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Conserved domains on  [gi|1176162545|gb|OQX78805|]
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ATP-dependent protease ATP-binding subunit ClpX [Bacteroidetes bacterium 4484_276]

Protein Classification

ATP-dependent Clp protease ATP-binding subunit ClpX( domain architecture ID 11440654)

ATP-dependent Clp protease ATP-binding subunit ClpX is an ATP-dependent specificity component of the Clp protease that uses cycles of ATP-binding and hydrolysis to unfold proteins and translocate them to the ClpP protease

CATH:  1.10.8.60
Gene Ontology:  GO:0005524|GO:0004176|GO:0016887|GO:0051082|GO:0008270|GO:0046983
SCOP:  4000283

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 1-402 0e+00

ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 731.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   1 MAKATDK---CSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELSAKQPDKyKQFKLLKPAEIKSYIDQYVIGQED 77
Cdd:COG1219     1 MAGDSKKelkCSFCGKSQDEVRKLIAGPGVYICDECVELCNEIIEEELKEEEAEE-ELKKLPKPKEIKAFLDEYVIGQER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  78 AKRILSVAVYNHYKRISQKgksiDKKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDV 157
Cdd:COG1219    80 AKKVLSVAVYNHYKRLNSG----SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 158 ESILSRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQI 237
Cdd:COG1219   156 ENILLKLLQAADYDVEKAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKHPQQEFIQI 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 238 NTENILFISGGAFGGIEKTIASRMRANVIGY-ASKNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQP 316
Cdd:COG1219   236 DTTNILFICGGAFDGLEKIIERRLGKKSIGFgAEVKSKKEKDEGELLKQVEPEDLIKFGLIPEFIGRLPVIATLEELDEE 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 317 ALKRILTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTR 396
Cdd:COG1219   316 ALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMYELPSRKDVKKVVITK 395


                  ....*.
gi 1176162545 397 TYASEK 402
Cdd:COG1219   396 EVVEGK 401
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 1-402 0e+00

ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 731.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   1 MAKATDK---CSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELSAKQPDKyKQFKLLKPAEIKSYIDQYVIGQED 77
Cdd:COG1219     1 MAGDSKKelkCSFCGKSQDEVRKLIAGPGVYICDECVELCNEIIEEELKEEEAEE-ELKKLPKPKEIKAFLDEYVIGQER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  78 AKRILSVAVYNHYKRISQKgksiDKKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDV 157
Cdd:COG1219    80 AKKVLSVAVYNHYKRLNSG----SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 158 ESILSRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQI 237
Cdd:COG1219   156 ENILLKLLQAADYDVEKAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKHPQQEFIQI 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 238 NTENILFISGGAFGGIEKTIASRMRANVIGY-ASKNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQP 316
Cdd:COG1219   236 DTTNILFICGGAFDGLEKIIERRLGKKSIGFgAEVKSKKEKDEGELLKQVEPEDLIKFGLIPEFIGRLPVIATLEELDEE 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 317 ALKRILTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTR 396
Cdd:COG1219   316 ALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMYELPSRKDVKKVVITK 395


                  ....*.
gi 1176162545 397 TYASEK 402
Cdd:COG1219   396 EVVEGK 401
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
3-402 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 668.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   3 KATDKCSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELsakQPDKYKQFKLLKPAEIKSYIDQYVIGQEDAKRIL 82
Cdd:PRK05342    7 KKLLYCSFCGKSQHEVRKLIAGPGVYICDECIELCNEIIREEL---KEEAVELKELPTPKEIKAHLDQYVIGQERAKKVL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  83 SVAVYNHYKRISQKGKsidkKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDVESILS 162
Cdd:PRK05342   84 SVAVYNHYKRLRHGDK----KDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 163 RLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQINTENI 242
Cdd:PRK05342  160 KLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNI 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 243 LFISGGAFGGIEKTIASRMRANVIGYAS--KNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQPALKR 320
Cdd:PRK05342  240 LFICGGAFDGLEKIIKQRLGKKGIGFGAevKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIGRLPVVATLEELDEEALVR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 321 ILTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTRTYAS 400
Cdd:PRK05342  320 ILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMFELPSREDVEKVVITKEVVE 399


                  ..
gi 1176162545 401 EK 402
Cdd:PRK05342  400 GK 401
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 7-396 4.17e-179

endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273047 [Multi-domain]  Cd Length: 413  Bit Score: 505.07  E-value: 4.17e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   7 KCSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELSAKQPDK-----YKQFKLLKPAEIKSYIDQYVIGQEDAKRI 81
Cdd:TIGR00382   9 YCSFCGKSQDEVRKLIAGPGVYICDECIELCHDILEEELGTRKESKeyeeeFELSYLPTPKEIKAHLDEYVIGQEQAKKV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  82 LSVAVYNHYKRISQKgkSIDKKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDVESIL 161
Cdd:TIGR00382  89 LSVAVYNHYKRLNFE--KNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENIL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 162 SRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQINTEN 241
Cdd:TIGR00382 167 LKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSN 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 242 ILFISGGAFGGIEKTIASRMRANVIGYASKNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQPALKRI 321
Cdd:TIGR00382 247 ILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAI 326

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1176162545 322 LTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTR 396
Cdd:TIGR00382 327 LTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVMFDLPSLEDLEKVVITK 401
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 59-310 4.59e-155

ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX 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: 410905 [Multi-domain]  Cd Length: 251  Bit Score: 437.80  E-value: 4.59e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  59 LKPAEIKSYIDQYVIGQEDAKRILSVAVYNHYKRISQKGKSIDkkkDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVP 138
Cdd:cd19497     1 PTPKEIKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNNLKQKD---DDVELEKSNILLIGPTGSGKTLLAQTLAKILDVP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 139 FAIADATILTEAGYVGEDVESILSRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSI 218
Cdd:cd19497    78 FAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 219 VNVPPQGGRKHPEQKMIQINTENILFISGGAFGGIEKTIASRMRANVIGY--ASKNTQEHIDKDNMLQYVAPPDLKKYGL 296
Cdd:cd19497   158 ANVPPQGGRKHPQQEFIQVDTTNILFICGGAFVGLEKIIARRLGKKSLGFgaETSSEKDEKERDELLSKVEPEDLIKFGL 237

