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Conserved domains on  [gi|663510451|gb|AIF01074|]
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ATPase, AAA family protein (rfcL) [uncultured marine group II/III euryarchaeote KM3_141_C05]

Protein Classification

ATP-binding protein( domain architecture ID 1005821)

ATP-binding protein with an AAA (ATPases Associated with various cellular Activities) domain, similar to human ATPase family AAA domain-containing protein 5 that is involved in DNA damage response

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK04195 super family cl35251
replication factor C large subunit; Provisional
 10-474 3.41e-85

replication factor C large subunit; Provisional


The actual alignment was detected with superfamily member PRK04195:

Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 271.02  E-value: 3.41e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  10 DWTERYRPSSEKELEGNDAVRKRIKNWLNTWADGIPdRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASI 89
Cdd:PRK04195   3 PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKP-KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  90 RKAALGGATNFTFGLDGsynpeatvRTLILLDEVDHLHGglrgvsearisdsisskqgieistselRGDSGGKAELLKLL 169
Cdd:PRK04195  82 ERVAGEAATSGSLFGAR--------RKLILLDEVDGIHG---------------------------NEDRGGARAILELI 126

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 170 KVSKQPIIMTCNDPmglWGRRNSNWRTArdrflkeAELIQFRRVTD----AALKRIARRvidgEKVTADPGAIELLISAN 245
Cdd:PRK04195 127 KKAKQPIILTANDP---YDPSLRELRNA-------CLMIEFKRLSTrsivPVLKRICRK----EGIECDDEALKEIAERS 192

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 246 PGDIRALVRDLQMIVEGNTsHIDIAAVEAQisrGLRDHQVDLFPGLEELYRCGSAKEASRLNMEMEKTPKELVAWISWNN 325
Cdd:PRK04195 193 GGDLRSAINDLQAIAEGYG-KLTLEDVKTL---GRRDREESIFDALDAVFKARNADQALEASYDVDEDPDDLIEWIDENI 268

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 326 GSVLKGREDLSRAAEASSRADQALHATFTNLAYRSWYWAGQLSALSASVAAEDIPQGRLSLSYPEFMR--------RGne 397
Cdd:PRK04195 269 PKEYDDPEDIARAYDALSRADIFLGRVKRTQNYDLWRYASDLMTAGVALAKEKKKRGFTRYQPPSYWRllsktkekRE-- 346

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451 398 pwRRVTLIEKMANLSGSSKQAAREELWPALAAIHEEAETIdPEDFRISLELGLEAEEHLLLHKLPSNRVSSKKLVER 474
Cdd:PRK04195 347 --TRDSIAKKIAEKLHTSKRKVRREVLPFLSIIFKHNPEL-AARLAAFLELTEEEIEFLTGSKKATKKIKKIVEKAE 420
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 10-474 3.41e-85

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 271.02  E-value: 3.41e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  10 DWTERYRPSSEKELEGNDAVRKRIKNWLNTWADGIPdRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASI 89
Cdd:PRK04195   3 PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKP-KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  90 RKAALGGATNFTFGLDGsynpeatvRTLILLDEVDHLHGglrgvsearisdsisskqgieistselRGDSGGKAELLKLL 169
Cdd:PRK04195  82 ERVAGEAATSGSLFGAR--------RKLILLDEVDGIHG---------------------------NEDRGGARAILELI 126

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 170 KVSKQPIIMTCNDPmglWGRRNSNWRTArdrflkeAELIQFRRVTD----AALKRIARRvidgEKVTADPGAIELLISAN 245
Cdd:PRK04195 127 KKAKQPIILTANDP---YDPSLRELRNA-------CLMIEFKRLSTrsivPVLKRICRK----EGIECDDEALKEIAERS 192

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 246 PGDIRALVRDLQMIVEGNTsHIDIAAVEAQisrGLRDHQVDLFPGLEELYRCGSAKEASRLNMEMEKTPKELVAWISWNN 325
Cdd:PRK04195 193 GGDLRSAINDLQAIAEGYG-KLTLEDVKTL---GRRDREESIFDALDAVFKARNADQALEASYDVDEDPDDLIEWIDENI 268

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 326 GSVLKGREDLSRAAEASSRADQALHATFTNLAYRSWYWAGQLSALSASVAAEDIPQGRLSLSYPEFMR--------RGne 397
Cdd:PRK04195 269 PKEYDDPEDIARAYDALSRADIFLGRVKRTQNYDLWRYASDLMTAGVALAKEKKKRGFTRYQPPSYWRllsktkekRE-- 346

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451 398 pwRRVTLIEKMANLSGSSKQAAREELWPALAAIHEEAETIdPEDFRISLELGLEAEEHLLLHKLPSNRVSSKKLVER 474
Cdd:PRK04195 347 --TRDSIAKKIAEKLHTSKRKVRREVLPFLSIIFKHNPEL-AARLAAFLELTEEEIEFLTGSKKATKKIKKIVEKAE 420
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 30-130 2.74e-12

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: 64.47  E-value: 2.74e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  30 RKRIKNWLNTWADGiPDRRGILLTGPPGIGKTSIVRAIAN---DNGWNVIELNASDARNAASIRKAALGGATNFTFGLDG 106
Cdd:cd00009    3 QEEAIEALREALEL-PPPKNLLLYGPPGTGKTTLARAIANelfRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAE 81

                         90       100
                 ....*....|....*....|....
gi 663510451 107 SYNPeatvrTLILLDEVDHLHGGL 130
Cdd:cd00009   82 KAKP-----GVLFIDEIDSLSRGA 100
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 50-183 1.48e-11

