPFCPMVGSEVYS 103
Cdd:cd19518  35 RGVLLHGPPGCGKTMLANAIAGEL--KVPFLKISATEIVS 72
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 40-91 2.50e-05

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 46.23  E-value: 2.50e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9790083    40 VGQENAREACGVIVELIKSKKMAgrAVLLAGPPGTGKTALALAIAQELGSKV 91
Cdd:PRK13342  15 VGQEHLLGPGKPLRRMIEAGRLS--SMILWGPPGTGKTTLARIIAGATDAPF 64
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 64-119 5.02e-05

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: 45.67  E-value: 5.02e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083     64 RAVLLAGPPGTGKTALALAIAQELGSKvpFCPMVGSEVYSTEIKKTE-VLMENFRRA 119
Cdd:TIGR01243 488 KGVLLFGPPGTGKTLLAKAVATESGAN--FIAVRGPEILSKWVGESEkAIREIFRKA 542
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 64-119 5.82e-05

first of two ATPase domains of CDC48 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. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like 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: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 43.58  E-value: 5.82e-05
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELGSKvpFCPMVGSEVYSTEIKKTEvlmENFRRA 119
Cdd:cd19519  35 RGILLYGPPGTGKTLIARAVANETGAF--FFLINGPEIMSKLAGESE---SNLRKA 85
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 64-100 1.05e-04

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN 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: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 42.71  E-value: 1.05e-04
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELGSKvpFCPMVGSE 100
Cdd:cd19502  38 KGVLLYGPPGTGKTLLAKAVANHTDAT--FIRVVGSE 72
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
39-87 1.39e-04

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 43.64  E-value: 1.39e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 9790083   39 LVGQENAREAcgvIVELIKSKKMAGrAVLLAGPPGTGKTALALAIAQEL 87
Cdd:COG2812  12 VVGQEHVVRT---LKNALASGRLAH-AYLFTGPRGVGKTTLARILAKAL 56
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 64-100 1.75e-04

26S protease regulatory subunit 6B-like protein; Provisional


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 43.60  E-value: 1.75e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 9790083    64 RAVLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSE 100
Cdd:PTZ00454 180 RGVLLYGPPGTGKTMLAKAVAHH--TTATFIRVVGSE 214
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 63-90 1.90e-04

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 41.59  E-value: 1.90e-04
                           10        20
                   ....*....|....*....|....*...
gi 9790083      63 GRAVLLAGPPGTGKTALALAIAQELGSK 90
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPP 29
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 40-90 3.21e-04

Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, recombination and repair];


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 42.74  E-value: 3.21e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 9790083   40 VGQENAREACGVIVELIKSKKMagRAVLLAGPPGTGKTALALAIAQELGSK 90
Cdd:COG2256  28 VGQEHLLGPGKPLRRAIEAGRL--SSMILWGPPGTGKTTLARLIANATDAE 76
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 54-89 4.45e-04

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. 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: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 41.12  E-value: 4.45e-04
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 9790083   54 ELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGS 89
Cdd:cd19522  24 EFFKGIRRPWKGVLMVGPPGTGKTLLAKAVATECGT 59
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 59-90 5.18e-04

lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain 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: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 41.00  E-value: 5.18e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 9790083   59 KKMAGRAVLLAGPPGTGKTALALAIAQELGSK 90
Cdd:cd19500  33 GSMKGPILCLVGPPGVGKTSLGKSIARALGRK 64
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 62-97 5.37e-04

IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was built to hit full-length AAA+ ATPases of IS21 family IS (insertion sequence) elements.


