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Conserved domains on  [gi|19115695|ref|NP_594783|]
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AAA family ATPase Rvb1 [Schizosaccharomyces pombe]

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 ...
 15-369 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: 621.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695    15 RITTHSHIKGLGLKEDGTCESVGGGFIGQEKAREACGIITDLIKSKKFGGKGVLFAGGAGTGKTALALAIAQELGPKVPF 94
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695    95 CPMVGSEVYSSEIKKTEALMENFRRAIGLRVKETKEVYEGEVTEMVPEEAENPLGGyGKTISHVLLGLKTHKGTKQLKLD 174
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSG-GKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   175 PSIYESLQREQVSTGDVIYIEANTGAVKRVGRSDAYATEFDLEAEEYVPMPKGEVHKRKEIVQDVTLHDLDIANARPqgg 254
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARP--- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   255 QDIMSMmgqlMKPKKTEITDKLRGEINKVVNKYIEQGIAELIPGVLFIDEVHMLDIECFTYLNQALESTISPIVIFASNR 334
Cdd:pfam06068 237 QGILSL----FSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNR 312

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 19115695   335 GICTIRGTeDIQAPHGIPTDLLDRLLIVRTLPYSE 369
Cdd:pfam06068 313 GICTIRGT-DIISPHGIPLDLLDRLLIITTEPYTR 346
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 375-440 2.37e-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: 103.88  E-value: 2.37e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19115695   375 ILQIRAKVENIILTDECLDKLAQEGSRTSLRYVIQLLTPVSIIASLHGNKEIGVQDIEECNDLFLD 440
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 ...
 15-369 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: 621.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695    15 RITTHSHIKGLGLKEDGTCESVGGGFIGQEKAREACGIITDLIKSKKFGGKGVLFAGGAGTGKTALALAIAQELGPKVPF 94
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695    95 CPMVGSEVYSSEIKKTEALMENFRRAIGLRVKETKEVYEGEVTEMVPEEAENPLGGyGKTISHVLLGLKTHKGTKQLKLD 174
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSG-GKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   175 PSIYESLQREQVSTGDVIYIEANTGAVKRVGRSDAYATEFDLEAEEYVPMPKGEVHKRKEIVQDVTLHDLDIANARPqgg 254
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARP--- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   255 QDIMSMmgqlMKPKKTEITDKLRGEINKVVNKYIEQGIAELIPGVLFIDEVHMLDIECFTYLNQALESTISPIVIFASNR 334
Cdd:pfam06068 237 QGILSL----FSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNR 312

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 19115695   335 GICTIRGTeDIQAPHGIPTDLLDRLLIVRTLPYSE 369
Cdd:pfam06068 313 GICTIRGT-DIISPHGIPLDLLDRLLIITTEPYTR 346
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
1-449 0e+00

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 515.68  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   1 MVQISEVKGNGRDNRITTHSHIKGLGLKEDGTCESVGGGFIGQEKAREACGIITDLIKSKKFGGKGVLFAGGAGTGKTAL 80
Cdd:COG1224   1 MSEIREIEKVKEFERISAHSHIRGLGLDENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTAL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  81 ALAIAQELGPKVPFCPMVGSEVYSSEIKKTEALMENFRRAIGLRVKETKEVYEGEVTEMVPEEAENPLGGYGKTISHVLL 160
Cdd:COG1224  81 AVAIARELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKIRYARHPYNPYVKVPREATI 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 161 GLKTHKGTKQLKLDPSIYESLQREQVSTGDVIYIEANTGAVKRVGRSDAYATE-FDLEAEEYVPMPKGEVHKRKEIVQDV 239
Cdd:COG1224 161 TLATKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAKGEGAKtYDIETKRIVEVPSGPVKKEKEIVRTL 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 240 TLHDLDIANARPQGGqdIMSMMGQlmkPKKTEITDKLRGEINKVVNKYIEQGIAELIPGVLFIDEVHMLDIECFTYLNQA 319
Cdd:COG1224 241 TLHDLDLYLAAQRAA--FSALFGF---FEEREIPSEVRKQVDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRA 315