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: 61.84  E-value: 1.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASIRKAALggaTNFTFGLDGSYNPeatvrTLILLDEVdhlhgg 129
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKR---LRELFEAAKKLAP-----CVIFIDEI------ 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 663510451  130 lrgvsearisDSISSKQGieisTSELRGDSGGKAELLKLL-----KVSKQPIIMTCNDP 183
Cdd:pfam00004  67 ----------DALAGSRG----SGGDSESRRVVNQLLTELdgftsSNSKVIVIAATNRP 111
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 2-258 8.44e-09

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 58.04  E-value: 8.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451    2 SGDEPvlsdWTERYRPSSEKELegndAVRKR----IKNWLNTWADGIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIE 77
Cdd:TIGR00602  69 DGNEP----WVEKYKPETQHEL----AVHKKkieeVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQE 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   78 -LNASDARNAASIRKAALGGATNFtfgldgsynpeatVRTLILLDEVDHLHGGLRGVSEARISDSISSKQGIEIST--SE 154
Cdd:TIGR00602 141 wSNPTLPDFQKNDHKVTLSLESCF-------------SNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDlpNQ 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  155 LRGDSGGKAELLKLLKVSKQ--PIIMTCNDpmGLWGRRNSNWRTARDRFLKEAELIQFRRVTDAA------------LKR 220
Cdd:TIGR00602 208 FYRDTRALHEILRWKYVSIGrcPLVFIITE--SLEGDNNQRRLLFPAETIMNKEILEEPRVSNISfnpiaptimkkfLNR 285

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 663510451  221 IARR--VIDGEKVTA-DPGAIELLISANPGDIRALVRDLQM 258
Cdd:TIGR00602 286 IVTIeaKKNGEKIKVpKKTSVELLCQGCSGDIRSAINSLQF 326
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 4-278 8.84e-09

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: 57.61  E-value: 8.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   4 DEPVLSDWTERYRPSSEKELEGNDAVRKRIK---NWLNTWAD-----GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNV 75
Cdd:COG0464  140 DIGGLEEELLELREAILDDLGGLEEVKEELRelvALPLKRPElreeyGLPPPRGLLLYGPPGTGKTLLARALAGELGLPL 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  76 IELNASD---------ARN-AASIRKAalggatnftfgldgsynpEATVRTLILLDEVDHLHGGLRGVSEArisdsiSSK 145
Cdd:COG0464  220 IEVDLSDlvskyvgetEKNlREVFDKA------------------RGLAPCVLFIDEADALAGKRGEVGDG------VGR 275

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 146 QGIeistselrgdsggkAELLKLL--KVSKQPIIMTCNDPmglwgrRNSN---WRtardRFlkeAELIQFRRVTDAALKR 220
Cdd:COG0464  276 RVV--------------NTLLTEMeeLRSDVVVIAATNRP------DLLDpalLR----RF---DEIIFFPLPDAEERLE 328

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663510451 221 IARRVIDGEKVT--ADPGAI-ELLISANPGDIRALVRDLQMI-VEGNTSHIDIAAVEAQISR 278
Cdd:COG0464  329 IFRIHLRKRPLDedVDLEELaEATEGLSGADIRNVVRRAALQaLRLGREPVTTEDLLEALER 390
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 47-184 2.87e-07

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: 50.06  E-value: 2.87e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451    47 RRGILLTGPPGIGKTSIVRAIAN---DNGWNVIELNASDARNAASIRKAALGGATNFTFGLDGSYN------PEATVRTL 117
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARelgPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLrlalalARKLKPDV 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451   118 ILLDEVDHLHgglrgvsearisDSISSKQGIEISTSELrgdsggkaeLLKLLKVSKQPIIMTCNDPM 184
Cdd:smart00382  82 LILDEITSLL------------DAEQEALLLLLEELRL---------LLLLKSEKNLTVILTTNDEK 127
BREX_3_BrxF NF033453
BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino ...
 50-80 1.74e-04

BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino acids in length includes BrxF from type 3 BREX (bacteriophage exclusion) systems. Most members have the P-loop motif GxxGxGKT, but the region is surprisingly poorly conserved in a sizable fraction of otherwise strongly similar proteins.


Pssm-ID: 468038  Cd Length: 149  Bit Score: 41.71  E-value: 1.74e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 663510451  50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNA 80
Cdd:NF033453  19 ILLVGPPGSGKTALLRELAAKRGAPVINVNL 49
 
Name Accession Description Interval E-value
PRK04195 PRK04195
replication factor C large subunit; Provisional
 10-474 3.41e-85

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 271.02  E-value: 3.41e-85
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  10 DWTERYRPSSEKELEGNDAVRKRIKNWLNTWADGIPdRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASI 89
Cdd:PRK04195   3 PWVEKYRPKTLSDVVGNEKAKEQLREWIESWLKGKP-KKALLLYGPPGVGKTSLAHALANDYGWEVIELNASDQRTADVI 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  90 RKAALGGATNFTFGLDGsynpeatvRTLILLDEVDHLHGglrgvsearisdsisskqgieistselRGDSGGKAELLKLL 169
Cdd:PRK04195  82 ERVAGEAATSGSLFGAR--------RKLILLDEVDGIHG---------------------------NEDRGGARAILELI 126

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 170 KVSKQPIIMTCNDPmglWGRRNSNWRTArdrflkeAELIQFRRVTD----AALKRIARRvidgEKVTADPGAIELLISAN 245
Cdd:PRK04195 127 KKAKQPIILTANDP---YDPSLRELRNA-------CLMIEFKRLSTrsivPVLKRICRK----EGIECDDEALKEIAERS 192

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 246 PGDIRALVRDLQMIVEGNTsHIDIAAVEAQisrGLRDHQVDLFPGLEELYRCGSAKEASRLNMEMEKTPKELVAWISWNN 325
Cdd:PRK04195 193 GGDLRSAINDLQAIAEGYG-KLTLEDVKTL---GRRDREESIFDALDAVFKARNADQALEASYDVDEDPDDLIEWIDENI 268

