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Conserved domains on  [gi|18426904|ref|NP_569079|]
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ATPase WRNIP1 isoform 2 [Homo sapiens]

Protein Classification

replication-associated recombination protein A( domain architecture ID 12219000)

replication-associated recombination protein A is a DNA-dependent ATPase that plays important roles in cellular responses to stalled DNA replication processes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-636 0e+00

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


:

Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 538.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256  13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQ-------------------------VNAALLSRCRVIVLEKLPVEA 359
Cdd:COG2256  90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQdallphvedgtitligattenpsfeVNSALLSRCRVFVLKPLSEED 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 360 MVTILMRAINSLGIHVLDSSRPtdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSrkmfckk 439
Cdd:COG2256 169 LEQLLERALADDERGLGGYKLE-----------------LDDEALEALARLADGDARRALNALELAVLSAPPD------- 224

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 440 sgqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFAS 519
Cdd:COG2256 225 -------GVIEITLELVEEALQRRALRYDKDGDEHYDLISAFIKSIRGSDPDAALYWLARMLEAGEDPRFIARRLVIMAS 297

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 520 EDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRnhQGPLPPVPLHLRNAPTR 599
Cdd:COG2256 298 EDIGLADPQALQIAVAAAQAVERLGMPEGRIALAQAVIYLATAPKSNAAYLAINAALADVR--EGGSLPVPLHLRNAPTK 375

                       410       420       430       440
                ....*....|....*....|....*....|....*....|
gi 18426904 600 LMKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 636
Cdd:COG2256 376 LMKELGYGKGYKY--PHDYPggyVGQQYLPDELKGRRYYE 413
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 3.23e-09

Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.


:

Pssm-ID: 128973 [Multi-domain]  Cd Length: 24  Bit Score: 52.22  E-value: 3.23e-09
                           10        20
                   ....*....|....*....|....
gi 18426904     17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
RAD18 super family cl35000
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 7.19e-04

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


The actual alignment was detected with superfamily member COG5432:

Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.38  E-value: 7.19e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426904  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432 161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
 
Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-636 0e+00

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 538.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256  13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQ-------------------------VNAALLSRCRVIVLEKLPVEA 359
Cdd:COG2256  90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQdallphvedgtitligattenpsfeVNSALLSRCRVFVLKPLSEED 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 360 MVTILMRAINSLGIHVLDSSRPtdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSrkmfckk 439
Cdd:COG2256 169 LEQLLERALADDERGLGGYKLE-----------------LDDEALEALARLADGDARRALNALELAVLSAPPD------- 224

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 440 sgqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFAS 519
Cdd:COG2256 225 -------GVIEITLELVEEALQRRALRYDKDGDEHYDLISAFIKSIRGSDPDAALYWLARMLEAGEDPRFIARRLVIMAS 297

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 520 EDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRnhQGPLPPVPLHLRNAPTR 599
Cdd:COG2256 298 EDIGLADPQALQIAVAAAQAVERLGMPEGRIALAQAVIYLATAPKSNAAYLAINAALADVR--EGGSLPVPLHLRNAPTK 375

                       410       420       430       440
                ....*....|....*....|....*....|....*....|
gi 18426904 600 LMKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 636
Cdd:COG2256 376 LMKELGYGKGYKY--PHDYPggyVGQQYLPDELKGRRYYE 413
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 226-636 0e+00

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 532.35  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  226 PLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTNDV 305
Cdd:PRK13342   1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP---FEALSAVTSGVKDL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  306 RDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQ-------------------------VNAALLSRCRVIVLEKLPVEAM 360
Cdd:PRK13342  78 REVIEEARQRRSA-GRRTILFIDEIHRFNKAQQdallphvedgtitligattenpsfeVNPALLSRAQVFELKPLSEEDI 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  361 VTILMRAINslgihvlDSSRPTDPlshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLarlssrkmfckks 440
Cdd:PRK13342 157 EQLLKRALE-------DKERGLVE--------------LDDEALDALARLANGDARRALNLLELAAL------------- 202

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  441 gqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFASE 520
Cdd:PRK13342 203 ------GVDSITLELLEEALQKRAARYDKDGDEHYDLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  521 DIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRL 600
Cdd:PRK13342 277 DIGLADPNALQVAVAAADAVERIGMPEGRIALAQAVIYLALAPKSNAAYTAINAALADVRE--GGSLPVPLHLRNAPTKL 354

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 18426904  601 MKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 636
Cdd:PRK13342 355 MKELGYGKGYKY--PHDYPngyVGQQYLPDELKGKRYYE 391
MgsA_C pfam12002
MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA ...
 487-636 4.92e-81

MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication. Additionally, MgsA may play a role in chromosomal segregation. This is consistent with a report that MgsA co-localizes with the replisome and affects chromosome segregation. This domain represents the C terminal region of MgsA.


Pssm-ID: 463426 [Multi-domain]  Cd Length: 158  Bit Score: 252.65  E-value: 4.92e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   487 GSDQNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSI 566
Cdd:pfam12002   1 GSDPDAALYWLARMLEAGEDPLFIARRLVIIASEDIGLADPQALVVAVAAAQAVERIGMPEARIPLAQAVIYLALAPKSN 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426904   567 EVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRLMKDLGYGKGYKYNPMYSE-PVDQEYLPEELRGVDFFK 636
Cdd:pfam12002  81 SAYLAIDAALADVRE--GGSLPVPLHLRNAPTKLMKKLGYGKGYKYPHDYPNgYVKQQYLPDELKGRRYYE 149
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 246-344 9.00e-15

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: 71.79  E-value: 9.00e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 246 VGQD---TLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRK 322
Cdd:cd00009   1 VGQEeaiEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA 80

                        90       100
                ....*....|....*....|....*..
gi 18426904 323 -----TILFIDEIHRFNKsqQVNAALL 344
Cdd:cd00009  81 ekakpGVLFIDEIDSLSR--GAQNALL 105
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 263-365 1.03e-11

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: 63.16  E-value: 1.03e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904    263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFF----------------KRKTILF 326
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASgsgelrlrlalalarkLKPDVLI 83

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 18426904    327 IDEIHRFNKSQQvNAALLSRCRVIVLEKLPVEAMVTILM 365
Cdd:smart00382  84 LDEITSLLDAEQ-EALLLLLEELRLLLLLKSEKNLTVIL 121
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 235-336 6.32e-10

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: 60.78  E-value: 6.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   235 TLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKKhSIRfVTLSATNAKTNDVRDVIkqa 312
Cdd:TIGR00635   2 LLAEFIGQEKVKEQlQLFIEAAKMRQEALDhLLLYGPPGLGKTTLAHIIANEMGV-NLK-ITSGPALEKPGDLAAIL--- 76

                          90       100
                  ....*....|....*....|....
gi 18426904   313 qnekSFFKRKTILFIDEIHRFNKS 336
Cdd:TIGR00635  77 ----TNLEEGDVLFIDEIHRLSPA 96
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 3.23e-09

Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.


Pssm-ID: 128973 [Multi-domain]  Cd Length: 24  Bit Score: 52.22  E-value: 3.23e-09
                           10        20
                   ....*....|....*....|....
gi 18426904     17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
zf-WRNIP1_ubi pfam18279
Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the ...
 16-36 4.70e-09

Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ.