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 320 LESTISPIVIFASNRGICTIRGTeDIQAPHGIPTDLLDRLLIVRTLPYSESEIRSILQIRAKVENIILTDECLDKLAQEG 399
Cdd:COG1224 316 MESELAPIIILATNRGITKIRGT-DIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIG 394

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|
gi 19115695 400 SRTSLRYVIQLLTPVSIIASLHGNKEIGVQDIEECNDLFLDARRSAQVVK 449
Cdd:COG1224 395 VERSLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESVEYVK 444
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 375-440 2.37e-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: 103.88  E-value: 2.37e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19115695   375 ILQIRAKVENIILTDECLDKLAQEGSRTSLRYVIQLLTPVSIIASLHGNKEIGVQDIEECNDLFLD 440
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 64-120 1.25e-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: 48.05  E-value: 1.25e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19115695  64 GKGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTEALMEN-FRRA 120
Cdd:cd19481  26 PKGILLYGPPGTGKTLLAKALAGELG--LPLIVVKLSSLLSKYVGESEKNLRKiFERA 81
ftsH CHL00176
cell division protein; Validated
 65-101 4.61e-05

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 45.81  E-value: 4.61e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 19115695   65 KGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSE 101
Cdd:CHL00176 217 KGVLLVGPPGTGKTLLAKAIAGEAE--VPFFSISGSE 251
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 65-120 1.47e-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: 41.05  E-value: 1.47e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695    65 KGVLFAGGAGTGKTALALAIAQELGPKvpFCPMVGSEVYSSEIKKTE-ALMENFRRA 120
Cdd:TIGR01243 488 KGVLLFGPPGTGKTLLAKAVATESGAN--FIAVRGPEILSKWVGESEkAIREIFRKA 542
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 64-91 2.42e-03

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: 38.51  E-value: 2.42e-03
                           10        20
                   ....*....|....*....|....*...
gi 19115695     64 GKGVLFAGGAGTGKTALALAIAQELGPK 91
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPP 29
 
Name Accession Description Interval E-value
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 15-369 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: 621.64  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695    15 RITTHSHIKGLGLKEDGTCESVGGGFIGQEKAREACGIITDLIKSKKFGGKGVLFAGGAGTGKTALALAIAQELGPKVPF 94
Cdd:pfam06068   1 RISAHSHIRGLGLDEDGEARYVSGGLVGQEKAREAAGVIVEMIKEGKIAGRAVLIAGPPGTGKTALAIAISKELGEDTPF 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695    95 CPMVGSEVYSSEIKKTEALMENFRRAIGLRVKETKEVYEGEVTEMVPEEAENPLGGyGKTISHVLLGLKTHKGTKQLKLD 174
Cdd:pfam06068  81 TSISGSEVYSLEMKKTEALTQAFRKAIGVRIKEEKEVYEGEVVELEIEEAENPLSG-GKTIKGGKITLKTTKMEKTLKLG 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   175 PSIYESLQREQVSTGDVIYIEANTGAVKRVGRSDAYATEFDLEAEEYVPMPKGEVHKRKEIVQDVTLHDLDIANARPqgg 254
Cdd:pfam06068 160 PKIYEQLQKEKVSAGDVIYIDKNTGRVKKLGRSFARATDFDLEATEFVPCPKGEVHKRKEVVQTVTLHDIDVANARP--- 236

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   255 QDIMSMmgqlMKPKKTEITDKLRGEINKVVNKYIEQGIAELIPGVLFIDEVHMLDIECFTYLNQALESTISPIVIFASNR 334
Cdd:pfam06068 237 QGILSL----FSPKKGEITSELREEINKKVNKWIEEGKAEIVPGVLFIDEVHMLDIECFSFLNRALESDLAPIVILATNR 312