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 326 GSVLKGREDLSRAAEASSRADQALHATFTNLAYRSWYWAGQLSALSASVAAEDIPQGRLSLSYPEFMR--------RGne 397
Cdd:PRK04195 269 PKEYDDPEDIARAYDALSRADIFLGRVKRTQNYDLWRYASDLMTAGVALAKEKKKRGFTRYQPPSYWRllsktkekRE-- 346

                        410       420       430       440       450       460       470
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451 398 pwRRVTLIEKMANLSGSSKQAAREELWPALAAIHEEAETIdPEDFRISLELGLEAEEHLLLHKLPSNRVSSKKLVER 474
Cdd:PRK04195 347 --TRDSIAKKIAEKLHTSKRKVRREVLPFLSIIFKHNPEL-AARLAAFLELTEEEIEFLTGSKKATKKIKKIVEKAE 420
rfc PRK00440
replication factor C small subunit; Reviewed
 11-257 1.32e-12

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 68.75  E-value: 1.32e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  11 WTERYRPSSEKELEGNDAVRKRIKNWLNTwaDGIPDrrgILLTGPPGIGKTSIVRAIAND---NGW--NVIELNASDARN 85
Cdd:PRK00440   7 WVEKYRPRTLDEIVGQEEIVERLKSYVKE--KNMPH---LLFAGPPGTGKTTAALALARElygEDWreNFLELNASDERG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  86 AASIRK--------AALGGATnFtfgldgsynpeatvrTLILLDEVDHLhgglrgVSEA-----RIsdsisskqgIEIST 152
Cdd:PRK00440  82 IDVIRNkikefartAPVGGAP-F---------------KIIFLDEADNL------TSDAqqalrRT---------MEMYS 130

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 153 SELRgdsggkaellkllkvskqpIIMTCN------DPMglwgrrNSnwRTArdrflkeaeLIQFRRVTDAALKRIARRVI 226
Cdd:PRK00440 131 QNTR-------------------FILSCNysskiiDPI------QS--RCA---------VFRFSPLKKEAVAERLRYIA 174

                        250       260       270
                 ....*....|....*....|....*....|.
gi 663510451 227 DGEKVTADPGAIELLISANPGDIRALVRDLQ 257
Cdd:PRK00440 175 ENEGIEITDDALEAIYYVSEGDMRKAINALQ 205
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 30-130 2.74e-12

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: 64.47  E-value: 2.74e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  30 RKRIKNWLNTWADGiPDRRGILLTGPPGIGKTSIVRAIAN---DNGWNVIELNASDARNAASIRKAALGGATNFTFGLDG 106
Cdd:cd00009    3 QEEAIEALREALEL-PPPKNLLLYGPPGTGKTTLARAIANelfRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAE 81

                         90       100
                 ....*....|....*....|....
gi 663510451 107 SYNPeatvrTLILLDEVDHLHGGL 130
Cdd:cd00009   82 KAKP-----GVLFIDEIDSLSRGA 100
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 50-183 1.48e-11

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: 61.84  E-value: 1.48e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASIRKAALggaTNFTFGLDGSYNPeatvrTLILLDEVdhlhgg 129
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKR---LRELFEAAKKLAP-----CVIFIDEI------ 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 663510451  130 lrgvsearisDSISSKQGieisTSELRGDSGGKAELLKLL-----KVSKQPIIMTCNDP 183
Cdd:pfam00004  67 ----------DALAGSRG----SGGDSESRRVVNQLLTELdgftsSNSKVIVIAATNRP 111
PLN03025 PLN03025
replication factor C subunit; Provisional
 11-263 9.51e-10

replication factor C subunit; Provisional


Pssm-ID: 178596 [Multi-domain]  Cd Length: 319  Bit Score: 60.13  E-value: 9.51e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  11 WTERYRPSSEKELEGN-DAVRKriknwLNTWA-DG-IPDrrgILLTGPPGIGKTSIVRAIANDN-GWN----VIELNASD 82
Cdd:PLN03025   3 WVEKYRPTKLDDIVGNeDAVSR-----LQVIArDGnMPN---LILSGPPGTGKTTSILALAHELlGPNykeaVLELNASD 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  83 ARNAASIRKAALGGATNFTFGLDGSYNpeatvrtLILLDEVDHLHGG----LRGVSEARisdSISSKQGIEISTSElrgd 158
Cdd:PLN03025  75 DRGIDVVRNKIKMFAQKKVTLPPGRHK-------IVILDEADSMTSGaqqaLRRTMEIY---SNTTRFALACNTSS---- 140

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 159 sggkaellKLLkvskQPIIMTCndpmglwgrrnsnwrtardrflkeaELIQFRRVTDA-ALKRIaRRVIDGEKVTADPGA 237
Cdd:PLN03025 141 --------KII----EPIQSRC-------------------------AIVRFSRLSDQeILGRL-MKVVEAEKVPYVPEG 182