Pssm-ID: 375706  Cd Length: 21  Bit Score: 51.75  E-value: 4.70e-09
                          10        20
                  ....*....|....*....|.
gi 18426904    16 HQVQCPVCQQMMPAAHINSHL 36
Cdd:pfam18279   1 HQVQCPVCQQMMPAAHINSHL 21
cell_div_CdvC NF041006
cell division protein CdvC;
264-330 3.70e-04

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 43.18  E-value: 3.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426904  264 LILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATN--------AKTNdVRDVIKQAQNEKSFFKRKTILFIDEI 330
Cdd:NF041006 137 ILLYGPPGCGKTMLAAAVANEIDSE---FIHVDAASimskwlgeAEKN-VAKIFKKAREKSKEEGKPAIIFIDEI 207
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 7.19e-04

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.38  E-value: 7.19e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426904  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432 161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
 
Name Accession Description Interval E-value
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 225-636 0e+00

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 538.87  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 225 KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTND 304
Cdd:COG2256  13 APLAERMRPRTLDEVVGQEHLLGPGKPLRRAIEAGRLSSMILWGPPGTGKTTLARLIANATDAE---FVALSAVTSGVKD 89

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 305 VRDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQ-------------------------VNAALLSRCRVIVLEKLPVEA 359
Cdd:COG2256  90 IREVIEEARERRAY-GRRTILFVDEIHRFNKAQQdallphvedgtitligattenpsfeVNSALLSRCRVFVLKPLSEED 168

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 360 MVTILMRAINSLGIHVLDSSRPtdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSrkmfckk 439
Cdd:COG2256 169 LEQLLERALADDERGLGGYKLE-----------------LDDEALEALARLADGDARRALNALELAVLSAPPD------- 224

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 440 sgqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFAS 519
Cdd:COG2256 225 -------GVIEITLELVEEALQRRALRYDKDGDEHYDLISAFIKSIRGSDPDAALYWLARMLEAGEDPRFIARRLVIMAS 297

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 520 EDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRnhQGPLPPVPLHLRNAPTR 599
Cdd:COG2256 298 EDIGLADPQALQIAVAAAQAVERLGMPEGRIALAQAVIYLATAPKSNAAYLAINAALADVR--EGGSLPVPLHLRNAPTK 375

                       410       420       430       440
                ....*....|....*....|....*....|....*....|
gi 18426904 600 LMKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 636
Cdd:COG2256 376 LMKELGYGKGYKY--PHDYPggyVGQQYLPDELKGRRYYE 413
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 226-636 0e+00

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 532.35  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  226 PLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATNAKTNDV 305
Cdd:PRK13342   1 PLAERMRPKTLDEVVGQEHLLGPGKPLRRMIEAGRLSSMILWGPPGTGKTTLARIIAGATDAP---FEALSAVTSGVKDL 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  306 RDVIKQAQNEKSFfKRKTILFIDEIHRFNKSQQ-------------------------VNAALLSRCRVIVLEKLPVEAM 360
Cdd:PRK13342  78 REVIEEARQRRSA-GRRTILFIDEIHRFNKAQQdallphvedgtitligattenpsfeVNPALLSRAQVFELKPLSEEDI 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  361 VTILMRAINslgihvlDSSRPTDPlshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLAVLarlssrkmfckks 440
Cdd:PRK13342 157 EQLLKRALE-------DKERGLVE--------------LDDEALDALARLANGDARRALNLLELAAL------------- 202

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  441 gqsyspSRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYVARRLVRFASE 520
Cdd:PRK13342 203 ------GVDSITLELLEEALQKRAARYDKDGDEHYDLISALHKSIRGSDPDAALYYLARMLEAGEDPLFIARRLVIIASE 276

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  521 DIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRL 600
Cdd:PRK13342 277 DIGLADPNALQVAVAAADAVERIGMPEGRIALAQAVIYLALAPKSNAAYTAINAALADVRE--GGSLPVPLHLRNAPTKL 354

                        410       420       430
                 ....*....|....*....|....*....|....*....
gi 18426904  601 MKDLGYGKGYKYnpMYSEP---VDQEYLPEELRGVDFFK 636
Cdd:PRK13342 355 MKELGYGKGYKY--PHDYPngyVGQQYLPDELKGKRYYE 391
PRK13341 PRK13341
AAA family ATPase;
220-635 8.63e-110

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 346.66  E-value: 8.63e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  220 QMLQG-KPLADTMRPDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHsirFVTLSAT 298
Cdd:PRK13341  10 QMSQSeAPLADRLRPRTLEEFVGQDHILGEGRLLRRAIKADRVGSLILYGPPGVGKTTLARIIANHTRAH---FSSLNAV 86

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  299 NAKTNDVRDVIKQAQNEKSFFKRKTILFIDEIHRFNKSQQ-------------------------VNAALLSRCRVIVLE 353
Cdd:PRK13341  87 LAGVKDLRAEVDRAKERLERHGKRTILFIDEVHRFNKAQQdallpwvengtitligattenpyfeVNKALVSRSRLFRLK 166

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  354 KLPVEAMVTILMRAINslgihvlDSSRPTDPLshssnsssepAMFIEDKAVDTLAYLSDGDARAGLNGLQLAVlarlssr 433
Cdd:PRK13341 167 SLSDEDLHQLLKRALQ-------DKERGYGDR----------KVDLEPEAEKHLVDVANGDARSLLNALELAV------- 222

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  434 kmfckksgQSYSP---SRVLITENDVKEGLQRSHILYDRAGEEHYNCISALHKSMRGSDQNASLYWLARMLEGGEDPLYV 510
Cdd:PRK13341 223 --------ESTPPdedGLIDITLAIAEESIQQRAVLYDKEGDAHFDTISAFIKSLRGSDPDAALYWLARMVEAGEDPRFI 294

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  511 ARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYSAYNNVKAClrnHQGPLPPVP 590
Cdd:PRK13341 295 FRRMLIAASEDVGLADPQALVVVEACAAAFERVGLPEGLYPLAQAALYLATAPKSNSVLGFFDALKKV---REEQVQDVP 371

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|....*.
gi 18426904  591 LHLRNaPTRLMKDLGYGKGYKYNPMYSEP-VDQEYLPEELRGVDFF 635
Cdd:PRK13341 372 NHLRD-ANRDGKAFGDGVGYRYPHAFRDHwVAQQYLPEALQGEVFW 416
MgsA_C pfam12002
MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA ...
 487-636 4.92e-81

MgsA AAA+ ATPase C terminal; The MgsA protein possesses DNA-dependent ATPase and ssDNA annealing activities. MgsA contributes to the recovery of stalled replication forks and therefore prevents genomic instability caused by aberrant DNA replication. Additionally, MgsA may play a role in chromosomal segregation. This is consistent with a report that MgsA co-localizes with the replisome and affects chromosome segregation. This domain represents the C terminal region of MgsA.