                         250
                  ....*....|....
gi 1176162545 297 IPEIVGRLPVVTYL 310
Cdd:cd19497   238 IPEFVGRLPVIVTL 251
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 110-307 7.93e-36

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: 129.24  E-value: 7.93e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 110 EKSNIIIVGETGTGKTLLARTIARML---EVPFAIADATILTEagyvgedvESILSRLLQASDYNVAAAEKG-------- 178
Cdd:pfam07724   2 PIGSFLFLGPTGVGKTELAKALAELLfgdERALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrr 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 179 ----IVFIDEIDKISRksdnpsitrdvsgeGVQQALLKLLEGSIVNvpPQGGRkhpeqkmiQINTENILFISGGAFGGIE 254
Cdd:pfam07724  74 kpysIVLIDEIEKAHP--------------GVQNDLLQILEGGTLT--DKQGR--------TVDFKNTLFIMTGNFGSEK 129

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1176162545 255 KTIASRMRAnvigyaskntqehiDKDNMLQYVAPPDLKKYGLIPEIVGRLPVV 307
Cdd:pfam07724 130 ISDASRLGD--------------SPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 313-403 1.04e-17

C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N at the N-terminus as well as AAA and AAA_2.


Pssm-ID: 198154 [Multi-domain]  Cd Length: 90  Bit Score: 77.48  E-value: 1.04e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  313 LGQPALKRILTEPKNALVKQFtklfAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSREL 392
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELILSGELKDG 76

                           90
                   ....*....|..
gi 1176162545  393 -KVTRTYASEKL 403
Cdd:smart01086  77 dTVVVDVDDGEL 88
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 1-402 0e+00

ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 731.08  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   1 MAKATDK---CSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELSAKQPDKyKQFKLLKPAEIKSYIDQYVIGQED 77
Cdd:COG1219     1 MAGDSKKelkCSFCGKSQDEVRKLIAGPGVYICDECVELCNEIIEEELKEEEAEE-ELKKLPKPKEIKAFLDEYVIGQER 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  78 AKRILSVAVYNHYKRISQKgksiDKKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDV 157
Cdd:COG1219    80 AKKVLSVAVYNHYKRLNSG----SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDV 155

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 158 ESILSRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQI 237
Cdd:COG1219   156 ENILLKLLQAADYDVEKAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKHPQQEFIQI 235

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 238 NTENILFISGGAFGGIEKTIASRMRANVIGY-ASKNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQP 316
Cdd:COG1219   236 DTTNILFICGGAFDGLEKIIERRLGKKSIGFgAEVKSKKEKDEGELLKQVEPEDLIKFGLIPEFIGRLPVIATLEELDEE 315

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 317 ALKRILTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTR 396
Cdd:COG1219   316 ALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMYELPSRKDVKKVVITK 395


                  ....*.
gi 1176162545 397 TYASEK 402
Cdd:COG1219   396 EVVEGK 401
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
3-402 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 668.40  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   3 KATDKCSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELsakQPDKYKQFKLLKPAEIKSYIDQYVIGQEDAKRIL 82
Cdd:PRK05342    7 KKLLYCSFCGKSQHEVRKLIAGPGVYICDECIELCNEIIREEL---KEEAVELKELPTPKEIKAHLDQYVIGQERAKKVL 83

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  83 SVAVYNHYKRISQKGKsidkKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDVESILS 162
Cdd:PRK05342   84 SVAVYNHYKRLRHGDK----KDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 163 RLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQINTENI 242
Cdd:PRK05342  160 KLLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNI 239

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 243 LFISGGAFGGIEKTIASRMRANVIGYAS--KNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQPALKR 320
Cdd:PRK05342  240 LFICGGAFDGLEKIIKQRLGKKGIGFGAevKSKKEKRTEGELLKQVEPEDLIKFGLIPEFIGRLPVVATLEELDEEALVR 319

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 321 ILTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTRTYAS 400
Cdd:PRK05342  320 ILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMFELPSREDVEKVVITKEVVE 399


                  ..
gi 1176162545 401 EK 402
Cdd:PRK05342  400 GK 401
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 7-396 4.17e-179

endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction. [Protein fate, Protein folding and stabilization, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273047 [Multi-domain]  Cd Length: 413  Bit Score: 505.07  E-value: 4.17e-179
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545   7 KCSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEELSAKQPDK-----YKQFKLLKPAEIKSYIDQYVIGQEDAKRI 81
Cdd:TIGR00382   9 YCSFCGKSQDEVRKLIAGPGVYICDECIELCHDILEEELGTRKESKeyeeeFELSYLPTPKEIKAHLDEYVIGQEQAKKV 88

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  82 LSVAVYNHYKRISQKgkSIDKKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDVESIL 161
Cdd:TIGR00382  89 LSVAVYNHYKRLNFE--KNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENIL 166

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 162 SRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQINTEN 241
Cdd:TIGR00382 167 LKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQIDTSN 246

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 242 ILFISGGAFGGIEKTIASRMRANVIGYASKNTQEHIDKDNMLQYVAPPDLKKYGLIPEIVGRLPVVTYLHPLGQPALKRI 321
Cdd:TIGR00382 247 ILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKSKEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEEALIAI 326

                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1176162545 322 LTEPKNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRELKVTR 396
Cdd:TIGR00382 327 LTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVMFDLPSLEDLEKVVITK 401
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 59-310 4.59e-155

ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent protease ClpXP. In ClpXP, ClpX ATPase serves to specifically recognize, unfold, and translocate protein substrates into the chamber of ClpP protease for degradation. This RecA-like_ClpX 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: 410905 [Multi-domain]  Cd Length: 251  Bit Score: 437.80  E-value: 4.59e-155
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  59 LKPAEIKSYIDQYVIGQEDAKRILSVAVYNHYKRISQKGKSIDkkkDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVP 138
Cdd:cd19497     1 PTPKEIKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNNLKQKD---DDVELEKSNILLIGPTGSGKTLLAQTLAKILDVP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 139 FAIADATILTEAGYVGEDVESILSRLLQASDYNVAAAEKGIVFIDEIDKISRKSDNPSITRDVSGEGVQQALLKLLEGSI 218
Cdd:cd19497    78 FAIADATTLTEAGYVGEDVENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTV 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 219 VNVPPQGGRKHPEQKMIQINTENILFISGGAFGGIEKTIASRMRANVIGY--ASKNTQEHIDKDNMLQYVAPPDLKKYGL 296
Cdd:cd19497   158 ANVPPQGGRKHPQQEFIQVDTTNILFICGGAFVGLEKIIARRLGKKSLGFgaETSSEKDEKERDELLSKVEPEDLIKFGL 237

                         250
                  ....*....|....
gi 1176162545 297 IPEIVGRLPVVTYL 310
Cdd:cd19497   238 IPEFVGRLPVIVTL 251
hslU PRK05201
ATP-dependent protease ATPase subunit HslU;
59-405 2.19e-54

ATP-dependent protease ATPase subunit HslU;


Pssm-ID: 235364 [Multi-domain]  Cd Length: 443  Bit Score: 186.44  E-value: 2.19e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  59 LKPAEIKSYIDQYVIGQEDAKRILSVAVYNHYKRiSQKGKSIdkkKDDIeIEKsNIIIVGETGTGKTLLARTIARMLEVP 138
Cdd:PRK05201    4 LTPREIVSELDKYIIGQDDAKRAVAIALRNRWRR-MQLPEEL---RDEV-TPK-NILMIGPTGVGKTEIARRLAKLANAP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 139 FAIADATILTEAGYVGEDVESIL----------------------------SRLLQA---------------SDYN---- 171
Cdd:PRK05201   78 FIKVEATKFTEVGYVGRDVESIIrdlveiavkmvreekrekvrekaeeaaeERILDAllppaknnwgeeeekEEISatrq 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 172 -------------------VAA--------------------------------------------------AEK----- 177
Cdd:PRK05201  158 kfrkklregelddkeieieVAEaapmmeimgppgmeemtiqlqdmfgnlgpkkkkkrklkvkearkilieeeAAKlidme 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 178 -------------GIVFIDEIDKISRKSDNPSitRDVSGEGVQQALLKLLEGSIVNVppqggrKHPeqkmiQINTENILF 244
Cdd:PRK05201  238 eikqeaierveqnGIVFIDEIDKIAARGGSSG--PDVSREGVQRDLLPLVEGSTVST------KYG-----MVKTDHILF 304

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 245 ISGGAFggiektiasrmranvigyaskntqeHIDKdnmlqyvaPPDlkkygLIPEIVGRLPVVTYLHPLGQPALKRILTE 324
Cdd:PRK05201  305 IASGAF-------------------------HVSK--------PSD-----LIPELQGRFPIRVELDALTEEDFVRILTE 346

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 325 PKNALVKQFTKLFAMDGIELSFTDGALE------YMVEKSVDfKLGARGLRSIMEAILNDAMFELPsDSTSRELKVTRTY 398
Cdd:PRK05201  347 PKASLIKQYQALLATEGVTLEFTDDAIRriaeiaYQVNEKTE-NIGARRLHTVMEKLLEDISFEAP-DMSGETVTIDAAY 424


                  ....*..
gi 1176162545 399 ASEKLGK 405
Cdd:PRK05201  425 VDEKLGD 431
HslU COG1220
ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, ...
 59-405 4.51e-51

ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440833 [Multi-domain]  Cd Length: 454  Bit Score: 177.93  E-value: 4.51e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  59 LKPAEIKSYIDQYVIGQEDAKRILSVAVYNHYKRiSQKGKSIdkkKDDIeIEKsNIIIVGETGTGKTLLARTIARMLEVP 138
Cdd:COG1220     4 LTPREIVAELDKYIIGQDEAKRAVAIALRNRWRR-QQLPEEL---RDEI-TPK-NILMIGPTGVGKTEIARRLAKLANAP 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 139 FAIADATILTEAGYVGEDVESIL----------------------------SRLL------------------------- 165
Cdd:COG1220    78 FIKVEATKFTEVGYVGRDVESMIrdlveiavkmvreekmekvrekaeeaaeERILdlllpppkkkagsnnpfeeeeeeee 157

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 166 QASDYN-----------------------------------------------------------------VAAAEK--- 177
Cdd:COG1220   158 EEEEISrtrekfrkklregelddreieieveessspgveimgppgmeemgmnlqdmfgnlmpkkkkkrkvkVKEARKilt 237

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 178 ------------------------GIVFIDEIDKISRKSDNPSItrDVSGEGVQQALLKLLEGSIVNVppqggrKHPeqk 233
Cdd:COG1220   238 qeeaaklidmdevkqeaieraeqnGIIFIDEIDKIASRGGGSGP--DVSREGVQRDLLPIVEGSTVNT------KYG--- 306

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 234 miQINTENILFISGGAFggiektiasrmranvigyaskntqeHIDKdnmlqyvaPPDlkkygLIPEIVGRLPVVTYLHPL 313
Cdd:COG1220   307 --MVKTDHILFIAAGAF-------------------------HVSK--------PSD-----LIPELQGRFPIRVELDSL 346

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 314 GQPALKRILTEPKNALVKQFTKLFAMDGIELSFTDGALE------YMVEKSVDfKLGARGLRSIMEAILNDAMFELPsDS 387
Cdd:COG1220   347 TEEDFVRILTEPKNALTKQYQALLATEGVELEFTDDAIReiaeiaFEVNERTE-NIGARRLHTVMEKLLEDISFEAP-DL 424

                         490
                  ....*....|....*...
gi 1176162545 388 TSRELKVTRTYASEKLGK 405
Cdd:COG1220   425 SGKTVVIDAAYVDEKLGD 442
RecA-like_HslU cd19498
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ...
 60-306 1.63e-45

ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease HslVU. In HslVU, HslU ATPase serves to unfold and translocate protein substrate, and the HslV protease degrades the unfolded proteins. This RecA-like_HslU 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: 410906 [Multi-domain]  Cd Length: 183  Bit Score: 155.23  E-value: 1.63e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  60 KPAEIKSYIDQYVIGQEDAKRILSVAVYNHYKRiSQKGKSIDKkkddiEIEKSNIIIVGETGTGKTLLARTIARMLEVPF 139
Cdd:cd19498     1 TPREIVSELDKYIIGQDEAKRAVAIALRNRWRR-MQLPEELRD-----EVTPKNILMIGPTGVGKTEIARRLAKLAGAPF 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 140 AIADATILTEAGYVGEDVESILSRLLqasdynvaaaeKGIVFIDEIDKISRKSDnpSITRDVSGEGVQQALLKLLEGSIV 219
Cdd:cd19498    75 IKVEATKFTEVGYVGRDVESIIRDLV-----------EGIVFIDEIDKIAKRGG--SSGPDVSREGVQRDLLPIVEGSTV 141

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 220 NVppqggrkhpeqKMIQINTENILFISGGAFggiektiasrmranvigyaskntqeHIDKdnmlqyvaPPDlkkygLIPE 299
Cdd:cd19498   142 ST-----------KYGPVKTDHILFIAAGAF-------------------------HVAK--------PSD-----LIPE 172


                  ....*..
gi 1176162545 300 IVGRLPV 306
Cdd:cd19498   173 LQGRFPI 179
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 110-307 7.93e-36

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: 129.24  E-value: 7.93e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 110 EKSNIIIVGETGTGKTLLARTIARML---EVPFAIADATILTEagyvgedvESILSRLLQASDYNVAAAEKG-------- 178
Cdd:pfam07724   2 PIGSFLFLGPTGVGKTELAKALAELLfgdERALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrr 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 179 ----IVFIDEIDKISRksdnpsitrdvsgeGVQQALLKLLEGSIVNvpPQGGRkhpeqkmiQINTENILFISGGAFGGIE 254
Cdd:pfam07724  74 kpysIVLIDEIEKAHP--------------GVQNDLLQILEGGTLT--DKQGR--------TVDFKNTLFIMTGNFGSEK 129

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1176162545 255 KTIASRMRAnvigyaskntqehiDKDNMLQYVAPPDLKKYGLIPEIVGRLPVV 307
Cdd:pfam07724 130 ISDASRLGD--------------SPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 78-216 5.75e-18

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: 80.40  E-value: 5.75e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  78 AKRILSVAVYNHYKRISQKGKSIDKKKddieieksNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEA--GYVGE 155
Cdd:cd19481     1 LKASLREAVEAPRRGSRLRRYGLGLPK--------GILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKyvGESEK 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1176162545 156 DVESILSRLLQASDynvaaaekGIVFIDEIDKISRKSDNPSITRDVSgeGVQQALLKLLEG 216
Cdd:cd19481    73 NLRKIFERARRLAP--------CILFIDEIDAIGRKRDSSGESGELR--RVLNQLLTELDG 123
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 313-403 1.04e-17

C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilise the functional assembly. The domain is associated with two Clp_N at the N-terminus as well as AAA and AAA_2.


Pssm-ID: 198154 [Multi-domain]  Cd Length: 90  Bit Score: 77.48  E-value: 1.04e-17
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  313 LGQPALKRILTEPKNALVKQFtklfAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSREL 392
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELILSGELKDG 76

                           90
                   ....*....|..
gi 1176162545  393 -KVTRTYASEKL 403
Cdd:smart01086  77 dTVVVDVDDGEL 88
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 73-215 2.98e-14

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: 69.87  E-value: 2.98e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  73 IGQEDAKRILSVAVYNHYKRisqkgksidkkkddieieksNIIIVGETGTGKTLLARTIARML---EVPFAIADATILTE 149
Cdd:cd00009     1 VGQEEAIEALREALELPPPK--------------------NLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLE 60

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1176162545 150 AGYVGEDVESILSRLLQAsdyNVAAAEKGIVFIDEIDKISRksdnpsitrdvsgeGVQQALLKLLE 215
Cdd:cd00009    61 GLVVAELFGHFLVRLLFE---LAEKAKPGVLFIDEIDSLSR--------------GAQNALLRVLE 109
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 114-216 2.78e-13

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: 66.46  E-value: 2.78e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTEaGYVGEDVESILSRLLQASDYNvaaaeKGIVFIDEIDKISRKSD 193
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVGESEKRLRELFEAAKKLA-----PCVIFIDEIDALAGSRG 74

                          90       100
                  ....*....|....*....|...
gi 1176162545 194 NPSitrDVSGEGVQQALLKLLEG 216
Cdd:pfam00004  75 SGG---DSESRRVVNQLLTELDG 94
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 72-216 4.08e-12

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: 67.24  E-value: 4.08e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  72 VIGQEDAKRIL---SVAVYNHYKRISQKGKSIDKKkddieieksnIIIVGETGTGKTLLARTIARMLEVPFAIAD-ATIL 147
Cdd:COG0464   159 LGGLEEVKEELrelVALPLKRPELREEYGLPPPRG----------LLLYGPPGTGKTLLARALAGELGLPLIEVDlSDLV 228

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1176162545 148 teAGYVGEdVESILSRLLQAsdynVAAAEKGIVFIDEIDKISRKSDNpsiTRDVSGEGVQQALLKLLEG 216
Cdd:COG0464   229 --SKYVGE-TEKNLREVFDK----ARGLAPCVLFIDEADALAGKRGE---VGDGVGRRVVNTLLTEMEE 287
zf-C4_ClpX pfam06689
ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the ...
 7-43 7.04e-12

ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type. This presumed zinc binding domain is found at the N-terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. The molecular function of this domain is now known.