                         330       340       350
                  ....*....|....*....|....*....|....*
gi 19115695   335 GICTIRGTeDIQAPHGIPTDLLDRLLIVRTLPYSE 369
Cdd:pfam06068 313 GICTIRGT-DIISPHGIPLDLLDRLLIITTEPYTR 346
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
1-449 0e+00

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 515.68  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   1 MVQISEVKGNGRDNRITTHSHIKGLGLKEDGTCESVGGGFIGQEKAREACGIITDLIKSKKFGGKGVLFAGGAGTGKTAL 80
Cdd:COG1224   1 MSEIREIEKVKEFERISAHSHIRGLGLDENGKAKFVADGLVGQVEAREAAGIVVKMIKEGKMAGKGILIVGPPGTGKTAL 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  81 ALAIAQELGPKVPFCPMVGSEVYSSEIKKTEALMENFRRAIGLRVKETKEVYEGEVTEMVPEEAENPLGGYGKTISHVLL 160
Cdd:COG1224  81 AVAIARELGEDTPFVAISGSEIYSAELKKTEFLMQALRKAIGVRVREKRKVYEGVVKEIKIRYARHPYNPYVKVPREATI 160

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 161 GLKTHKGTKQLKLDPSIYESLQREQVSTGDVIYIEANTGAVKRVGRSDAYATE-FDLEAEEYVPMPKGEVHKRKEIVQDV 239
Cdd:COG1224 161 TLATKDEEKTLTVGEEIAQQLVELGIRKGDVIWIDAETGRVSKLGRAKGEGAKtYDIETKRIVEVPSGPVKKEKEIVRTL 240

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 240 TLHDLDIANARPQGGqdIMSMMGQlmkPKKTEITDKLRGEINKVVNKYIEQGIAELIPGVLFIDEVHMLDIECFTYLNQA 319
Cdd:COG1224 241 TLHDLDLYLAAQRAA--FSALFGF---FEEREIPSEVRKQVDELVKKWIEEGKAELVPGVLFIDDAHMLDIEAFSFLTRA 315

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 320 LESTISPIVIFASNRGICTIRGTeDIQAPHGIPTDLLDRLLIVRTLPYSESEIRSILQIRAKVENIILTDECLDKLAQEG 399
Cdd:COG1224 316 MESELAPIIILATNRGITKIRGT-DIESPHGIPLDLLDRLLIIPTRPYTEDEIREIIKIRAEEEDIELSDDALEELTKIG 394

                       410       420       430       440       450
                ....*....|....*....|....*....|....*....|....*....|
gi 19115695 400 SRTSLRYVIQLLTPVSIIASLHGNKEIGVQDIEECNDLFLDARRSAQVVK 449
Cdd:COG1224 395 VERSLRYAVQLLEPAYIIAKRRGRSKVTVEDVEEASKLFADVKESVEYVK 444
TIP49_C pfam17856
TIP49 AAA-lid domain; This family consists of the C-terminal region of several eukaryotic and ...
 375-440 2.37e-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: 103.88  E-value: 2.37e-27
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 19115695   375 ILQIRAKVENIILTDECLDKLAQEGSRTSLRYVIQLLTPVSIIASLHGNKEIGVQDIEECNDLFLD 440
Cdd:pfam17856   1 ILKIRAQEEGVKIDEEALDLLAKIGTETSLRYAIQLLTPASILAKKRGGKEVEVQDVEEAYELFLD 66
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 64-120 1.25e-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: 48.05  E-value: 1.25e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19115695  64 GKGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTEALMEN-FRRA 120
Cdd:cd19481  26 PKGILLYGPPGTGKTLLAKALAGELG--LPLIVVKLSSLLSKYVGESEKNLRKiFERA 81
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 44-120 2.34e-06