                        250       260
                 ....*....|....*....|....*.
gi 663510451 238 IELLISANPGDIRALVRDLQMIVEGN 263
Cdd:PLN03025 183 LEAIIFTADGDMRQALNNLQATHSGF 208
PRK12402 PRK12402
replication factor C small subunit 2; Reviewed
 11-286 1.24e-09

replication factor C small subunit 2; Reviewed


Pssm-ID: 237090 [Multi-domain]  Cd Length: 337  Bit Score: 59.62  E-value: 1.24e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  11 WTERYRPSSEKELEGNDAVRKRIKNWLNTwadgiPDRRGILLTGPPGIGKTSIVRAIAN---DNGW--NVIELNASD--- 82
Cdd:PRK12402   5 WTEKYRPALLEDILGQDEVVERLSRAVDS-----PNLPHLLVQGPPGSGKTAAVRALARelyGDPWenNFTEFNVADffd 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  83 ------------ARNAASIRKAALGGATNFTF---------GLDGSYNpeatvrtLILLDEVDHL----HGGLRgvseaR 137
Cdd:PRK12402  80 qgkkylvedprfAHFLGTDKRIRSSKIDNFKHvlkeyasyrPLSADYK-------TILLDNAEALredaQQALR-----R 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 138 ISDSISSKQGIEISTSELRgdsggkaellKLLkvskQPIimtcndpmglwgrrnsnwrtaRDRFLKeaelIQFRRVTDAA 217
Cdd:PRK12402 148 IMEQYSRTCRFIIATRQPS----------KLI----PPI---------------------RSRCLP----LFFRAPTDDE 188

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663510451 218 LKRIARRVIDGEKVTADPGAIELLISANPGDIRALVRDLQMIVEGNTSHIDIAAVEAqISRGLRDHQVD 286
Cdd:PRK12402 189 LVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEA-LGDVGTDEVIE 256
rad24 TIGR00602
checkpoint protein rad24; All proteins in this family for which functions are known are ...
 2-258 8.44e-09

checkpoint protein rad24; All proteins in this family for which functions are known are involved in DNA damage tolerance (likely cell cycle checkpoints).This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129690 [Multi-domain]  Cd Length: 637  Bit Score: 58.04  E-value: 8.44e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451    2 SGDEPvlsdWTERYRPSSEKELegndAVRKR----IKNWLNTWADGIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIE 77
Cdd:TIGR00602  69 DGNEP----WVEKYKPETQHEL----AVHKKkieeVETWLKAQVLENAPKRILLITGPSGCGKSTTIKILSKELGIQVQE 140

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   78 -LNASDARNAASIRKAALGGATNFtfgldgsynpeatVRTLILLDEVDHLHGGLRGVSEARISDSISSKQGIEIST--SE 154
Cdd:TIGR00602 141 wSNPTLPDFQKNDHKVTLSLESCF-------------SNFQSQIEVFSEFLLRATNKLQMLGDDLMTDKKIILVEDlpNQ 207

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  155 LRGDSGGKAELLKLLKVSKQ--PIIMTCNDpmGLWGRRNSNWRTARDRFLKEAELIQFRRVTDAA------------LKR 220
Cdd:TIGR00602 208 FYRDTRALHEILRWKYVSIGrcPLVFIITE--SLEGDNNQRRLLFPAETIMNKEILEEPRVSNISfnpiaptimkkfLNR 285

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|.
gi 663510451  221 IARR--VIDGEKVTA-DPGAIELLISANPGDIRALVRDLQM 258
Cdd:TIGR00602 286 IVTIeaKKNGEKIKVpKKTSVELLCQGCSGDIRSAINSLQF 326
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 4-278 8.84e-09

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: 57.61  E-value: 8.84e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   4 DEPVLSDWTERYRPSSEKELEGNDAVRKRIK---NWLNTWAD-----GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNV 75
Cdd:COG0464  140 DIGGLEEELLELREAILDDLGGLEEVKEELRelvALPLKRPElreeyGLPPPRGLLLYGPPGTGKTLLARALAGELGLPL 219

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  76 IELNASD---------ARN-AASIRKAalggatnftfgldgsynpEATVRTLILLDEVDHLHGGLRGVSEArisdsiSSK 145
Cdd:COG0464  220 IEVDLSDlvskyvgetEKNlREVFDKA------------------RGLAPCVLFIDEADALAGKRGEVGDG------VGR 275

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 146 QGIeistselrgdsggkAELLKLL--KVSKQPIIMTCNDPmglwgrRNSN---WRtardRFlkeAELIQFRRVTDAALKR 220
Cdd:COG0464  276 RVV--------------NTLLTEMeeLRSDVVVIAATNRP------DLLDpalLR----RF---DEIIFFPLPDAEERLE 328

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 663510451 221 IARRVIDGEKVT--ADPGAI-ELLISANPGDIRALVRDLQMI-VEGNTSHIDIAAVEAQISR 278
Cdd:COG0464  329 IFRIHLRKRPLDedVDLEELaEATEGLSGADIRNVVRRAALQaLRLGREPVTTEDLLEALER 390
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
26-351 1.63e-08

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


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 55.75  E-value: 1.63e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  26 NDAVRKRIKNWLNTWadgiPDRRGILLTGPPGIGKTSIVRAIANDNGW-----------------------NVIELNA-- 80
Cdd:COG0470    1 QEEAWEQLLAAAESG----RLPHALLLHGPPGIGKTTLALALARDLLCenpeggkacgqchsrlmaagnhpDLLELNPee 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  81 -SDARNAASIRkaALGGATNFTfGLDGSYNpeatvrtLILLDEVDHLHGglrgvSEARIsdsisskqgieistselrgds 159
Cdd:COG0470   77 kSDQIGIDQIR--ELGEFLSLT-PLEGGRK-------VVIIDEADAMNE-----AAANA--------------------- 120

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 160 ggkaeLLKLL-KVSKQ-PIIMTCNDPMGLwgrrnsnWRTARDRflkeAELIQFRRVTDAAlkriARRVIDGEKVTADpgA 237
Cdd:COG0470  121 -----LLKTLeEPPKNtPFILIANDPSRL-------LPTIRSR----CQVIRFRPPSEEE----ALAWLREEGVDED--A 178