Pssm-ID: 461988 [Multi-domain]  Cd Length: 39  Bit Score: 59.47  E-value: 7.04e-12
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1176162545   7 KCSFCGRARNETEILIAGING-NICEGCVEQAKLIIGE 43
Cdd:pfam06689   2 RCSFCGKSEDEVKKLIAGPNGvYICDECVELCYEILEE 39
zf-C4_ClpX smart00994
ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the ...
 7-44 2.79e-11

ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type. This presumed zinc binding domain is found at the N-terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. The molecular function of this domain is now known.


Pssm-ID: 198062 [Multi-domain]  Cd Length: 39  Bit Score: 57.96  E-value: 2.79e-11
                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 1176162545    7 KCSFCGRARNETEILIAGINGNICEGCVEQAKLIIGEE 44
Cdd:smart00994   2 RCSFCGKSESEVRKLIAGPGVYICDECVELCYEILEEE 39
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
72-216 3.08e-11

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 62.98  E-value: 3.08e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  72 VIGQEDAKRILSVAV--YNHYKRISQKGKSIDKkkddieieksNIIIVGETGTGKTLLARTIARMLEVPFAIADAT-ILT 148
Cdd:COG1223     4 VVGQEEAKKKLKLIIkeLRRRENLRKFGLWPPR----------KILFYGPPGTGKTMLAEALAGELKLPLLTVRLDsLIG 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1176162545 149 EagYVGEDVesilSRLLQASDYnvAAAEKGIVFIDEIDKI----SRKSDNPSITRDVSgegvqqALLKLLEG 216
Cdd:COG1223    74 S--YLGETA----RNLRKLFDF--ARRAPCVIFFDEFDAIakdrGDQNDVGEVKRVVN------ALLQELDG 131
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 114-216 4.91e-10

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: 58.07  E-value: 4.91e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPF-AIADATILteAGYVGEDvESILSRLLQASdynvAAAEKGIVFIDEIDKI--SR 190
Cdd:cd19503    37 VLLHGPPGTGKTLLARAVANEAGANFlSISGPSIV--SKYLGES-EKNLREIFEEA----RSHAPSIIFIDEIDALapKR 109

                          90       100
                  ....*....|....*....|....*.
gi 1176162545 191 KSDNPSITRDVsgegVQQaLLKLLEG 216
Cdd:cd19503   110 EEDQREVERRV----VAQ-LLTLMDG 130
ClpB_D2-small pfam10431
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 313-391 2.54e-09

C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, referred to as the D2-small domain, and is a mixed alpha-beta structure. Compared with the D1-small domain (included in AAA, pfam00004) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerization, forming a tight interface with the D2-large domain of a neighbouring subunit and thereby providing enough binding energy to stabilize the functional assembly. The domain is associated with two Clp_N, pfam02861, at the N-terminus as well as AAA, pfam00004 and AAA_2, pfam07724.


Pssm-ID: 463090 [Multi-domain]  Cd Length: 81  Bit Score: 53.56  E-value: 2.54e-09
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1176162545 313 LGQPALKRILTEpknALVKQFTKLFAmDGIELSFTDGALEYMVEKSVDFKLGARGLRSIMEAILNDAMFELPSDSTSRE 391
Cdd:pfam10431   1 LSKEELRKIVDL---QLKELQKRLAE-RGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREIEDPLAEEILSGELKE 75
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 113-237 3.30e-07

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: 49.21  E-value: 3.30e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 113 NIIIVGETGTGKTLLARTIARMLE--VPFAIADATILTEAGYVG---------EDVESILSRllqasdynvAAAEKGIVF 181
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSnrPVFYVQLTRDTTEEDLFGrrnidpggaSWVDGPLVR---------AAREGEIAV 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1176162545 182 IDEIDKISRKsdnpsitrdvsgegVQQALLKLLEGSIVNVPPQGGRKHPEQKMIQI 237
Cdd:pfam07728  72 LDEINRANPD--------------VLNSLLSLLDERRLLLPDGGELVKAAPDGFRL 113
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 114-227 3.93e-07

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: 49.71  E-value: 3.93e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTeAGYVGEDVESILSRLLQASDYNVAaaekgIVFIDEIDKISRKSD 193
Cdd:cd19518    37 VLLHGPPGCGKTMLANAIAGELKVPFLKISATEIV-SGVSGESEEKIRELFDQAISNAPC-----IVFIDEIDAITPKRE 110

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1176162545 194 NPSitRDVSGEGVQQaLLKLLEGsIVNVPPQGGR 227
Cdd:cd19518   111 SAQ--REMERRIVSQ-LLTCMDE-LNNEKTAGGP 140
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 111-191 4.49e-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: 49.29  E-value: 4.49e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  111 KSNIIIVGETGTGKTLLARTIARMLEVP---FAIADATILTEAGYVGEDVESILSRLLQASDYN-----VAAAEK---GI 179
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVLDQLLLIIVGGKKASGSGELrlrlaLALARKlkpDV 81

                           90
                   ....*....|..
gi 1176162545  180 VFIDEIDKISRK 191
Cdd:smart00382  82 LILDEITSLLDA 93
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 114-216 9.35e-07

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 50.39  E-value: 9.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAgYVGEDvESILSRLLQasdynvAAAEKG--IVFIDEIDKISRK 191
Cdd:COG1222   115 VLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSK-YIGEG-ARNVREVFE------LAREKApsIIFIDEIDAIAAR 186

                          90       100
                  ....*....|....*....|....*..
gi 1176162545 192 SDNpSITrdvSGEG--VQQALLKLLEG 216
Cdd:COG1222   187 RTD-DGT---SGEVqrTVNQLLAELDG 209
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 72-191 9.95e-07

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: 48.38  E-value: 9.95e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  72 VIGQEDAKRILSVAVynHYKRISQKGKSIDKKkddieIEKSnIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAg 151
Cdd:cd19501     6 VAGCEEAKEELKEVV--EFLKNPEKFTKLGAK-----IPKG-VLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1176162545 152 YVGEDVESILSRLLQASDYNVAaaekgIVFIDEIDKISRK 191
Cdd:cd19501    77 FVGVGASRVRDLFEQAKKNAPC-----IVFIDEIDAVGRK 111
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 114-216 4.54e-06