Pssm-ID: 463426 [Multi-domain]  Cd Length: 158  Bit Score: 252.65  E-value: 4.92e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   487 GSDQNASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSI 566
Cdd:pfam12002   1 GSDPDAALYWLARMLEAGEDPLFIARRLVIIASEDIGLADPQALVVAVAAAQAVERIGMPEARIPLAQAVIYLALAPKSN 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426904   567 EVYSAYNNVKACLRNhqGPLPPVPLHLRNAPTRLMKDLGYGKGYKYNPMYSE-PVDQEYLPEELRGVDFFK 636
Cdd:pfam12002  81 SAYLAIDAALADVRE--GGSLPVPLHLRNAPTKLMKKLGYGKGYKYPHDYPNgYVKQQYLPDELKGRRYYE 149
PRK14700 PRK14700
recombination factor protein RarA; Provisional
 334-630 2.04e-34

recombination factor protein RarA; Provisional


Pssm-ID: 173163 [Multi-domain]  Cd Length: 300  Bit Score: 132.83  E-value: 2.04e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  334 NKSQQVNAALLSRCRVIVLEKLPVEAMVTILMRAINS---LGIHVLDssrptdplshssnsssepamfIEDKAVDTLAYL 410
Cdd:PRK14700  18 NPTYYLNDALVSRLFILRLKRLSLVATQKLIEKALSQdevLAKHKFK---------------------IDDGLYNAMHNY 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  411 SDGDARAGLNGLQLAVLARLSSRKMFCKKSgqsyspsrvlITENDVKEGLQRSHilydRAGEEHYNCISALHKSMRGSDQ 490
Cdd:PRK14700  77 NEGDCRKILNLLERMFLISTRGDEIYLNKE----------LFDQAVGETSRDFH----REGKEFYEQLSAFHKSVRGTDP 142

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  491 NASLYWLARMLEGGEDPLYVARRLVRFASEDIGLADPSALTQAVAAYQGCHFIGMPECEVLLAQCVVYFARAPKSIEVYS 570
Cdd:PRK14700 143 DAAIFWLSVMLDNGVDPLVIARRMLCIASEDIGNADPQALRVAMDAWNAYEKLGMPEGRLVLAQAAIYLAVAPKSNACYK 222

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  571 AYNNVKACLRNhQGPLpPVPLHLRNaptrlMKDLGYGKGYKYNPMYsepVDQEYLPEELR 630
Cdd:PRK14700 223 ALAQAQQLVKS-LGNI-DVPQHLKN-----YKDSNYLYPHNYPNSY---VIQQYLPDNII 272
AAA_assoc_2 pfam16193
AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA ...
 399-486 2.24e-29

AAA C-terminal domain; AAA_assoc_2 is found at the C-terminus of a relatively small set of AAA domains in proteins ranging from archaeal to fungi, plants and mammals.


Pssm-ID: 465057  Cd Length: 81  Bit Score: 111.02  E-value: 2.24e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   399 IEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSRKmfckksgqsyspsRVLITENDVKEGLQRSHILYDRAGEEHYNCI 478
Cdd:pfam16193   7 LDDEALEALAELADGDARRALNALELAVLSTPPDDG-------------GIHITLEILEEALQRKALRYDKDGDEHYDLI 73


                  ....*...
gi 18426904   479 SALHKSMR 486
Cdd:pfam16193  74 SAFHKSIR 81
PRK04195 PRK04195
replication factor C large subunit; Provisional
 226-462 7.04e-15

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 77.65  E-value: 7.04e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  226 PLADTMRPDTLQDYFGQSKAVGQdtlLRSLLET--NEIPS--LILWGPPGCGKTTLAHIIAsnskkHSIRF--VTLSATN 299
Cdd:PRK04195   3 PWVEKYRPKTLSDVVGNEKAKEQ---LREWIESwlKGKPKkaLLLYGPPGVGKTSLAHALA-----NDYGWevIELNASD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  300 AKTNDV-RDVIKQAQNEKSFF-KRKTILFIDE---IHR-------------FNKSQQ--VNAA----------LLSRCRV 349
Cdd:PRK04195  75 QRTADViERVAGEAATSGSLFgARRKLILLDEvdgIHGnedrggarailelIKKAKQpiILTAndpydpslreLRNACLM 154

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  350 IVLEKLPVEAMVTILMRAINSLGIhvldssrptdplshssnsssepamFIEDKAVDTLAYLSDGDARAGLNGLQLAVLAR 429
Cdd:PRK04195 155 IEFKRLSTRSIVPVLKRICRKEGI------------------------ECDDEALKEIAERSGGDLRSAINDLQAIAEGY 210

                        250       260       270
                 ....*....|....*....|....*....|...
gi 18426904  430 LSsrkmfckksgqsyspsrvlITENDVKEGLQR 462
Cdd:PRK04195 211 GK-------------------LTLEDVKTLGRR 224
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 246-344 9.00e-15

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: 71.79  E-value: 9.00e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 246 VGQD---TLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRK 322
Cdd:cd00009   1 VGQEeaiEALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA 80

                        90       100
                ....*....|....*....|....*..
gi 18426904 323 -----TILFIDEIHRFNKsqQVNAALL 344
Cdd:cd00009  81 ekakpGVLFIDEIDSLSR--GAQNALL 105
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 264-346 1.93e-14

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: 70.31  E-value: 1.93e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNeksffKRKTILFIDEIHRFNKS 336
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELG---APFIEISGSElvskyvgESEKRLRELFEAAKK-----LAPCVIFIDEIDALAGS 72

                          90
                  ....*....|
gi 18426904   337 QQVNAALLSR 346
Cdd:pfam00004  73 RGSGGDSESR 82
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
230-336 1.49e-13

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 72.09  E-value: 1.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  230 TMRPDTLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIAsNSKKHSIRFVT---------LSA- 297
Cdd:PRK00080  18 SLRPKSLDEFIGQEKVKENlKIFIEAAKKRGEALDhVLLYGPPGLGKTTLANIIA-NEMGVNIRITSgpalekpgdLAAi 96

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 18426904  298 -TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKS 336
Cdd:PRK00080  97 lTNLEEGDV-------------------LFIDEIHRLSPV 117
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 230-336 6.83e-13

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 70.11  E-value: 6.83e-13
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 230 TMRPDTLQDYFGQSKAVGQ-DTLLRSLLETNE-IPSLILWGPPGCGKTTLAHIIAsNSKKHSIRfVT----------LSA 297
Cdd:COG2255  21 SLRPKRLDEYIGQEKVKENlKIFIEAAKKRGEaLDHVLLYGPPGLGKTTLAHIIA-NEMGVNIR-ITsgpaiekpgdLAA 98

                        90       100       110       120
                ....*....|....*....|....*....|....*....|.
gi 18426904 298 --TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKS 336
Cdd:COG2255  99 ilTNLEEGDV-------------------LFIDEIHRLSRV 120
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 231-336 7.46e-13

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: 66.75  E-value: 7.46e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   231 MRPDTLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIAsNSKKHSIRfVT----------LSA- 297
Cdd:pfam05496   1 LRPRTLDEYIGQEKVKENlKIFIEAAKQRGEALDhVLLYGPPGLGKTTLANIIA-NEMGVNIR-ITsgpaierpgdLAAi 78

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 18426904   298 -TNAKTNDVrdvikqaqneksffkrktiLFIDEIHRFNKS 336
Cdd:pfam05496  79 lTNLEPGDV-------------------LFIDEIHRLNRA 99
rfc PRK00440
replication factor C small subunit; Reviewed
 232-425 3.12e-12

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 67.98  E-value: 3.12e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  232 RPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTTLAHIIAsnskkHSI-------RFVTLSATNAKTND 304
Cdd:PRK00440  12 RPRTLDEIVGQEEIVER---LKSYVKEKNMPHLLFAGPPGTGKTTAALALA-----RELygedwreNFLELNASDERGID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  305 V-RDVIKQAQNEKSF----FKrktILFIDE---------------------IHRF----NKSQQVNAALLSRCRVIVLEK 354
Cdd:PRK00440  84 ViRNKIKEFARTAPVggapFK---IIFLDEadnltsdaqqalrrtmemysqNTRFilscNYSSKIIDPIQSRCAVFRFSP 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426904  355 LPVEAMVTILMRAINSLGIHvldssrptdplshssnsssepamfIEDKAVDTLAYLSDGDARAGLNGLQLA 425
Cdd:PRK00440 161 LKKEAVAERLRYIAENEGIE------------------------ITDDALEAIYYVSEGDMRKAINALQAA 207
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 263-365 1.03e-11