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 238 IELLISANPGDIRALVRDLQMIVEGNTSHIDIAAVEAqisrglRDHQVDLFPGLEElyrcgsAKEASRLNMemektpkeL 317
Cdd:COG0470  179 LEAILRLAGGDPRAAINLLQALAGRKELLEDLAALLS------RDRALELLDALLK------AEALELLDW--------L 238

                        330       340       350
                 ....*....|....*....|....*....|....
gi 663510451 318 VAWISWNNGSVLKGrEDLSRAAEASSRADQALHA 351
Cdd:COG0470  239 LKWLLDNLPLEYAG-EDLARAYEALSEADRRLGR 271
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 43-126 2.29e-08

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: 53.45  E-value: 2.29e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIelnasdARNAASIRKAALGGATNftfGLDGSYN-PEATVRTLILLD 121
Cdd:cd19503   30 GLKPPRGVLLHGPPGTGKTLLARAVANEAGANFL------SISGPSIVSKYLGESEK---NLREIFEeARSHAPSIIFID 100


                 ....*
gi 663510451 122 EVDHL 126
Cdd:cd19503  101 EIDAL 105
44 PHA02544
clamp loader, small subunit; Provisional
 11-257 4.03e-08

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 55.00  E-value: 4.03e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  11 WTERYRPSSEKELEGNDAVRKRIKNWLNtwaDG-IPDRrgILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARnAASI 89
Cdd:PHA02544  11 WEQKYRPSTIDECILPAADKETFKSIVK---KGrIPNM--LLHSPSPGTGKTTVAKALCNEVGAEVLFVNGSDCR-IDFV 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  90 RkaalGGATNF--TFGLDGSynpeatvRTLILLDEVDHLhgglrGVSEARISdsisskqgieistseLRGdsggkaellK 167
Cdd:PHA02544  85 R----NRLTRFasTVSLTGG-------GKVIIIDEFDRL-----GLADAQRH---------------LRS---------F 124

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 168 LLKVSKQ-PIIMTCNDPMGLWGRRNSNWRTardrflkeaelIQFRRVTDAALKRIARRVI-------DGEKVTADPGAIE 239
Cdd:PHA02544 125 MEAYSKNcSFIITANNKNGIIEPLRSRCRV-----------IDFGVPTKEEQIEMMKQMIvrckgilEAEGVEVDMKVLA 193

                        250
                 ....*....|....*...
gi 663510451 240 LLISANPGDIRALVRDLQ 257
Cdd:PHA02544 194 ALVKKNFPDFRRTINELQ 211
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 43-82 1.35e-07

Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of mitochondrial respiratory chain complex III and plays an important role in the maintenance of mitochondrial tubular networks, respiratory chain assembly and formation of the LETM1 complex. RecA-like NTPases. This family includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. This group also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 50.81  E-value: 1.35e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:cd19510   19 GIPYRRGYLLYGPPGTGKSSFIAALAGELDYDICDLNLSE 58
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 27-82 2.36e-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: 50.36  E-value: 2.36e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 663510451  27 DAVRKRIKNWLNTW---ADGIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:cd19481    3 ASLREAVEAPRRGSrlrRYGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSS 61
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 47-184 2.87e-07

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: 50.06  E-value: 2.87e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451    47 RRGILLTGPPGIGKTSIVRAIAN---DNGWNVIELNASDARNAASIRKAALGGATNFTFGLDGSYN------PEATVRTL 117
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARelgPPGGGVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLrlalalARKLKPDV 81

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451   118 ILLDEVDHLHgglrgvsearisDSISSKQGIEISTSELrgdsggkaeLLKLLKVSKQPIIMTCNDPM 184
Cdd:smart00382  82 LILDEITSLL------------DAEQEALLLLLEELRL---------LLLLKSEKNLTVILTTNDEK 127
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 50-123 8.74e-07

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 51.24  E-value: 8.74e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 663510451  50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNASDArNAASIRKAALGGATNFTFGLdgsynpeatvRTLILLDEV 123
Cdd:PRK13342  39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVTS-GVKDLREVIEEARQRRSAGR----------RTILFIDEI 101
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 50-132 2.46e-06

lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an evolutionarily conserved ATP-dependent serine protease, present in bacteria and eukaryotic mitochondria and peroxisomes, which mediates the selective degradation of mutant and abnormal proteins as well as certain short-lived regulatory proteins. Lon protease is both an ATP-dependent peptidase and a protein-activated ATPase. This RecA-like Lon domain subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 47.94  E-value: 2.46e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASIRK------AALGGatNFTFGLD--GSYNPeatvrtLILLD 121
Cdd:cd19500   40 LCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRGhrrtyvGAMPG--RIIQALKkaGTNNP------VFLLD 111

                         90
                 ....*....|.
gi 663510451 122 EVDHLHGGLRG 132
Cdd:cd19500  112 EIDKIGSSFRG 122
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 43-79 5.07e-06

first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r1-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 46.66  E-value: 5.07e-06
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELN 79
Cdd:cd19519   30 GIKPPRGILLYGPPGTGKTLIARAVANETGAFFFLIN 66
Rad17 pfam03215
Rad17 P-loop domain;
11-77 6.83e-06

Rad17 P-loop domain;


Pssm-ID: 367398 [Multi-domain]  Cd Length: 186  Bit Score: 46.88  E-value: 6.83e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663510451   11 WTERYRPSSEKELegndAVRKR----IKNWLNtwADGIPDR--RGILLTGPPGIGKTSIVRAIANDNGWNVIE 77
Cdd:pfam03215   9 WYEKYKPNCLEQL----AVHKRkikdVQEWLD--AMFLENAkhRILLISGPSGCGKSTVIKELSKELGPKYRE 75
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 43-82 9.69e-06