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 49.23  E-value: 2.34e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  44 EKAREAcgIITDLIKS---KKFG---GKGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTEALMEN- 116
Cdd:COG1222  88 EEIREA--VELPLKNPelfRKYGiepPKGVLLYGPPGTGKTLLAKAVAGELG--APFIRVRGSELVSKYIGEGARNVREv 163


                ....
gi 19115695 117 FRRA 120
Cdd:COG1222 164 FELA 167
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 42-101 3.02e-06

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: 47.23  E-value: 3.02e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695  42 GQEKAREACGIITDLIKS-KKF---GG---KGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSE 101
Cdd:cd19501   8 GCEEAKEELKEVVEFLKNpEKFtklGAkipKGVLLVGPPGTGKTLLAKAVAGEAG--VPFFSISGSD 72
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 41-131 3.74e-06

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: 46.76  E-value: 3.74e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  41 IGQEKAREAcgiITDLIKSKKfgGKGVLFAGGAGTGKTALALAIAQELG-PKVPFCPMVGSEVYSSEIKKTEALMENFRR 119
Cdd:cd00009   1 VGQEEAIEA---LREALELPP--PKNLLLYGPPGTGKTTLARAIANELFrPGAPFLYLNASDLLEGLVVAELFGHFLVRL 75

                        90
                ....*....|..
gi 19115695 120 AIGLRVKETKEV 131
Cdd:cd00009  76 LFELAEKAKPGV 87
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 67-120 4.20e-06

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: 46.05  E-value: 4.20e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 19115695    67 VLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTEALMEN-FRRA 120
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG--APFIEISGSELVSKYVGESEKRLRElFEAA 53
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 283-433 5.40e-06

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: 48.37  E-value: 5.40e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 283 VVNKYI---EQGIAELI-------PGVLFIDEVHML-----------DIECFTYLNQALESTISP-IVIFASNRgictir 340
Cdd:COG0464 227 LVSKYVgetEKNLREVFdkarglaPCVLFIDEADALagkrgevgdgvGRRVVNTLLTEMEELRSDvVVIAATNR------ 300

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695 341 gtediqaPHGIPTDLLDRL-LIVRTLPYSESEIRSILQIRAKvENIILTDECLDKLAQEGSRTSLRYVIQLLTPVSIIAS 419
Cdd:COG0464 301 -------PDLLDPALLRRFdEIIFFPLPDAEERLEIFRIHLR-KRPLDEDVDLEELAEATEGLSGADIRNVVRRAALQAL 372

                       170
                ....*....|....
gi 19115695 420 LHGNKEIGVQDIEE 433
Cdd:COG0464 373 RLGREPVTTEDLLE 386
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
41-140 6.67e-06

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 47.19  E-value: 6.67e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  41 IGQEKAREACGIITDLIKS----KKFGG---KGVLFAGGAGTGKTALALAIAQELgpKVPFCPMVGSEVYSSEI----KK 109
Cdd:COG1223   5 VGQEEAKKKLKLIIKELRRrenlRKFGLwppRKILFYGPPGTGKTMLAEALAGEL--KLPLLTVRLDSLIGSYLgetaRN 82

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 19115695 110 TEALMENFRR-----------AIGLRVKETKEVyeGEVTEMV 140
Cdd:COG1223  83 LRKLFDFARRapcviffdefdAIAKDRGDQNDV--GEVKRVV 122
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 64-120 8.17e-06

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: 47.98  E-value: 8.17e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19115695  64 GKGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTE-ALMENFRRA 120
Cdd:COG0464 191 PRGLLLYGPPGTGKTLLARALAGELG--LPLIEVDLSDLVSKYVGETEkNLREVFDKA 246
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 65-120 9.00e-06

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: 45.75  E-value: 9.00e-06
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695  65 KGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTE-ALMENFRRA 120
Cdd:cd19503  35 RGVLLHGPPGTGKTLLARAVANEAG--ANFLSISGPSIVSKYLGESEkNLREIFEEA 89
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 40-89 3.48e-05