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: 63.16  E-value: 1.03e-11
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904    263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFF----------------KRKTILF 326
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASgsgelrlrlalalarkLKPDVLI 83

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 18426904    327 IDEIHRFNKSQQvNAALLSRCRVIVLEKLPVEAMVTILM 365
Cdd:smart00382  84 LDEITSLLDAEQ-EALLLLLEELRLLLLLKSEKNLTVIL 121
DnaX COG2812
DNA polymerase III, gamma/tau subunits [Replication, recombination and repair];
233-419 2.73e-11

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


Pssm-ID: 442061 [Multi-domain]  Cd Length: 340  Bit Score: 65.21  E-value: 2.73e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 233 PDTLQDYFGQSKAVgqdTLLRSLLETNEIP-SLILWGPPGCGKTTLAHIIA-----------------SNSKKHS----- 289
Cdd:COG2812   6 PQTFDDVVGQEHVV---RTLKNALASGRLAhAYLFTGPRGVGKTTLARILAkalncengptgepcgecESCRAIAagshp 82

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 290 -IRFVTLSATNAKTNDVRDVIKQAQNeKSFFKRKTILFIDEIHRFNKSQQvNAAL------------------------- 343
Cdd:COG2812  83 dVIEIDAEASNIGVDDIRELIEKVSY-APVEGRYKVYIIDEAHMLTTEAF-NALLktleeppphvvfilattepqkllpt 160

                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426904 344 -LSRCRVIVLEKLPVEAMVTILMRAINSLGIHvldssrptdplshssnsssepamfIEDKAVDTLAYLSDGDARAGL 419
Cdd:COG2812 161 iLSRCQRFDFRRLPPEEIAEHLAKIAEREGIE------------------------IEPEALALIARAADGSMRDAL 213
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 235-336 6.32e-10

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: 60.78  E-value: 6.32e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   235 TLQDYFGQSKAVGQ-DTLLRSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKKhSIRfVTLSATNAKTNDVRDVIkqa 312
Cdd:TIGR00635   2 LLAEFIGQEKVKEQlQLFIEAAKMRQEALDhLLLYGPPGLGKTTLAHIIANEMGV-NLK-ITSGPALEKPGDLAAIL--- 76

                          90       100
                  ....*....|....*....|....
gi 18426904   313 qnekSFFKRKTILFIDEIHRFNKS 336
Cdd:TIGR00635  77 ----TNLEEGDVLFIDEIHRLSPA 96
PLN03025 PLN03025
replication factor C subunit; Provisional
 226-423 8.70e-10

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 60.51  E-value: 8.70e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  226 PLADTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTT----LAHIIASNSKKHSIrfVTLSATNAK 301
Cdd:PLN03025   2 PWVEKYRPTKLDDIVGNEDAVSR---LQVIARDGNMPNLILSGPPGTGKTTsilaLAHELLGPNYKEAV--LELNASDDR 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  302 TND-VRDVIKQ-AQNEKSFFK-RKTILFID-----------------EIH----RF----NKSQQVNAALLSRCRVIVLE 353
Cdd:PLN03025  77 GIDvVRNKIKMfAQKKVTLPPgRHKIVILDeadsmtsgaqqalrrtmEIYsnttRFalacNTSSKIIEPIQSRCAIVRFS 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  354 KLPVEAMVTILMRAINSLGIhvldssrPTDPlshssnsssepamfiedKAVDTLAYLSDGDARAGLNGLQ 423
Cdd:PLN03025 157 RLSDQEILGRLMKVVEAEKV-------PYVP-----------------EGLEAIIFTADGDMRQALNNLQ 202
HLD_clamp_RarA cd18139
helical lid domain of recombination factor protein RarA; Recombination factor RarA ...
 355-461 2.66e-09

helical lid domain of recombination factor protein RarA; Recombination factor RarA (Replication associated recombination gene/protein A, also known as MgsA (Maintenance of genome stability A) or Mgs1 in yeast and WRNIP1 in mammals) is a member of the clamp-loader clade of the AAA+ superfamily. It functions as a tetramer. RarA co-localize with the replication fork throughout the cell cycle and may play a role in the rescue of stalled replication forks.


Pssm-ID: 350841 [Multi-domain]  Cd Length: 75  Bit Score: 53.79  E-value: 2.66e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 355 LPVEAMVTILMRAINSLGIHvldssrptdplshssnssSEPAMFIEDKAVDTLAYLSDGDARAGLNGLQLAVLARLSSRk 434
Cdd:cd18139   1 LSEEDLEKLLKRALEDKERG------------------GDRKVTIDDEALELLAEAADGDARSALNLLELAVLSAEEDG- 61

                        90       100
                ....*....|....*....|....*..
gi 18426904 435 mfckksgqsyspsRVLITENDVKEGLQ 461
Cdd:cd18139  62 -------------GIVITLEDLEEVLQ 75
ZnF_Rad18 smart00734
Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative ...
 17-40 3.23e-09

Rad18-like CCHC zinc finger; Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.


Pssm-ID: 128973 [Multi-domain]  Cd Length: 24  Bit Score: 52.22  E-value: 3.23e-09
                           10        20
                   ....*....|....*....|....
gi 18426904     17 QVQCPVCQQMMPAAHINSHLDRCL 40
Cdd:smart00734   1 LVQCPVCFREVPENLINSHLDSCL 24
44 PHA02544
clamp loader, small subunit; Provisional
 250-350 4.50e-09

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 58.46  E-value: 4.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  250 TLLRSLLETNEIPSLILWGP-PGCGKTTLAHIIASNSkkhSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKRKTILFID 328
Cdd:PHA02544  31 ETFKSIVKKGRIPNMLLHSPsPGTGKTTVAKALCNEV---GAEVLFVNGSDCRIDFVRNRLTRFASTVSLTGGGKVIIID 107

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 18426904  329 EIHRF--------------------------NKSQQVNAALLSRCRVI 350
Cdd:PHA02544 108 EFDRLgladaqrhlrsfmeayskncsfiitaNNKNGIIEPLRSRCRVI 155
zf-WRNIP1_ubi pfam18279
Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the ...
 16-36 4.70e-09

Werner helicase-interacting protein 1 ubiquitin-binding domain; This domain is found in the Werner helicase-interacting protein 1 present in Homo sapiens. The domain is a zinc finger responsible and has a zinc-coordinating B-B-A fold. WRNIP1 UBZ binds ubiquitin in a similar manner to Rad18 UBZ.