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 47.69  E-value: 9.69e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:COG1222  108 GIEPPKGVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSE 147
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 43-82 1.42e-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: 45.35  E-value: 1.42e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:cd19511   23 GIRPPKGVLLYGPPGCGKTLLAKALASEAGLNFISVKGPE 62
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 43-76 5.45e-05

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


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 43.64  E-value: 5.45e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVI 76
Cdd:cd19529   23 GIRPPKGILLYGPPGTGKTLLAKAVATESNANFI 56
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 50-123 8.59e-05

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 45.05  E-value: 8.59e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 663510451  50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNASDArNAASIRKAALGGATNFTFGldgsynpeatVRTLILLDEV 123
Cdd:COG2256   52 MILWGPPGTGKTTLARLIANATDAEFVALSAVTS-GVKDIREVIEEARERRAYG----------RRTILFVDEI 114
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 43-82 8.91e-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: 43.16  E-value: 8.91e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:cd19518   30 GVEPPRGVLLHGPPGCGKTMLANAIAGELKVPFLKISATE 69
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 48-135 1.06e-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: 42.72  E-value: 1.06e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  48 RGILLTGPPGIGKTSIVRAIANDNGWNVIELNASdarnaaSIRKAALGGATNFT---FGLDGSYNPeatvrTLILLDEVD 124
Cdd:cd19509   33 RGILLYGPPGTGKTLLARAVASESGSTFFSISAS------SLVSKWVGESEKIVralFALARELQP-----SIIFIDEID 101

                         90
                 ....*....|.
gi 663510451 125 HLhGGLRGVSE 135
Cdd:cd19509  102 SL-LSERGSGE 111
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 23-85 1.15e-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: 42.48  E-value: 1.15e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 663510451  23 LEGNDAVRKRIKNWLNTWADGIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASDARN 85
Cdd:cd19530    6 EELTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANESGANFISVKGPELLN 68
PRK10787 PRK10787
DNA-binding ATP-dependent protease La; Provisional
 25-158 1.19e-04

DNA-binding ATP-dependent protease La; Provisional


Pssm-ID: 182730 [Multi-domain]  Cd Length: 784  Bit Score: 44.93  E-value: 1.19e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  25 GNDAVRKRIKNWLNTWADGIPDRRGIL-LTGPPGIGKTSIVRAIANDNGWNVIELNASDARNAASIRK------AALGGA 97
Cdd:PRK10787 326 GLERVKDRILEYLAVQSRVNKIKGPILcLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGhrrtyiGSMPGK 405

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 663510451  98 TNFTFGLDGSYNPeatvrtLILLDEVDHLHGGLRGVSEARISDSISSKQGIEISTSELRGD 158
Cdd:PRK10787 406 LIQKMAKVGVKNP------LFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVD 460
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
21-137 1.27e-04

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 43.72  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  21 KELEGNDAVRKRIKNWLNTWAD-------GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASdarnaaSIRKAA 93
Cdd:COG1223    2 DDVVGQEEAKKKLKLIIKELRRrenlrkfGLWPPRKILFYGPPGTGKTMLAEALAGELKLPLLTVRLD------SLIGSY 75

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 663510451  94 LG-GATN----FTFGldgsynpeATVRTLILLDEVDHLhGGLRGVSEAR 137
Cdd:COG1223   76 LGeTARNlrklFDFA--------RRAPCVIFFDEFDAI-AKDRGDQNDV 115
BREX_3_BrxF NF033453
BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino ...
 50-80 1.74e-04

BREX-3 system P-loop-containing protein BrxF; This family of proteins that are about 150 amino acids in length includes BrxF from type 3 BREX (bacteriophage exclusion) systems. Most members have the P-loop motif GxxGxGKT, but the region is surprisingly poorly conserved in a sizable fraction of otherwise strongly similar proteins.


Pssm-ID: 468038  Cd Length: 149  Bit Score: 41.71  E-value: 1.74e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 663510451  50 ILLTGPPGIGKTSIVRAIANDNGWNVIELNA 80
Cdd:NF033453  19 ILLVGPPGSGKTALLRELAAKRGAPVINVNL 49
HLD_clamp_RFC cd18140
helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein ...
 218-274 1.79e-04

helical lid domain of replication factor C subunit; Replication factor C (RFC) is five-protein clamp loader complex that forms a stable ATP-dependent complex with the sliding clamp, PCNA, which binds specifically to primed DNA. RFC subunits belong to the clamp loader clade of the AAA+ superfamily.


Pssm-ID: 350842 [Multi-domain]  Cd Length: 63  Bit Score: 39.43  E-value: 1.79e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451 218 LKRIARRvidgEKVTADPGAIELLISANPGDIRALVRDLQMIVEGNTsHIDIAAVEA 274
Cdd:cd18140   10 LREICKK----EGVKIDEEALEAIAEKSEGDMRKAINDLQAAAAGGG-VITEEDVYE 61
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 44-82 2.07e-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: 42.22  E-value: 2.07e-04
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 663510451  44 IPdrRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:cd19501   36 IP--KGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSD 72
PRK13341 PRK13341
AAA family ATPase;
12-123 2.30e-04

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 43.89  E-value: 2.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  12 TERYRPSSEKELEGNDAVrkriknwlntWADGIPDRRGI--------LLTGPPGIGKTSIVRAIANDNGWNVIELNA--- 80
Cdd:PRK13341  19 ADRLRPRTLEEFVGQDHI----------LGEGRLLRRAIkadrvgslILYGPPGVGKTTLARIIANHTRAHFSSLNAvla 88