Pssm-ID: 439516  Cd Length: 232  Bit Score: 41.30  E-value: 5.37e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 9790083    62 AGRAVLLAGPPGTGKTALALAIAQEL---GSKVPFCPMV 97
Cdd:NF038214  89 RAENVLLLGPPGTGKTHLAIALGYAAcrqGYRVRFTTAA 127
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 64-88 5.49e-04

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. 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: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 40.49  E-value: 5.49e-04
                        10        20
                ....*....|....*....|....*
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELG 88
Cdd:cd19520  36 KGVLLYGPPGCGKTMLAKATAKEAG 60
COG3903 COG3903
Predicted ATPase [General function prediction only];
62-87 6.33e-04

Predicted ATPase [General function prediction only];


Pssm-ID: 443109 [Multi-domain]  Cd Length: 933  Bit Score: 42.31  E-value: 6.33e-04
                        10        20
                ....*....|....*....|....*.
gi 9790083   62 AGRAVLLAGPPGTGKTALALAIAQEL 87
Cdd:COG3903 175 AARLVTLTGPGGVGKTRLALEVAHRL 200
rfc PRK00440
replication factor C small subunit; Reviewed
 40-87 7.20e-04

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 41.40  E-value: 7.20e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 9790083    40 VGQENareacgvIVELIKS----KKMAgrAVLLAGPPGTGKTALALAIAQEL 87
Cdd:PRK00440  20 VGQEE-------IVERLKSyvkeKNMP--HLLFAGPPGTGKTTAALALAREL 62
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 64-110 7.92e-04

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in 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 second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like 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: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 40.19  E-value: 7.92e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSEVYSTEIKKTE 110
Cdd:cd19528  28 KGVLFYGPPGCGKTLLAKAIANE--CQANFISVKGPELLTMWFGESE 72
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 64-119 7.97e-04

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: 41.82  E-value: 7.97e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 9790083     64 RAVLLAGPPGTGKTALALAIAQELGSKvpFCPMVGSEVYSTEIKKTEV-LMENFRRA 119
Cdd:TIGR01243 213 KGVLLYGPPGTGKTLLAKAVANEAGAY--FISINGPEIMSKYYGESEErLREIFKEA 267
bpMoxR pfam20030
MoxR domain in the MoxR-vWA-beta-propeller ternary systems; Core MoxR component domain of the ...
 33-90 8.04e-04

MoxR domain in the MoxR-vWA-beta-propeller ternary systems; Core MoxR component domain of the MoxR-vWA-beta-propeller ternary systems, a class of NTP-dependent biological conflict systems.


Pssm-ID: 437862 [Multi-domain]  Cd Length: 205  Bit Score: 40.69  E-value: 8.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 9790083     33 KQAASGLVGQENareacgvIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSK 90
Cdd:pfam20030   8 RPLKTGFVGKDE-------IIDLLGLALVARENLFLLGPPGTAKSALVRRLAARLGGR 58
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 28-87 9.02e-04

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: 41.75  E-value: 9.02e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 9790083     28 ESGLAKQAASGLVGQENAREACGVIVELIKSK---KMAGRA--VLLAGPPGTGKTALALAIAQEL 87
Cdd:TIGR03922 272 EAELAEQIGLERVKRQVAALKSSTAMALARAErglPVAQTSnhMLFAGPPGTGKTTIARVVAKIY 336
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 64-87 9.47e-04

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. 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: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 40.51  E-value: 9.47e-04
                        10        20
                ....*....|....*....|....
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQEL 87
Cdd:cd19508  53 RLVLLHGPPGTGKTSLCKALAQKL 76
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
62-87 1.14e-03

DNA replication protein DnaC [Replication, recombination and repair];


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 40.53  E-value: 1.14e-03
                        10        20
                ....*....|....*....|....*.
gi 9790083   62 AGRAVLLAGPPGTGKTALALAIAQEL 87
Cdd:COG1484  98 RGENLILLGPPGTGKTHLAIALGHEA 123
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 39-113 1.39e-03

ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in microtubule dynamics; it specifically recognizes and cuts microtubules that are polyglutamylated. 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: 410932 [Multi-domain]  Cd Length: 164  Bit Score: 39.45  E-value: 1.39e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   39 LVGQENAREACGVIV-------ELIKSKKMAGRAVLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSEVYSTEIKKTEV 111
Cdd:cd19524   2 IAGQDLAKQALQEMVilpslrpELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAE--SNATFFNISAASLTSKYVGEGEK 79