Pssm-ID: 375706  Cd Length: 21  Bit Score: 51.75  E-value: 4.70e-09
                          10        20
                  ....*....|....*....|.
gi 18426904    16 HQVQCPVCQQMMPAAHINSHL 36
Cdd:pfam18279   1 HQVQCPVCQQMMPAAHINSHL 21
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 229-428 1.42e-08

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 56.92  E-value: 1.42e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  229 DTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGKTT----LAHIIASNSKKHSI-------------- 290
Cdd:PRK12402   7 EKYRPALLEDILGQDEVVER---LSRAVDSPNLPHLLVQGPPGSGKTAavraLARELYGDPWENNFtefnvadffdqgkk 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  291 ------RFVTLSATNAKTN-DVRDVIKQAQNEKSFFKR-----KTILFiDEIHRFNKSQQvnAAL-------LSRCRVIV 351
Cdd:PRK12402  84 ylvedpRFAHFLGTDKRIRsSKIDNFKHVLKEYASYRPlsadyKTILL-DNAEALREDAQ--QALrrimeqySRTCRFII 160

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18426904  352 LEKLPveamvTILMRAINSLGIHVLDSSRPTDPLSHSSNSSSEP-AMFIEDKAVDTLAYLSDGDARAGLNGLQLAVLA 428
Cdd:PRK12402 161 ATRQP-----SKLIPPIRSRCLPLFFRAPTDDELVDVLESIAEAeGVDYDDDGLELIAYYAGGDLRKAILTLQTAALA 233
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
242-429 3.11e-08

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 55.37  E-value: 3.11e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 242 QSKAVGQdtlLRSLLETNEIP-SLILWGPPGCGKTTLAHIIA------------SNSKKHSIR--------FVTLSATNA 300
Cdd:COG0470   1 QEEAWEQ---LLAAAESGRLPhALLLHGPPGIGKTTLALALArdllcenpeggkACGQCHSRLmaagnhpdLLELNPEEK 77

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 301 KT----NDVRDVIKQAQNeKSFFKRKTILFIDEIHRFNksqqVNAA-----------------------------LLSRC 347
Cdd:COG0470  78 SDqigiDQIRELGEFLSL-TPLEGGRKVVIIDEADAMN----EAAAnallktleeppkntpfiliandpsrllptIRSRC 152

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 348 RVIVLEKLPVEAMVTILMRAinslgihvldssrptdplshssnsssepamFIEDKAVDTLAYLSDGDARAGLNGLQLAVL 427
Cdd:COG0470 153 QVIRFRPPSEEEALAWLREE------------------------------GVDEDALEAILRLAGGDPRAAINLLQALAG 202


                ..
gi 18426904 428 AR 429
Cdd:COG0470 203 RK 204
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 232-330 3.35e-08

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 55.78  E-value: 3.35e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 232 RPDTLQDYFGqskavGQDTLLRSLLETNEIP----------------SLILWGPPGCGKTTLAHIIASNSKKHSIR---- 291
Cdd:COG1222  72 SPDVTFDDIG-----GLDEQIEEIREAVELPlknpelfrkygieppkGVLLYGPPGTGKTLLAKAVAGELGAPFIRvrgs 146

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 18426904 292 -----FVTLSATNaktndVRDVIKQAQNeksffKRKTILFIDEI 330
Cdd:COG1222 147 elvskYIGEGARN-----VREVFELARE-----KAPSIIFIDEI 180
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 264-330 4.04e-08

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: 55.69  E-value: 4.04e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426904 264 LILWGPPGCGKTTLAHIIASNSKKHSIRfVTLSA--------TNAKtndVRDVIKQAQNEKsffkrKTILFIDEI 330
Cdd:COG0464 194 LLLYGPPGTGKTLLARALAGELGLPLIE-VDLSDlvskyvgeTEKN---LREVFDKARGLA-----PCVLFIDEA 259
PRK08691 PRK08691
DNA polymerase III subunits gamma and tau; Validated
 227-374 1.33e-07

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236333 [Multi-domain]  Cd Length: 709  Bit Score: 54.71  E-value: 1.33e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  227 LADTMRPDTLQDYFGQSKAVgqDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIA------------------SNSKKH 288
Cdd:PRK08691   6 LARKWRPKTFADLVGQEHVV--KALQNALDEGRLHHAYLLTGTRGVGKTTIARILAkslncenaqhgepcgvcqSCTQID 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  289 SIRFVTL----SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKS-------------------------QQV 339
Cdd:PRK08691  84 AGRYVDLleidAASNTGIDNIREVLENAQYAPTAGKYK-VYIIDEVHMLSKSafnamlktleeppehvkfilattdpHKV 162

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 18426904  340 NAALLSRCRVIVLEKLPVEAMVTILMRAINSLGIH 374
Cdd:PRK08691 163 PVTVLSRCLQFVLRNMTAQQVADHLAHVLDSEKIA 197
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
249-335 2.47e-07

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 53.41  E-value: 2.47e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 249 DTLLRSLLETNEIpsLILWGPPGCGKTTLA-HIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQAqneKSFFKRKTILFI 327
Cdd:COG1373  10 LDKLLKLLDNRKA--VVITGPRQVGKTTLLkQLAKELENILYINLDDPRLRALAEEDPDDLLEAL---KELYPGKTYLFL 84


                ....*...
gi 18426904 328 DEIHRFNK 335
Cdd:COG1373  85 DEIQRVPE 92
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 262-331 5.30e-07

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: 49.59  E-value: 5.30e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426904 262 PSLILWGPPGCGKTTLAHIIASNSKKHSIRfVTLSATNAKTND-----VRDVIKQAQNeksffKRKTILFIDEIH 331
Cdd:cd19481  27 KGILLYGPPGTGKTLLAKALAGELGLPLIV-VKLSSLLSKYVGeseknLRKIFERARR-----LAPCILFIDEID 95
PRK14970 PRK14970
DNA polymerase III subunits gamma and tau; Provisional
 228-440 1.40e-06

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 184934 [Multi-domain]  Cd Length: 367  Bit Score: 51.03  E-value: 1.40e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  228 ADTMRPDTLQDYFGQSKAVgqDTLLRSLlETNEIPSLILW-GPPGCGKTTLAHIIASNSKKHSIR----------FVTLS 296
Cdd:PRK14970   8 ARKYRPQTFDDVVGQSHIT--NTLLNAI-ENNHLAQALLFcGPRGVGKTTCARILARKINQPGYDdpnedfsfniFELDA 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  297 ATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNkSQQVNAALLSrcrvivLEKLPVEAMV------------TIL 364
Cdd:PRK14970  85 ASNNSVDDIRNLIDQVRIPPQTGKYK-IYIIDEVHMLS-SAAFNAFLKT------LEEPPAHAIFilattekhkiipTIL 156

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 18426904  365 MRAinslgiHVLDSSRPT--DPLSHSSNSSSEPAMFIEDKAVDTLAYLSDGDARAGlnglqLAVLARLSSrkmFCKKS 440
Cdd:PRK14970 157 SRC------QIFDFKRITikDIKEHLAGIAVKEGIKFEDDALHIIAQKADGALRDA-----LSIFDRVVT---FCGKN 220
PRK05896 PRK05896
DNA polymerase III subunits gamma and tau; Validated
 232-423 1.86e-06

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 235638 [Multi-domain]  Cd Length: 605  Bit Score: 51.00  E-value: 1.86e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  232 RPDTLQDYFGQSKAvgQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIAS-----NSKK----------------HSI 290
Cdd:PRK05896  11 RPHNFKQIIGQELI--KKILVNAILNNKLTHAYIFSGPRGIGKTSIAKIFAKainclNPKDgdccnscsvcesintnQSV 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  291 RFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFnkSQQVNAALLSRCR-----VIVL------EKLPve 358
Cdd:PRK05896  89 DIVELdAASNNGVDEIRNIIDNINYLPTTFKYK-VYIIDEAHML--STSAWNALLKTLEeppkhVVFIfattefQKIP-- 163

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426904  359 amVTILMRAiNSLGIHVLDSSRPTDPLshsSNSSSEPAMFIEDKAVDTLAYLSDGDARAGLNGLQ 423
Cdd:PRK05896 164 --LTIISRC-QRYNFKKLNNSELQELL---KSIAKKEKIKIEDNAIDKIADLADGSLRDGLSILD 222
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
264-331 8.76e-06