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 663510451  81 --SDARNAASIRKAALGgatnfTFGLdgsynpeatvRTLILLDEV 123
Cdd:PRK13341  89 gvKDLRAEVDRAKERLE-----RHGK----------RTILFIDEV 118
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 48-81 2.45e-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: 41.64  E-value: 2.45e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 663510451  48 RGILLTGPPGIGKTSIVRAIANDNGWNVIELNAS 81
Cdd:cd19520   36 KGVLLYGPPGCGKTMLAKATAKEAGARFINLQVS 69
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 43-82 2.65e-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: 2.65e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELNASD 82
Cdd:cd19502   33 GIEPPKGVLLYGPPGTGKTLLAKAVANHTDATFIRVVGSE 72
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 43-76 3.10e-04

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: 41.26  E-value: 3.10e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVI 76
Cdd:cd19526   23 PLRLRSGILLYGPPGCGKTLLASAIASECGLNFI 56
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 43-79 3.70e-04

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 43.36  E-value: 3.70e-04
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 663510451   43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVIELN 79
Cdd:TIGR01243 208 GIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISIN 244
HolA COG1466
DNA polymerase III, delta subunit [Replication, recombination and repair];
190-278 3.94e-04

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


Pssm-ID: 441075 [Multi-domain]  Cd Length: 305  Bit Score: 42.55  E-value: 3.94e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451 190 RNSNWRTArdrFLKEAELIQFRRVTDAALKRIARRVIDGEKVTADPGAIELLISANPGDIRALVRDLQMIVE--GNTSHI 267
Cdd:COG1466  106 KRKKLFKA---LEKAGVVVECYPLKERELPAWIRQRLKAAGLRIDPDAAQLLAERVGGDLLALAQELEKLALyaGDGGTI 182

                         90
                 ....*....|.
gi 663510451 268 DIAAVEAQISR 278
Cdd:COG1466  183 TLEDVEALVGD 193
AAA_22 pfam13401
AAA domain;
46-130 6.02e-04

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 40.02  E-value: 6.02e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   46 DRRGILLTGPPGIGKTSIVRAIAN-DNGWN--VIELNASDARNAASIRKA---ALGGATNFTFGLDGSYN------PEAT 113
Cdd:pfam13401   4 GAGILVLTGESGTGKTTLLRRLLEqLPEVRdsVVFVDLPSGTSPKDLLRAllrALGLPLSGRLSKEELLAalqqllLALA 83

                          90
                  ....*....|....*..
gi 663510451  114 VRTLILLDEVDHLHGGL 130
Cdd:pfam13401  84 VAVVLIIDEAQHLSLEA 100
PRK04132 PRK04132
replication factor C small subunit; Provisional
 11-69 7.65e-04

replication factor C small subunit; Provisional


Pssm-ID: 235223 [Multi-domain]  Cd Length: 846  Bit Score: 42.13  E-value: 7.65e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 663510451  11 WTERYRPSSEKELEGNDAVRKRIKNWLNTwaDGIPDrrgILLTGPPGIGK--TSIVRAIAN 69
Cdd:PRK04132   9 WVEKYRPQRLDDIVGQEHIVKRLKHYVKT--GSMPH---LLFAGPPGVGKclTGDTKVIAN 64
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 43-76 9.69e-04

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 41.82  E-value: 9.69e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 663510451   43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVI 76
Cdd:TIGR01243 483 GIRPPKGVLLFGPPGTGKTLLAKAVATESGANFI 516
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 43-76 1.07e-03

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: 39.80  E-value: 1.07e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIANDNGWNVI 76
Cdd:cd19528   23 GMTPSKGVLFYGPPGCGKTLLAKAIANECQANFI 56
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 28-68 1.10e-03

ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 41.54  E-value: 1.10e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 663510451  28 AVRKRIKnwlntwadgipDRRG--ILLTGPPGIGKTSIVRAIA 68
Cdd:COG0466  342 AVRKLKK-----------KLKGpiLCLVGPPGVGKTSLGKSIA 373
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 36-166 1.35e-03

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 39.58  E-value: 1.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  36 WLNTWADGIpdRR---GILLTGPPGIGKTSIVRAIANDNGWNVieLNASDARNAASIRKAAlGGATNFTFGLDGSYNPea 112
Cdd:cd19522   21 WMPEFFKGI--RRpwkGVLMVGPPGTGKTLLAKAVATECGTTF--FNVSSSTLTSKYRGES-EKLVRLLFEMARFYAP-- 93

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 663510451 113 tvrTLILLDEVdhlhgglrgvsearisDSISSKQGieiSTSELRGDSGGKAELL 166
Cdd:cd19522   94 ---TTIFIDEI----------------DSICSRRG---TSEEHEASRRVKSELL 125
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 25-82 1.38e-03

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


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 39.41  E-value: 1.38e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 663510451   25 GNDAVRKRIKNWLNTWADGIPdrRGILLTGPPGIGKTSIVRAI---ANDNGWNVIELNASD 82
Cdd:pfam13191   4 GREEELEQLLDALDRVRSGRP--PSVLLTGEAGTGKTTLLRELlraLERDGGYFLRGKCDE 62
ycf46 CHL00195
Ycf46; Provisional
 33-160 1.56e-03

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 41.16  E-value: 1.56e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  33 IKNWLNTWAD---------GIPDRRGILLTGPPGIGKTSIVRAIANDngWNVielnasdarnaasirkaalggatnftfg 103
Cdd:CHL00195 236 LKDWLKKRSTsfskqasnyGLPTPRGLLLVGIQGTGKSLTAKAIAND--WQL---------------------------- 285

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 663510451 104 ldgsynpeatvrTLILLDeVDHLHGGLRGVSEARISDSISSKQGI--------EI----STSELRGDSG 160
Cdd:CHL00195 286 ------------PLLRLD-VGKLFGGIVGESESRMRQMIRIAEALspcilwidEIdkafSNSESKGDSG 341
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 40-74 1.86e-03

second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as Peroxin61)/PEX1 is a protein unfoldase; PEX6 and PEX1 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. This subfamily represents the second ATPase domain of PEX6. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 39.03  E-value: 1.86e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 663510451  40 WADGIPDRRGILLTGPPGIGKTSIVRAIANDNGWN 74
Cdd:cd19527   19 FSSGLRKRSGILLYGPPGTGKTLLAKAIATECSLN 53
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 43-69 3.30e-03