                ..
gi 9790083  112 LM 113
Cdd:cd19524  80 LV 81
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 59-118 1.61e-03

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. 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: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 39.03  E-value: 1.61e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   59 KKMAGraVLLAGPPGTGKTALALAIAQELgsKVPFCPMVGSEVYSTEIKKTEvlmENFRR 118
Cdd:cd19527  24 RKRSG--ILLYGPPGTGKTLLAKAIATEC--SLNFLSVKGPELINMYIGESE---ANVRE 76
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 66-119 1.63e-03

second 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: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 39.01  E-value: 1.63e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 9790083   66 VLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSEVYSTEIKKTEVLMEN-FRRA 119
Cdd:cd19530  33 VLLYGPPGCGKTLLAKAVANE--SGANFISVKGPELLNKYVGESERAVRQvFQRA 85
COG0645 COG0645
Predicted kinase, contains AAA domain [General function prediction only];
66-88 1.79e-03

Predicted kinase, contains AAA domain [General function prediction only];


Pssm-ID: 440410 [Multi-domain]  Cd Length: 164  Bit Score: 39.13  E-value: 1.79e-03
                        10        20
                ....*....|....*....|...
gi 9790083   66 VLLAGPPGTGKTALALAIAQELG 88
Cdd:COG0645   2 ILVCGLPGSGKSTLARALAERLG 24
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 298-413 1.92e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 40.45  E-value: 1.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   298 VLFVDEVHMLDIECFTYLHRALESSiAPIVIFasnrgncvIRGTEDItspHGIPLDLLDRVMIIRTMLYTPQEMKQIIKI 377
Cdd:PRK14957 122 VYLIDEVHMLSKQSFNALLKTLEEP-PEYVKF--------ILATTDY---HKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 9790083   378 RAQTEGINISEEALNHLGeIGTKTTLRYSVQLLTPA 413
Cdd:PRK14957 190 ILAKENINSDEQSLEYIA-YHAKGSLRDALSLLDQA 224
PRK14965 PRK14965
DNA polymerase III subunits gamma and tau; Provisional
 298-391 2.08e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237871 [Multi-domain]  Cd Length: 576  Bit Score: 40.50  E-value: 2.08e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083   298 VLFVDEVHMLDIECFTYLHRALESSIAPI-VIFASnrgncvirgtediTSPHGIPLDLLDRVM---IIRTMLytPQEMKQ 373
Cdd:PRK14965 122 IFIIDEVHMLSTNAFNALLKTLEEPPPHVkFIFAT-------------TEPHKVPITILSRCQrfdFRRIPL--QKIVDR 186

                         90
                 ....*....|....*...
gi 9790083   374 IIKIRAQtEGINISEEAL 391
Cdd:PRK14965 187 LRYIADQ-EGISISDAAL 203
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 64-110 2.12e-03

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 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: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 39.03  E-value: 2.12e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQEL---GSKVPFCPMVGSEVYSTEIKKTE 110
Cdd:cd19517  35 RGVLFHGPPGTGKTLMARALAAECskgGQKVSFFMRKGADCLSKWVGEAE 84
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 66-119 3.29e-03

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. 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: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 38.18  E-value: 3.29e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 9790083   66 VLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEVYSTEIKKTEVLMEN-FRRA 119
Cdd:cd19526  30 ILLYGPPGCGKTLLASAIASECG--LNFISVKGPELLNKYIGASEQNVRDlFSRA 82
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 64-119 4.22e-03

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 39.37  E-value: 4.22e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 9790083    64 RAVLLAGPPGTGKTALALAIAQElgSKVPFCPMVGSEV---YSTEIKKteVLMENFRRA 119
Cdd:PTZ00361 218 KGVILYGPPGTGKTLLAKAVANE--TSATFLRVVGSELiqkYLGDGPK--LVRELFRVA 272
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 64-88 4.52e-03