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 47.57  E-value: 8.76e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426904 264 LILWGPPGCGKTTLAHIIASNSKKHSI---------RFVTLSATNaktndVRDVIKQAQNeksffkRKTILFIDEIH 331
Cdd:COG1223  38 ILFYGPPGTGKTMLAEALAGELKLPLLtvrldsligSYLGETARN-----LRKLFDFARR------APCVIFFDEFD 103
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 264-330 1.49e-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: 45.86  E-value: 1.49e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18426904 264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:cd19518  37 VLLHGPPGCGKTMLANAIAGELK---VPFLKISATEivsgvsgESEEKIRELFDQAISNAP-----CIVFIDEI 102
DnaA COG0593
Chromosomal replication initiation ATPase DnaA [Replication, recombination and repair];
264-351 2.64e-05

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


Pssm-ID: 440358 [Multi-domain]  Cd Length: 303  Bit Score: 46.72  E-value: 2.64e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 264 LILWGPPGCGKTTLAHIIA----SNSKKHSIRFVTLSA-TNAKTNDVRDviKQAQNEKSFFKRKTILFIDEIHRF---NK 335
Cdd:COG0593  37 LFLYGGVGLGKTHLLHAIGnealENNPGARVVYLTAEEfTNDFINAIRN--NTIEEFKEKYRSVDVLLIDDIQFLagkEA 114

                        90       100
                ....*....|....*....|.
gi 18426904 336 SQQ-----VNAALLSRCRVIV 351
Cdd:COG0593 115 TQEeffhtFNALREAGKQIVL 135
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 264-329 3.94e-05

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: 44.34  E-value: 3.94e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18426904 264 LILWGPPGCGKTTLAHIIASNSkkhSIRFVTLSA-------TNAKTNDVRDVIKQAQNEKSffkrkTILFIDE 329
Cdd:cd19526  30 ILLYGPPGCGKTLLASAIASEC---GLNFISVKGpellnkyIGASEQNVRDLFSRAQSAKP-----CILFFDE 94
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 265-330 4.96e-05

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: 44.20  E-value: 4.96e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18426904 265 ILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATNAKT-------NDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:cd19511  31 LLYGPPGCGKTLLAKALASEAG---LNFISVKGPELFSkyvgeseRAVREIFQKARQAAP-----CIIFFDEI 95
AAA_14 pfam13173
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 264-332 5.54e-05

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


Pssm-ID: 463799 [Multi-domain]  Cd Length: 128  Bit Score: 43.35  E-value: 5.54e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 18426904   264 LILWGPPGCGKTTLA-HIIASNSKKHSIRFVTL---SATNAKTNDVRDVIkqaqnEKSFFKRKTILFIDEIHR 332
Cdd:pfam13173   5 LVITGPRQVGKTTLLlQLIKELLPPENILYINLddpRLLKLADFELLELF-----LELLYPGKTYLFLDEIQR 72
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 266-330 9.81e-05

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 45.21  E-value: 9.81e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426904  266 LWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATN------AKTndVRDVIKQAQnEKSffkrKTILFIDEI 330
Cdd:PRK03992 170 LYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQkfigegARL--VRELFELAR-EKA----PSIIFIDEI 233
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 264-338 1.20e-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: 43.18  E-value: 1.20e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426904 264 LILWGPPGCGKTTLAHIIAsnsKKHSIRFVTLSATNAKTNDVRDVIKQAQNEKSFFKR--KTILFIDEIHRFNKSQQ 338
Cdd:cd19520  38 VLLYGPPGCGKTMLAKATA---KEAGARFINLQVSSLTDKWYGESQKLVAAVFSLASKlqPSIIFIDEIDSFLRQRS 111
ftsH CHL00176
cell division protein; Validated
 253-330 1.28e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 45.04  E-value: 1.28e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  253 RSLLETNEIPS-LILWGPPGCGKTTLAHIIASNSKK--HSI-------RFVTLSATNaktndVRDVIKQAQNeksffKRK 322
Cdd:CHL00176 207 RFTAVGAKIPKgVLLVGPPGTGKTLLAKAIAGEAEVpfFSIsgsefveMFVGVGAAR-----VRDLFKKAKE-----NSP 276


                 ....*...
gi 18426904  323 TILFIDEI 330
Cdd:CHL00176 277 CIVFIDEI 284
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 265-330 2.78e-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: 41.94  E-value: 2.78e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 265 ILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTND----VRDVIKQAQNeksffKRKTILFIDEI 330
Cdd:cd19502  41 LLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKYIGEgarlVRELFEMARE-----KAPSIIFIDEI 105
cell_div_CdvC NF041006
cell division protein CdvC;
264-330 3.70e-04

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 43.18  E-value: 3.70e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426904  264 LILWGPPGCGKTTLAHIIASNSKKHsirFVTLSATN--------AKTNdVRDVIKQAQNEKSFFKRKTILFIDEI 330
Cdd:NF041006 137 ILLYGPPGCGKTMLAAAVANEIDSE---FIHVDAASimskwlgeAEKN-VAKIFKKAREKSKEEGKPAIIFIDEI 207
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 263-330 4.06e-04

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: 41.57  E-value: 4.06e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 18426904 263 SLILWGPPGCGKTTLAHIIASNSkkhSIRFVTLSATN-------AKTNDVRDVIKQAQneksfFKRKTILFIDEI 330
Cdd:cd19509  34 GILLYGPPGTGKTLLARAVASES---GSTFFSISASSlvskwvgESEKIVRALFALAR-----ELQPSIIFIDEI 100
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 264-330 4.28e-04

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: 41.51  E-value: 4.28e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 18426904 264 LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSA----------TNAKtndVRDVIKQAQNEKsffkrKTILFIDEI 330
Cdd:cd19503  37 VLLHGPPGTGKTLLARAVANEAG---ANFLSISGpsivskylgeSEKN---LREIFEEARSHA-----PSIIFIDEI 102
PRK14971 PRK14971
DNA polymerase III subunit gamma/tau;
232-361 4.44e-04

DNA polymerase III subunit gamma/tau;


Pssm-ID: 237874 [Multi-domain]  Cd Length: 614  Bit Score: 43.23  E-value: 4.44e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  232 RPDTLQDYFGQSKAVgqdTLLRSLLETNEIPSLILW-GPPGCGKTTLAHIIA----------------------SNSKKH 288
Cdd:PRK14971  12 RPSTFESVVGQEALT---TTLKNAIATNKLAHAYLFcGPRGVGKTTCARIFAktincqnltadgeacnecescvAFNEQR 88

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  289 SIRFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNkSQQVNAAL------------------------ 343
Cdd:PRK14971  89 SYNIHELdAASNNSVDDIRNLIEQVRIPPQIGKYK-IYIIDEVHMLS-QAAFNAFLktleeppsyaifilattekhkilp 166

                        170       180
                 ....*....|....*....|
gi 18426904  344 --LSRCRVIVLEKLPVEAMV 361
Cdd:PRK14971 167 tiLSRCQIFDFNRIQVADIV 186
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 260-330 4.70e-04

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: 41.45  E-value: 4.70e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 260 EIP-SLILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATN---------AKTndVRDVIKQAqneksffKRKT--ILFI 327
Cdd:cd19501  35 KIPkGVLLVGPPGTGKTLLAKAVAGEAG---VPFFSISGSDfvemfvgvgASR--VRDLFEQA-------KKNApcIVFI 102