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 39.75  E-value: 3.30e-03
                         10        20
                 ....*....|....*....|....*..
gi 663510451  43 GIPDRRGILLTGPPGIGKTSIVRAIAN 69
Cdd:PTZ00454 175 GIDPPRGVLLYGPPGTGKTMLAKAVAH 201
Fap7 COG1936
Broad-specificity NMP kinase [Nucleotide transport and metabolism];
50-79 3.78e-03

Broad-specificity NMP kinase [Nucleotide transport and metabolism];


Pssm-ID: 441539 [Multi-domain]  Cd Length: 173  Bit Score: 38.26  E-value: 3.78e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 663510451  50 ILLTGPPGIGKTSIVRAIANDNGWNVIELN 79
Cdd:COG1936    3 IAITGTPGTGKTTVAKLLAERLGLEVIHLN 32
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
44-68 4.37e-03

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 39.63  E-value: 4.37e-03
                         10        20
                 ....*....|....*....|....*
gi 663510451  44 IPdrRGILLTGPPGIGKTSIVRAIA 68
Cdd:COG0465  174 IP--KGVLLVGPPGTGKTLLAKAVA 196
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 32-74 5.00e-03

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. 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: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 37.73  E-value: 5.00e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 663510451  32 RIKNWLN----TWAD-----GIPDRRGILLTGPPGIGKTSIVRAIANDngWN 74
Cdd:cd19507    7 NLKDWLKkrkaAFSKqasayGLPTPKGLLLVGIQGTGKSLTAKAIAGV--WQ 56
PRK14964 PRK14964
DNA polymerase III subunits gamma and tau; Provisional
 14-68 5.49e-03

DNA polymerase III subunits gamma and tau; Provisional


Pssm-ID: 237870 [Multi-domain]  Cd Length: 491  Bit Score: 39.38  E-value: 5.49e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 663510451  14 RYRPSSEKELEGNDAVRKRIKNWLNTwaDGIPdrRGILLTGPPGIGKTSIVRAIA 68
Cdd:PRK14964   6 KYRPSSFKDLVGQDVLVRILRNAFTL--NKIP--QSILLVGASGVGKTTCARIIS 56
NTPase_1 pfam03266
NTPase; This domain is found across all species from bacteria to human, and the function was ...
 50-75 7.35e-03

NTPase; This domain is found across all species from bacteria to human, and the function was determined first in a hyperthermophilic bacterium to be an NTPase. The structure of one member-sequence represents a variation of the RecA fold, and implies that the function might be that of a DNA/RNA modifying enzyme. The sequence carries both a Walker A and Walker B motif which together are characteriztic of ATPases or GTPases. The protein exhibits an increased expression profile in human liver cholangiocarcinoma when compared to normal tissue.


Pssm-ID: 460869  Cd Length: 168  Bit Score: 37.61  E-value: 7.35e-03
                          10        20
                  ....*....|....*....|....*....
gi 663510451   50 ILLTGPPGIGKTSIVRAIAN---DNGWNV 75
Cdd:pfam03266   2 IFITGPPGVGKTTLVLKVAEllkSSGVKV 30
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 50-152 8.65e-03

AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 37.17  E-value: 8.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451   50 ILLTGPPGIGKTSIVRAIAN---DNGWNVIELNASDARNAASIrkAALGGATNFTFGLD-GSYNPEATVR---TLILLDE 122
Cdd:pfam07724   6 FLFLGPTGVGKTELAKALAEllfGDERALIRIDMSEYMEEHSV--SRLIGAPPGYVGYEeGGQLTEAVRRkpySIVLIDE 83

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 663510451  123 VDHLHGG-----LRGVSEARISDsissKQGIEIST 152
Cdd:pfam07724  84 IEKAHPGvqndlLQILEGGTLTD----KQGRTVDF 114
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 48-126 8.86e-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: 37.14  E-value: 8.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 663510451  48 RGILLTGPPGIGKTSIVRAIANDNgwNVIELNASdarnAASIRKAALGGATNFT---FGLDGSYNPeatvrTLILLDEVD 124
Cdd:cd19524   34 RGLLLFGPPGNGKTMLAKAVAAES--NATFFNIS----AASLTSKYVGEGEKLVralFAVARELQP-----SIIFIDEVD 102


                 ..
gi 663510451 125 HL 126
Cdd:cd19524  103 SL 104
AAA_28 pfam13521
AAA domain;
50-77 8.90e-03

AAA domain;


Pssm-ID: 433278 [Multi-domain]  Cd Length: 164  Bit Score: 37.24  E-value: 8.90e-03
                          10        20
                  ....*....|....*....|....*...
gi 663510451   50 ILLTGPPGIGKTSIVRAIANDNGWNVIE 77
Cdd:pfam13521   2 IVITGGPSTGKTTLAEALAARFGYPVVP 29
PRK13764 PRK13764
ATPase; Provisional
 16-69 9.04e-03

ATPase; Provisional


Pssm-ID: 184311 [Multi-domain]  Cd Length: 602  Bit Score: 38.67  E-value: 9.04e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 663510451  16 RPSSEKELEG---NDAVRKRIKNwlntwadgipDRRGILLTGPPGIGKTSIVRAIAN 69
Cdd:PRK13764 233 RPVVKLSLEDynlSEKLKERLEE----------RAEGILIAGAPGAGKSTFAQALAE 279
 
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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