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: 48.75  E-value: 4.54e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVGEDvESILSRLLQASDYNVAAaekgIVFIDEIDKISRKS 192
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEAGAYFiSINGPEIMSK--YYGES-EERLREIFKEAEENAPS----IIFIDEIDAIAPKR 287

                          90       100
                  ....*....|....*....|....
gi 1176162545 193 DnpSITRDVSGEGVQQaLLKLLEG 216
Cdd:TIGR01243 288 E--EVTGEVEKRVVAQ-LLTLMDG 308
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 114-216 5.02e-06

ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This subfamily includes the ATPase domains of vacuolar protein sorting-associated protein 4 (VPS4), ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase), Katanin p60 ATPase-containing subunit A1 (KTNA1), Spastin, and Fidgetin-Like 1 (FIGL-1). This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 46.19  E-value: 5.02e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTeAGYVGEDvESILSRLlqasdYNVAAAEK-GIVFIDEIDKI--SR 190
Cdd:cd19509    35 ILLYGPPGTGKTLLARAVASESGSTFFSISASSLV-SKWVGES-EKIVRAL-----FALARELQpSIIFIDEIDSLlsER 107

                          90       100
                  ....*....|....*....|....*.
gi 1176162545 191 KSDNPSITRDVSGEgvqqaLLKLLEG 216
Cdd:cd19509   108 GSGEHEASRRVKTE-----FLVQMDG 128
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 62-215 7.00e-06

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


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 47.47  E-value: 7.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  62 AEIKSYIDQYVIGQEDAKRILSVAVynhykrISQKgksidkkkddieieksNIIIVGETGTGKTLLARTIARMLEVPFAI 141
Cdd:COG0714     4 ARLRAEIGKVYVGQEELIELVLIAL------LAGG----------------HLLLEGVPGVGKTTLAKALARALGLPFIR 61

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 142 ADATI-LTEAGYVGEdvesilsrllqaSDYNVAAAE---------KGIVFIDEIDKISRKsdnpsitrdvsgegVQQALL 211
Cdd:COG0714    62 IQFTPdLLPSDILGT------------YIYDQQTGEfefrpgplfANVLLADEINRAPPK--------------TQSALL 115


                  ....
gi 1176162545 212 KLLE 215
Cdd:COG0714   116 EAME 119
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
114-191 7.19e-06

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 48.11  E-value: 7.19e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAgYVGEDVESILSRLLQASDynvaaAEKGIVFIDEIDKISRK 191
Cdd:PRK10733  188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM-FVGVGASRVRDMFEQAKK-----AAPCIIFIDEIDAVGRQ 259
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 114-214 1.36e-05

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: 45.02  E-value: 1.36e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAgYVGEDvesilSRLLQasDYNVAAAEKG--IVFIDEIDKI--S 189
Cdd:cd19502    40 VLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQK-YIGEG-----ARLVR--ELFEMAREKApsIIFIDEIDAIgaK 111

                          90       100
                  ....*....|....*....|....*
gi 1176162545 190 RKSDNPSITRDvsgegVQQALLKLL 214
Cdd:cd19502   112 RFDSGTGGDRE-----VQRTMLELL 131
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 114-216 1.47e-05

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


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 45.12  E-value: 1.47e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVGEDvESILSRLLQASDYNVAAaekgIVFIDEIDKISRKS 192
Cdd:cd19519    37 ILLYGPPGTGKTLIARAVANETGAFFfLINGPEIMSK--LAGES-ESNLRKAFEEAEKNAPA----IIFIDEIDAIAPKR 109

                          90       100
                  ....*....|....*....|....
gi 1176162545 193 DNpsITRDVSGEGVQQaLLKLLEG 216
Cdd:cd19519   110 EK--THGEVERRIVSQ-LLTLMDG 130
AcoR COG3284
Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];
112-228 1.78e-05

Transcriptional regulator DhaR of acetoin/glycerol metabolism [Transcription];


Pssm-ID: 442514 [Multi-domain]  Cd Length: 625  Bit Score: 46.82  E-value: 1.78e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 112 SNIIIVGETGTGKTLLARTIARMLEV---PF------AIADATILTE-AGYV-----GEDVESILSRLLQASdynvaaae 176
Cdd:COG3284   345 IPVLILGETGTGKELFARAIHAASPRadgPFvavncaAIPEELIESElFGYEpgaftGARRKGRPGKIEQAD-------- 416

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1176162545 177 KGIVFIDEIDkisrksDNPsitrdvsgEGVQQALLKLLEGSIVNvpPQGGRK 228
Cdd:COG3284   417 GGTLFLDEIG------DMP--------LALQARLLRVLQEREVT--PLGGTK 452
AAA_22 pfam13401
AAA domain;
107-194 2.64e-05

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 43.48  E-value: 2.64e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 107 IEIEKSNIIIVGETGTGKTLLARTIARML---EVPFAIADAT--------------ILTEAGYVGEDVESILSRLLQASd 169
Cdd:pfam13401   1 IRFGAGILVLTGESGTGKTTLLRRLLEQLpevRDSVVFVDLPsgtspkdllrallrALGLPLSGRLSKEELLAALQQLL- 79

                          90       100
                  ....*....|....*....|....*
gi 1176162545 170 ynVAAAEKGIVFIDEIDKISRKSDN 194
Cdd:pfam13401  80 --LALAVAVVLIIDEAQHLSLEALE 102
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 298-373 2.91e-05

ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 46.23  E-value: 2.91e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1176162545 298 PEIVGRLPVVTYLHPLGQPALKRILtepkNALVKQFTKLFAMDGIELSFTDGALEYMVEKSVDFKLGARGLRSIME 373
Cdd:COG0542   733 PEFLNRIDEIIVFHPLSKEELRKIV----DLQLKRLRKRLAERGITLELTDAAKDFLAEKGYDPEYGARPLKRAIQ 804
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
66-190 2.93e-05