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. 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: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 37.72  E-value: 4.52e-03
                        10        20
                ....*....|....*....|....*
gi 9790083   64 RAVLLAGPPGTGKTALALAIAQELG 88
Cdd:cd19510  24 RGYLLYGPPGTGKSSFIAALAGELD 48
RAD55 COG0467
RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];
62-86 4.59e-03

RecA-superfamily ATPase, KaiC/GvpD/RAD55 family [Signal transduction mechanisms];


Pssm-ID: 440235 [Multi-domain]  Cd Length: 221  Bit Score: 38.36  E-value: 4.59e-03
                        10        20
                ....*....|....*....|....*
gi 9790083   62 AGRAVLLAGPPGTGKTALALAIAQE 86
Cdd:COG0467  19 RGSSTLLSGPPGTGKTTLALQFLAE 43
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 39-87 4.61e-03

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 37.87  E-value: 4.61e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 9790083     39 LVGQENAREAcgvIVELIKSKKM-AGRAVLLAGPPGTGKTALALAIAQEL 87
Cdd:pfam13191   2 LVGREEELEQ---LLDALDRVRSgRPPSVLLTGEAGTGKTTLLRELLRAL 48
COG3899 COG3899
Predicted ATPase [General function prediction only];
62-89 4.85e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443106 [Multi-domain]  Cd Length: 1244  Bit Score: 39.46  E-value: 4.85e-03
                         10        20
                 ....*....|....*....|....*...
gi 9790083    62 AGRAVLLAGPPGTGKTALALAIAQELGS 89
Cdd:COG3899  310 RGELVLVSGEAGIGKSRLVRELARRARA 337
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 56-101 4.88e-03

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. 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: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 37.51  E-value: 4.88e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 9790083   56 IKSKKMAGRAVLLAGPPGTGKTALALAIAQELGskVPFCPMVGSEV 101
Cdd:cd19512  15 TKKNKGLYRNILFYGPPGTGKTLFAKKLALHSG--MDYAIMTGGDV 58
dnaX_nterm TIGR02397
DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ ...
 301-433 6.45e-03

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: 38.70  E-value: 6.45e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 9790083    301 VDEVHMLDIECFTYLHRALESsiAP---IVIFASnrgncvirgtediTSPHGIPLDLLDRVMIIRTMLYTPQEMKQIIKI 377
Cdd:TIGR02397 123 IDEVHMLSKSAFNALLKTLEE--PPehvVFILAT-------------TEPHKIPATILSRCQRFDFKRIPLEDIVERLKK 187

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 9790083    378 RAQTEGINISEEALNHLGEIGtKTTLRYSVQLLTPANLLakinGKDSIEKEHVEEI 433
Cdd:TIGR02397 188 ILDKEGIKIEDEALELIARAA-DGSLRDALSLLDQLISF----GNGKITYEDVNEL 238
DnaA COG0593
Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];
39-92 8.38e-03

Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];


Pssm-ID: 440358 [Multi-domain]  Cd Length: 303  Bit Score: 38.25  E-value: 8.38e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 9790083   39 LVGQENaREACGVIVELIKSKKMAGRAVLLAGPPGTGKTALALAIAQELGSKVP 92
Cdd:COG0593  11 VVGPSN-RLAHAAALAVAEWPGKAYNPLFLYGGVGLGKTHLLHAIGNEALENNP 63
PRK09270 PRK09270
nucleoside triphosphate hydrolase domain-containing protein; Reviewed
 62-88 8.88e-03

nucleoside triphosphate hydrolase domain-containing protein; Reviewed


Pssm-ID: 236442  Cd Length: 229  Bit Score: 37.61  E-value: 8.88e-03
                         10        20
                 ....*....|....*....|....*...
gi 9790083    62 AGRAVL-LAGPPGTGKTALALAIAQELG 88
Cdd:PRK09270  31 QRRTIVgIAGPPGAGKSTLAEFLEALLQ 58
 
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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