                ...
gi 18426904 328 DEI 330
Cdd:cd19501 103 DEI 105
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 216-290 4.91e-04

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: 41.32  E-value: 4.91e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 18426904 216 EEIRQMLQGKPLADTMRPDtlqdyfgQSKAVGQDTllrslletneiPS-LILWGPPGCGKTTLAHIIASNSKKHSI 290
Cdd:cd19530   2 DHVREELTMSILRPIKRPD-------IYKALGIDL-----------PTgVLLYGPPGCGKTLLAKAVANESGANFI 59
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
260-330 6.42e-04

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 42.71  E-value: 6.42e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 18426904  260 EIPSLILW-GPPGCGKTTLAHIIASNSKkhsIRFVTLSATN-------AKTNDVRDVIKQAQNEKSffkrkTILFIDEI 330
Cdd:PRK10733 183 KIPKGVLMvGPPGTGKTLLAKAIAGEAK---VPFFTISGSDfvemfvgVGASRVRDMFEQAKKAAP-----CIIFIDEI 253
RAD18 COG5432
RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];
18-83 7.19e-04

RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms];


Pssm-ID: 227719 [Multi-domain]  Cd Length: 391  Bit Score: 42.38  E-value: 7.19e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 18426904  18 VQCPVCQQMMPAAHINSHLDRCLLLH--PAGHAEP---AAGSH-RAGERAKGPSPPGAKRRRLSESSALKQP 83
Cdd:COG5432 161 VHCPACSNLVPHNQINQHLDSCLNSPssPSSSSSPyknKDNSKsNSLLSFKTDDDSITKRRLRSFNSADELP 232
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 264-342 7.32e-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: 7.32e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 264 LILWGPPGCGKTTLAHIIASNSKKHSI-----RFVTLSATNAKTNdVRDVIKQAQNEKSffkrkTILFIDEIHRFNKSQQ 338
Cdd:cd19528  30 VLFYGPPGCGKTLLAKAIANECQANFIsvkgpELLTMWFGESEAN-VRDIFDKARAAAP-----CVLFFDELDSIAKARG 103


                ....
gi 18426904 339 VNAA 342
Cdd:cd19528 104 GNIG 107
DEXDc smart00487
DEAD-like helicases superfamily;
248-351 8.27e-04

DEAD-like helicases superfamily;


Pssm-ID: 214692 [Multi-domain]  Cd Length: 201  Bit Score: 40.94  E-value: 8.27e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904    248 QDTLLRSLLETNEipSLILWGPPGCGKTT--LAHIIASNSKKHSIRFVTLSATNAKTNDVRDVIKQaqneksFFKRKTIL 325
Cdd:smart00487  13 QKEAIEALLSGLR--DVILAAPTGSGKTLaaLLPALEALKRGKGGRVLVLVPTRELAEQWAEELKK------LGPSLGLK 84

                           90       100
                   ....*....|....*....|....*.
gi 18426904    326 FIDEIHRFNKSQQVNAALLSRCRVIV 351
Cdd:smart00487  85 VVGLYGGDSKREQLRKLESGKTDILV 110
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 263-345 9.42e-04

AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 39.97  E-value: 9.42e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   263 SLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSAtNAKTNDVRDVIKQAQNEKSF--------FKRKTILFIDEIHRFN 334
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNRPVFYVQLTR-DTTEEDLFGRRNIDPGGASWvdgplvraAREGEIAVLDEINRAN 79

                          90
                  ....*....|.
gi 18426904   335 KSqqVNAALLS 345
Cdd:pfam07728  80 PD--VLNSLLS 88
PRK08451 PRK08451
DNA polymerase III subunits gamma and tau; Validated
 227-343 1.31e-03

DNA polymerase III subunits gamma and tau; Validated


Pssm-ID: 236267 [Multi-domain]  Cd Length: 535  Bit Score: 41.56  E-value: 1.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  227 LADTMRPDTLqdyfgqSKAVGQDTLLRSL---LETNEIPSLILW-GPPGCGKTTLAHI---------------------- 280
Cdd:PRK08451   4 LALKYRPKHF------DELIGQESVSKTLslaLDNNRLAHAYLFsGLRGSGKTSSARIfaralvceqgpsstpcdtciqc 77

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 18426904  281 IASNSKKHsIRFVTL-SATNAKTNDVRDVIKQAQNEKSFFKRKtILFIDEIHRFNKsQQVNAAL 343
Cdd:PRK08451  78 QSALENRH-IDIIEMdAASNRGIDDIRELIEQTKYKPSMARFK-IFIIDEVHMLTK-EAFNALL 138
Rad17 pfam03215
Rad17 P-loop domain;
223-356 1.64e-03

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 39.94  E-value: 1.64e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   223 QGKPLADTMRPDTLQDYFGQSKAVG--QDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIasnSKKHSIRFVT-LSATN 299
Cdd:pfam03215   5 GGEQWYEKYKPNCLEQLAVHKRKIKdvQEWLDAMFLENAKHRILLISGPSGCGKSTVIKEL---SKELGPKYREwSNPTS 81

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426904   300 AKT--NDVRDVIKQAQNEKSFFKRKTIL--FIDEIHRFNKSQQVNAALLSRCRVIVLEKLP 356
Cdd:pfam03215  82 FRSppNQVTDFRGDCIVNSRFLSQMESFseFELKGARYLVMQKRGKNAQGNKKLILIEDLP 142
AAA_7 pfam12775
P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 ...
 251-331 1.68e-03

P-loop containing dynein motor region; This domain is found in human cytoplasmic dynein-2 proteins. Cytoplasmic dynein-2 (dynein-2) performs intraflagellar transport and is associated with human skeletal ciliopathies. Dyneins share a conserved motor domain that couples cycles of ATP hydrolysis with conformational changes to produce movement. Structural analysis reveal that the motor's ring consists of six AAA+ domains (ATPases associated with various cellular activities (AAA1-AAA6). This is the third nucleotide binding sites in the dynein motor. However, AAA3 has lost the catalytic residues necessary for ATP hydrolysis (the Walker B glutamate, the arginine finger, sensor-I and sensor-II motifs).


Pssm-ID: 463698 [Multi-domain]  Cd Length: 179  Bit Score: 39.68  E-value: 1.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   251 LLRSLLeTNEIPSLiLWGPPGCGKTTLAH--IIASNSKKHSIRFVTLSA-TNAktNDVRDVIkqaqnEKSFFKR------ 321
Cdd:pfam12775  23 LLDLLL-KNGKPVL-LVGPTGTGKTVIIQnlLRKLDKEKYLPLFINFSAqTTS--NQTQDII-----ESKLEKRrkgvyg 93

                          90
                  ....*....|....*
gi 18426904   322 -----KTILFIDEIH 331
Cdd:pfam12775  94 ppggkKLVVFIDDLN 108
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 264-330 1.72e-03

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 41.29  E-value: 1.72e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18426904  264 LILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSATNAKTND----VRDVIKQAQnEKSffkrKTILFIDEI 330
Cdd:PTZ00454 182 VLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLGEgprmVRDVFRLAR-ENA----PSIIFIDEV 247
Bac_DnaA pfam00308
Bacterial dnaA protein;
264-340 1.77e-03

Bacterial dnaA protein;