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 45.51  E-value: 2.93e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  66 SYIDQYvIGQEDAKRILSVAVYNHYKRisqkGKSIDkkkddieieksNIIIVGETGTGKTLLARTIARMLEVPFAIADAT 145
Cdd:PRK00080   22 KSLDEF-IGQEKVKENLKIFIEAAKKR----GEALD-----------HVLLYGPPGLGKTTLANIIANEMGVNIRITSGP 85

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1176162545 146 ILTEAGyvgeDVESILSRLlqasdynvaaaEKG-IVFIDEIDKISR 190
Cdd:PRK00080   86 ALEKPG----DLAAILTNL-----------EEGdVLFIDEIHRLSP 116
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 72-204 4.22e-05

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: 43.82  E-value: 4.22e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  72 VIGQEDAKRILSVAVY------NHYKRISQKGKSIdkkkddieieksniIIVGETGTGKTLLARTIARMLEVPFAIADAT 145
Cdd:cd19522     2 IADLEEAKKLLEEAVVlpmwmpEFFKGIRRPWKGV--------------LMVGPPGTGKTLLAKAVATECGTTFFNVSSS 67

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1176162545 146 ILTeAGYVGEDvESILSRLLQASDYNVAAAekgiVFIDEIDKI-SRK--SDNPSITRDVSGE 204
Cdd:cd19522    68 TLT-SKYRGES-EKLVRLLFEMARFYAPTT----IFIDEIDSIcSRRgtSEEHEASRRVKSE 123
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 114-213 4.84e-05

first of two ATPase domains of NSF and SEC18, and similar ATPase domains; N-ethylmaleimide-sensitive factor (NSF) and Saccharomyces cerevisiae Vesicular-fusion protein Sec18, key factors for eukaryotic trafficking, are ATPases and SNARE disassembly chaperones. NSF/Sec18 activate or prime SNAREs, the terminal catalysts of membrane fusion. Sec18/NSF associates with SNARE complexes through binding Sec17/alpha-SNAP. Sec18 has an N-terminal cap domain and two nucleotide-binding domains (D1 and D2) which form the two rings of the hexameric complex. The hydrolysis of ATP by D1 generates most of the energy necessary to disassemble inactive SNARE bundles, while the D2 ring binds ATP to stabilize the homohexamer. This subfamily includes the first (D1) ATPase domain of NSF/Sec18, 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: 410912 [Multi-domain]  Cd Length: 177  Bit Score: 43.63  E-value: 4.84e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEV--PFAIADATILTEagYVGEDVESILSRLLQA-SDYNVAAAEKG--IVFIDEIDKI 188
Cdd:cd19504    38 ILLYGPPGTGKTLMARQIGKMLNArePKIVNGPEILNK--YVGESEANIRKLFADAeEEQRRLGANSGlhIIIFDEIDAI 115

                          90       100
                  ....*....|....*....|....*...
gi 1176162545 189 SRKSDNpsiTRDVSGEG---VQQALLKL 213
Cdd:cd19504   116 CKQRGS---MAGSTGVHdtvVNQLLSKI 140
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 114-187 4.84e-05

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: 43.51  E-value: 4.84e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTeAGYVGEDvESILSRLLQASDynvaAAEKGIVFIDEIDK 187
Cdd:cd19507    34 LLLVGIQGTGKSLTAKAIAGVWQLPLLRLDMGRLF-GGLVGES-ESRLRQMIQTAE----AIAPCVLWIDEIEK 101
MCM8 cd17759
DNA helicase Mcm8; Mcm8 plays an important role homologous recombination repair. It forms a ...
 96-225 6.06e-05

DNA helicase Mcm8; Mcm8 plays an important role homologous recombination repair. It forms a complex with Mcm9 that is required for homologous recombination (HR) repair induced by DNA interstrand crosslinks (ICLs).


Pssm-ID: 350665 [Multi-domain]  Cd Length: 289  Bit Score: 44.45  E-value: 6.06e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  96 KGKSIDKKKDDIEIEKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGEDVESILSRLLQASDYNVaAA 175
Cdd:cd17759    28 KQKYADDKNRIPIRGDPHVLIVGDPGLGKSQMLQAACNIAPRGVYVCGNTTTTSGLTVTLTKDGRSGDFALEAGALV-LG 106

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1176162545 176 EKGIVFIDEIDKISRKsdnpsitrdvsgegvQQALLKLLEGSIVNVPPQG 225
Cdd:cd17759   107 DQGICGIDEFDKMGSQ---------------HQALLEAMEQQSVSLAKAG 141
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 105-214 1.32e-04

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 43.67  E-value: 1.32e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 105 DDIEIEK-SNIIIVGETGTGKTLLARTIARMlevpfaiADATILTEAG------YVGEDvesilSRLLQasDYNVAAAEK 177
Cdd:PRK03992  158 EEVGIEPpKGVLLYGPPGTGKTLLAKAVAHE-------TNATFIRVVGselvqkFIGEG-----ARLVR--ELFELAREK 223

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 1176162545 178 --GIVFIDEIDKI-SRKSDnpSITrdvSGEG-VQQALLKLL 214
Cdd:PRK03992  224 apSIIFIDEIDAIaAKRTD--SGT---SGDReVQRTLMQLL 259
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 72-187 1.48e-04

Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_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: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 42.16  E-value: 1.48e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  72 VIGQEDAKRILSVAVynhykRISQKGKSiDKKKDDIeieksNIIIVGETGTGKTLLARTIARMLevpFAIADATI----- 146
Cdd:cd19499    13 VVGQDEAVKAVSDAI-----RRARAGLS-DPNRPIG-----SFLFLGPTGVGKTELAKALAELL---FGDEDNLIridms 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1176162545 147 ----------LTEA--GYVGEDVESILSRLLQASDYNVaaaekgiVFIDEIDK 187
Cdd:cd19499    79 eymekhsvsrLIGAppGYVGYTEGGQLTEAVRRKPYSV-------VLLDEIEK 124
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
112-194 2.01e-04

Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 43.30  E-value: 2.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 112 SNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEagYV---GEDVE-SILSRLLQASDYNVAAAEKG--------- 178
Cdd:COG1474    52 SNVLIYGPTGTGKTAVAKYVLEELEEEAEERGVDVRVV--YVncrQASTRyRVLSRILEELGSGEDIPSTGlstdelfdr 129