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: 44.03  E-value: 3.48e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 19115695    40 FIGQEKAREACGIitdLIKSKKFGGKG---VLFAGGAGTGKTALALAIAQELG 89
Cdd:pfam05496   9 YIGQEKVKENLKI---FIEAAKQRGEAldhVLLYGPPGLGKTTLANIIANEMG 58
ftsH CHL00176
cell division protein; Validated
 65-101 4.61e-05

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 45.81  E-value: 4.61e-05
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 19115695   65 KGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSE 101
Cdd:CHL00176 217 KGVLLVGPPGTGKTLLAKAIAGEAE--VPFFSISGSE 251
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
42-101 1.05e-04

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 44.64  E-value: 1.05e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695   42 GQEKAREACGIITDLIKS----KKFGGK---GVLFAGGAGTGKTALALAIAQElgPKVPFCPMVGSE 101
Cdd:PRK10733 156 GCDEAKEEVAELVEYLREpsrfQKLGGKipkGVLMVGPPGTGKTLLAKAIAGE--AKVPFFTISGSD 220
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
40-89 1.15e-04

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 43.97  E-value: 1.15e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 19115695   40 FIGQEKAREACGIitdLIKSKKFGGKG---VLFAGGAGTGKTALALAIAQELG 89
Cdd:PRK00080  27 FIGQEKVKENLKI---FIEAAKKRGEAldhVLLYGPPGLGKTTLANIIANEMG 76
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 65-120 1.74e-04

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: 41.89  E-value: 1.74e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695  65 KGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSEVYSSEIKKTE-ALMENFRRA 120
Cdd:cd19511  28 KGVLLYGPPGCGKTLLAKALASEAG--LNFISVKGPELFSKYVGESErAVREIFQKA 82
PRK04195 PRK04195
replication factor C large subunit; Provisional
 41-89 1.74e-04

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 43.76  E-value: 1.74e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 19115695   41 IGQEKAREAcgiITDLIKS--KKFGGKGVLFAGGAGTGKTALALAIAQELG 89
Cdd:PRK04195  17 VGNEKAKEQ---LREWIESwlKGKPKKALLLYGPPGVGKTSLAHALANDYG 64
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
43-89 2.15e-04

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 43.04  E-value: 2.15e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*..
gi 19115695  43 QEKAREAcgiITDLIKSKKfGGKGVLFAGGAGTGKTALALAIAQELG 89
Cdd:COG0470   1 QEEAWEQ---LLAAAESGR-LPHALLLHGPPGIGKTTLALALARDLL 43
PRK14957 PRK14957
DNA polymerase III subunits gamma and tau; Provisional
 299-411 2.87e-04

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184921 [Multi-domain]  Cd Length: 546  Bit Score: 43.15  E-value: 2.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  299 VLFIDEVHMLDIECFTYLNQALESTiSPIVIFasnrgictIRGTEDIqapHGIPTDLLDRLLIVRTLPYSESEIRSILQI 378
Cdd:PRK14957 122 VYLIDEVHMLSKQSFNALLKTLEEP-PEYVKF--------ILATTDY---HKIPVTILSRCIQLHLKHISQADIKDQLKI 189

                         90       100       110
                 ....*....|....*....|....*....|...
gi 19115695  379 RAKVENIILTDECLDKLAQEgSRTSLRYVIQLL 411
Cdd:PRK14957 190 ILAKENINSDEQSLEYIAYH-AKGSLRDALSLL 221
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 58-112 5.96e-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: 40.57  E-value: 5.96e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 19115695  58 KSKKFG---GKGVLFAGGAGTGKTALALAIAQELgpKVPFCPMVGSEVYSSEIKKTEA 112
Cdd:cd19528  18 KFLKFGmtpSKGVLFYGPPGCGKTLLAKAIANEC--QANFISVKGPELLTMWFGESEA 73
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
42-101 6.38e-04