Pssm-ID: 278724 [Multi-domain]  Cd Length: 219  Bit Score: 40.39  E-value: 1.77e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   264 LILWGPPGCGKTTLAHIIASN--SKKHSIRFVTLSATNAkTNDVRDVIKqaQNEKSFFKRK----TILFIDEIHRFNKSQ 337
Cdd:pfam00308  37 LFIYGGVGLGKTHLLHAIGNYalQNAPNLRVVYLTAEEF-LNDFVDAIR--DNKTNQFKEKyrnvDVLLIDDIQFLAGKE 113


                  ...
gi 18426904   338 QVN 340
Cdd:pfam00308 114 GTQ 116
DEXXQc_Upf1-like cd17934
DEXXQ-box helicase domain of Upf1-like helicase; The Upf1-like helicase family includes UPF1, ...
 264-352 1.88e-03

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


Pssm-ID: 438708 [Multi-domain]  Cd Length: 121  Bit Score: 38.76  E-value: 1.88e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 264 LILWGPPGCGKT-TLAHIIASNSKKHSIRFVTLSATnakTNDVRDVIkqaqneksffkrkTILFIDEIhrfnkSQQVNAA 342
Cdd:cd17934   2 SLIQGPPGTGKTtTIAAIVLQLLKGLRGKRVLVTAQ---SNVAVDNV-------------DVVIIDEA-----SQITEPE 60

                        90
                ....*....|...
gi 18426904 343 LL---SRCRVIVL 352
Cdd:cd17934  61 LLialIRAKKVVL 73
IstB_IS21 pfam01695
IstB-like ATP binding protein; This protein contains an ATP/GTP binding P-loop motif. It is ...
 235-330 2.05e-03

IstB-like ATP binding protein; This protein contains an ATP/GTP binding P-loop motif. It is found associated with IS21 family insertion sequences. The function of this protein is unknown, but it may perform a transposase function.


Pssm-ID: 426385 [Multi-domain]  Cd Length: 238  Bit Score: 40.12  E-value: 2.05e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   235 TLQDY-FGQSKAVGQDTL--LRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKH--SIRFVTlsatnakTNDVRDVI 309
Cdd:pfam01695  63 TLEDFdFTFAPGLDQRIVaeLASLSFIDRAQNVVLLGPPGVGKTHLAIALGVEACRAgySVRFTS-------AADLVNQL 135

                          90       100
                  ....*....|....*....|....*..
gi 18426904   310 KQAQNEKSF------FKRKTILFIDEI 330
Cdd:pfam01695 136 KRAHGDGKLtrklqqLLKPDVLILDEW 162
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 246-330 2.16e-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: 2.16e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 246 VGQDTLLRSLLETNEIPS---------------LILWGPPGCGKTTLAHIIASNSKkhsIRFVTLSATNAKTNDVRDVIK 310
Cdd:cd19524   3 AGQDLAKQALQEMVILPSlrpelftglrapargLLLFGPPGNGKTMLAKAVAAESN---ATFFNISAASLTSKYVGEGEK 79

                        90       100
                ....*....|....*....|....*
gi 18426904 311 QAqneKSFFK-----RKTILFIDEI 330
Cdd:cd19524  80 LV---RALFAvarelQPSIIFIDEV 101
RecD COG0507
ATPase/5#-3# helicase helicase subunit RecD of the DNA repair enzyme RecBCD (exonuclease V) ...
 205-376 2.42e-03

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


Pssm-ID: 440273 [Multi-domain]  Cd Length: 514  Bit Score: 40.73  E-value: 2.42e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 205 GGRPHPRALAAEE-----IRQmLQGKPLADTMRPDTLQDYFGQSKAV---GQDTLLRSLLETNEIpsLILWGPPGCGKTT 276
Cdd:COG0507  79 GRRYLTRLLEAEQrlarrLRR-LARPALDEADVEAALAALEPRAGITlsdEQREAVALALTTRRV--SVLTGGAGTGKTT 155

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 277 LAHIIASNSKKHSIRFVTLSATNaktndvrdviKQAQN--EKSFFKRKTilfideIHRF------NKSQQVNA-ALLSRC 347
Cdd:COG0507 156 TLRALLAALEALGLRVALAAPTG----------KAAKRlsESTGIEART------IHRLlglrpdSGRFRHNRdNPLTPA 219

                       170       180       190
                ....*....|....*....|....*....|....*
gi 18426904 348 RVIVLEklpvEA-MVTI-----LMRAINSLGIHVL 376
Cdd:COG0507 220 DLLVVD----EAsMVDTrlmaaLLEALPRAGARLI 250
PRK04132 PRK04132
replication factor C small subunit; Provisional
 225-274 2.66e-03

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 40.98  E-value: 2.66e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 18426904  225 KPLADTMRPDTLQDYFGQSKAVGQdtlLRSLLETNEIPSLILWGPPGCGK 274
Cdd:PRK04132   7 KPWVEKYRPQRLDDIVGQEHIVKR---LKHYVKTGSMPHLLFAGPPGVGK 53
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 264-283 3.54e-03

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 37.20  E-value: 3.54e-03
                          10        20
                  ....*....|....*....|
gi 18426904   264 LILWGPPGCGKTTLAHIIAS 283
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLAR 20
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 265-365 3.55e-03

RecA-like_NTPases; RecA-like NTPases. This superfamily 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: 410865 [Multi-domain]  Cd Length: 119  Bit Score: 37.87  E-value: 3.55e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904 265 ILW-GPPGCGKTTLAHIIASNSKKHSIRFVTLSAtnaktndVRDVIKQAQNEKsFFKRKTILFIDEIHRFNKSQQVNAAL 343
Cdd:cd01120   1 ILItGPPGSGKTTLLLQFAEQALLSDEPVIFISF-------LDTILEAIEDLI-EEKKLDIIIIDSLSSLARASQGDRSS 72

                        90       100
                ....*....|....*....|..
gi 18426904 344 LSRCRVIVLEKLPVEAMVTILM 365
Cdd:cd01120  73 ELLEDLAKLLRAARNTGITVIA 94
AAA_22 pfam13401
AAA domain;
263-333 4.44e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 37.71  E-value: 4.44e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904   263 SLILWGPPGCGKTTLAHIIASNSKKHSIR--FVTLSATNAKTNDVRDVIKQAQNEKSFFKRKTILF-------------- 326
Cdd:pfam13401   7 ILVLTGESGTGKTTLLRRLLEQLPEVRDSvvFVDLPSGTSPKDLLRALLRALGLPLSGRLSKEELLaalqqlllalavav 86

                          90
                  ....*....|
gi 18426904   327 ---IDEIHRF 333
Cdd:pfam13401  87 vliIDEAQHL 96
PRK08903 PRK08903
DnaA regulatory inactivator Hda; Validated
 233-339 6.56e-03

DnaA regulatory inactivator Hda; Validated


Pssm-ID: 236347 [Multi-domain]  Cd Length: 227  Bit Score: 38.42  E-value: 6.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18426904  233 PDTLQDYFGQSKAVGQDTLLRSLLETNEIPSLILWGPPGCGKTTLAHIIASNSKKHSIRFVTLSAtnaktndvrdviKQA 312
Cdd:PRK08903  14 PPTFDNFVAGENAELVARLRELAAGPVADRFFYLWGEAGSGRSHLLQALVADASYGGRNARYLDA------------ASP 81

                         90       100
                 ....*....|....*....|....*..
gi 18426904  313 QNEKSFFKRKTILFIDEIHRFNKSQQV 339
Cdd:PRK08903  82 LLAFDFDPEAELYAVDDVERLDDAQQI 108
 
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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