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 41.95  E-value: 6.38e-04
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695  42 GQEKAREACGIITDLIKS-KKF---GG---KGVLFAGGAGTGKTALALAIAQELGpkVPFCPMVGSE 101
Cdd:COG0465 146 GVDEAKEELQEIVDFLKDpEKFtrlGAkipKGVLLVGPPGTGKTLLAKAVAGEAG--VPFFSISGSD 210
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 65-120 7.43e-04

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: 40.17  E-value: 7.43e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695  65 KGVLFAGGAGTGKTALALAIAQELGPKvpFCPMVGSEVYSSEIKKTE-ALMENFRRA 120
Cdd:cd19529  28 KGILLYGPPGTGKTLLAKAVATESNAN--FISVKGPELLSKWVGESEkAIREIFRKA 82
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 40-89 8.76e-04

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 41.61  E-value: 8.76e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 19115695   40 FIGQEKAREACGIITDLIKSKKFGGkgVLFAGGAGTGKTALALAIAQELG 89
Cdd:PRK13342  14 VVGQEHLLGPGKPLRRMIEAGRLSS--MILWGPPGTGKTTLARIIAGATD 61
PRK14953 PRK14953
DNA polymerase III subunits gamma and tau; Provisional
 299-433 1.11e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237867 [Multi-domain]  Cd Length: 486  Bit Score: 41.35  E-value: 1.11e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  299 VLFIDEVHMLDIECFTYLNQALESTiSPIVIFAsnrgICTirgTEdiqaPHGIPTDLLDRLLIVRTLPYSESEIRSILQI 378
Cdd:PRK14953 122 VYIIDEAHMLTKEAFNALLKTLEEP-PPRTIFI----LCT---TE----YDKIPPTILSRCQRFIFSKPTKEQIKEYLKR 189

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 19115695  379 RAKVENIILTDECLDKLAQEgSRTSLRYVIQLLTPvsiiASLHGNKEIGVQDIEE 433
Cdd:PRK14953 190 ICNEEKIEYEEKALDLLAQA-SEGGMRDAASLLDQ----ASTYGEGKVTIKVVEE 239
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 65-120 1.47e-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: 41.05  E-value: 1.47e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 19115695    65 KGVLFAGGAGTGKTALALAIAQELGPKvpFCPMVGSEVYSSEIKKTE-ALMENFRRA 120
Cdd:TIGR01243 488 KGVLLFGPPGTGKTLLAKAVATESGAN--FIAVRGPEILSKWVGESEkAIREIFRKA 542
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 65-101 1.76e-03

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 40.59  E-value: 1.76e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 19115695   65 KGVLFAGGAGTGKTALALAIAQElgPKVPFCPMVGSE 101
Cdd:PRK03992 166 KGVLLYGPPGTGKTLLAKAVAHE--TNATFIRVVGSE 200
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 40-89 2.29e-03

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 40.06  E-value: 2.29e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
gi 19115695  40 FIGQEKAREACGIitdLIKSKKfgGKG-----VLFAGGAGTGKTALALAIAQELG 89
Cdd:COG2255  30 YIGQEKVKENLKI---FIEAAK--KRGealdhVLLYGPPGLGKTTLAHIIANEMG 79
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 64-91 2.42e-03

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: 38.51  E-value: 2.42e-03
                           10        20
                   ....*....|....*....|....*...
gi 19115695     64 GKGVLFAGGAGTGKTALALAIAQELGPK 91
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPP 29
rfc PRK00440
replication factor C small subunit; Reviewed
 68-88 2.53e-03

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 39.86  E-value: 2.53e-03
                         10        20
                 ....*....|....*....|.
gi 19115695   68 LFAGGAGTGKTALALAIAQEL 88
Cdd:PRK00440  42 LFAGPPGTGKTTAALALAREL 62
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 65-123 2.62e-03

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: 38.54  E-value: 2.62e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  65 KGVLFAGGAGTGKTALALAIAQELgpKVPFCPMVGSEVYSSEIKKTEA-LMENFRRAIGL 123
Cdd:cd19518  35 RGVLLHGPPGCGKTMLANAIAGEL--KVPFLKISATEIVSGVSGESEEkIRELFDQAISN 92
dnaX_nterm TIGR02397
DNA polymerase III, subunit gamma and tau; This model represents the well-conserved first ~ ...
 302-433 3.14e-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: 39.47  E-value: 3.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695   302 IDEVHMLDIECFTYLNQALESTISPIV-IFASnrgictirgTEdiqaPHGIPTDLLDRLLIVRTLPYSESEIRSILQIRA 380
Cdd:TIGR02397 123 IDEVHMLSKSAFNALLKTLEEPPEHVVfILAT---------TE----PHKIPATILSRCQRFDFKRIPLEDIVERLKKIL 189

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 19115695   381 KVENIILTDECLDKLAQ--EGS-RTSLryviqlltpvSII--ASLHGNKEIGVQDIEE 433
Cdd:TIGR02397 190 DKEGIKIEDEALELIARaaDGSlRDAL----------SLLdqLISFGNGKITYEDVNE 237
PRK14962 PRK14962
DNA polymerase III subunits gamma and tau; Provisional
 299-433 3.98e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237869 [Multi-domain]  Cd Length: 472  Bit Score: 39.36  E-value: 3.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  299 VLFIDEVHMLDIECFTYLNQALESTISPIV-IFASNRgictirgtediqaPHGIPTDLLDRLLIVRTLPYSESEIRSILQ 377
Cdd:PRK14962 120 VYIIDEVHMLTKEAFNALLKTLEEPPSHVVfVLATTN-------------LEKVPPTIISRCQVIEFRNISDELIIKRLQ 186

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 19115695  378 IRAKVENIILTDECLDKLAQEGSrTSLRYVIQLLTPVSIIASlhgnKEIGVQDIEE 433
Cdd:PRK14962 187 EVAEAEGIEIDREALSFIAKRAS-GGLRDALTMLEQVWKFSE----GKITLETVHE 237
PRK08451 PRK08451
DNA polymerase III subunits gamma and tau; Validated
 302-411 5.29e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236267 [Multi-domain]  Cd Length: 535  Bit Score: 39.25  E-value: 5.29e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  302 IDEVHMLDIECFTYLNQALESTISpIVIFasnrgictIRGTEDiqaPHGIPTDLLDRLLIVRTLPYSESEIRSILQIRAK 381
Cdd:PRK08451 123 IDEVHMLTKEAFNALLKTLEEPPS-YVKF--------ILATTD---PLKLPATILSRTQHFRFKQIPQNSIISHLKTILE 190

                         90       100       110
                 ....*....|....*....|....*....|
gi 19115695  382 VENIILTDECLDKLAQEGSrTSLRYVIQLL 411
Cdd:PRK08451 191 KEGVSYEPEALEILARSGN-GSLRDTLTLL 219
PRK07133 PRK07133
DNA polymerase III subunits gamma and tau; Validated
 302-433 8.18e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235943 [Multi-domain]  Cd Length: 725  Bit Score: 38.65  E-value: 8.18e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19115695  302 IDEVHMLDIECFTYLNQALESTISPiVIFasnrgictIRGTEDiqaPHGIPTDLLDRLLIVRTLPYSESEIRSILQIRAK 381
Cdd:PRK07133 124 IDEVHMLSKSAFNALLKTLEEPPKH-VIF--------ILATTE---VHKIPLTILSRVQRFNFRRISEDEIVSRLEFILE 191

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 19115695  382 VENIILTDECLDKLAQEGSrTSLRYVIQLLTPVSIiaslHGNKEIGVQDIEE 433
Cdd:PRK07133 192 KENISYEKNALKLIAKLSS-GSLRDALSIAEQVSI----FGNNKITLKNVEE 238
 
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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