                          90       100
                  ....*....|....*....|....*...
gi 1176162545 179 ------------IVFIDEIDKISRKSDN 194
Cdd:COG1474   130 lyealderdgvlVVVLDEIDYLVDDEGD 157
ftsH CHL00176
cell division protein; Validated
 114-191 2.38e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 43.50  E-value: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFaiadatiLTEAGyvGEDVESILSrllqasdynVAAA------EKG------IVF 181
Cdd:CHL00176  219 VLLVGPPGTGKTLLAKAIAGEAEVPF-------FSISG--SEFVEMFVG---------VGAArvrdlfKKAkenspcIVF 280

                          90
                  ....*....|
gi 1176162545 182 IDEIDKISRK 191
Cdd:CHL00176  281 IDEIDAVGRQ 290
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 112-185 2.64e-04

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 42.76  E-value: 2.64e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1176162545 112 SNIIIVGETGTGKTLLARTIARMLEVPFAIADATIlteAGyVgEDVESILSRLLQASDYNvaaaEKGIVFIDEI 185
Cdd:PRK13342   37 SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVT---SG-V-KDLREVIEEARQRRSAG----RRTILFIDEI 101
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 111-213 2.72e-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: 2.72e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 111 KSNIIIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVG---EDVESILSRllqasdynVAAAEKGIVFIDEID 186
Cdd:cd19526    27 RSGILLYGPPGCGKTLLASAIASECGLNFiSVKGPELLNK--YIGaseQNVRDLFSR--------AQSAKPCILFFDEFD 96

                          90       100
                  ....*....|....*....|....*....
gi 1176162545 187 KIS--RKSDNPSITRDVsgegVQQALLKL 213
Cdd:cd19526    97 SIApkRGHDSTGVTDRV----VNQLLTQL 121
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 110-213 6.23e-04

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: 40.19  E-value: 6.23e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 110 EKSNIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAgYVGEDVESILSRLLQASDynvaaAEKGIVFIDEIDKIS 189
Cdd:cd19527    25 KRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINM-YIGESEANVREVFQKARD-----AKPCVIFFDELDSLA 98

                          90       100
                  ....*....|....*....|....
gi 1176162545 190 RKSDNPSITRDVSGEGVQQALLKL 213
Cdd:cd19527    99 PSRGNSGDSGGVMDRVVSQLLAEL 122
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 114-216 7.01e-04

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 39.96  E-value: 7.01e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVGEDvESILSRLLQASdynvAAAEKGIVFIDEIDKI-SRK 191
Cdd:cd19511    30 VLLYGPPGCGKTLLAKALASEAGLNFiSVKGPELFSK--YVGES-ERAVREIFQKA----RQAAPCIIFFDEIDSLaPRR 102

                          90       100
                  ....*....|....*....|....*
gi 1176162545 192 SDNPSITrdvSGEGVQQALLKLLEG 216
Cdd:cd19511   103 GQSDSSG---VTDRVVSQLLTELDG 124
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 114-193 8.77e-04

ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. 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: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 39.97  E-value: 8.77e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTeAGYVGEDvESILSRLLQASDYNVAAaekgIVFIDEIDK-ISRKS 192
Cdd:cd19525    58 ILLFGPPGTGKTLIGKCIASQSGATFFSISASSLT-SKWVGEG-EKMVRALFSVARCKQPA----VIFIDEIDSlLSQRG 131


                  .
gi 1176162545 193 D 193
Cdd:cd19525   132 E 132
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 105-214 1.02e-03

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 41.30  E-value: 1.02e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 105 DDIEIEK-SNIIIVGETGTGKTLLARTIARMlevpfaiADATILTEAG------YVGEDvESILSRLLQASDYNVAAaek 177
Cdd:PTZ00361  210 DDIGIKPpKGVILYGPPGTGKTLLAKAVANE-------TSATFLRVVGseliqkYLGDG-PKLVRELFRVAEENAPS--- 278

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1176162545 178 gIVFIDEIDKISRKSDNPsitrDVSGEG-VQQALLKLL 214
Cdd:PTZ00361  279 -IVFIDEIDAIGTKRYDA----TSGGEKeIQRTMLELL 311
DppD COG0444
ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid ...
 116-157 1.49e-03

ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism, Inorganic ion transport and metabolism];


Pssm-ID: 440213 [Multi-domain]  Cd Length: 320  Bit Score: 40.42  E-value: 1.49e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1176162545 116 IVGETGTGKTLLARTIARMLEvPFAIADATILteagYVGEDV 157
Cdd:COG0444    36 LVGESGSGKSTLARAILGLLP-PPGITSGEIL----FDGEDL 72
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 111-190 1.98e-03

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: 39.08  E-value: 1.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 111 KSNII-IVGETGTGKTLLARTIARMLEVPFA-IADATILTEA-------GYVGedveSILSRLLQAsdYNVAAAEKGIVF 181
Cdd:cd19500    36 KGPILcLVGPPGVGKTSLGKSIARALGRKFVrISLGGVRDEAeirghrrTYVG----AMPGRIIQA--LKKAGTNNPVFL 109


                  ....*....
gi 1176162545 182 IDEIDKISR 190
Cdd:cd19500   110 LDEIDKIGS 118
Sigma54_activat pfam00158
Sigma-54 interaction domain;
112-131 2.22e-03

Sigma-54 interaction domain;


Pssm-ID: 425491 [Multi-domain]  Cd Length: 168  Bit Score: 38.54  E-value: 2.22e-03
                          10        20
                  ....*....|....*....|
gi 1176162545 112 SNIIIVGETGTGKTLLARTI 131
Cdd:pfam00158  23 APVLITGESGTGKELFARAI 42
clpA PRK11034
ATP-dependent Clp protease ATP-binding subunit; Provisional
 111-188 2.46e-03

ATP-dependent Clp protease ATP-binding subunit; Provisional


Pssm-ID: 236828 [Multi-domain]  Cd Length: 758  Bit Score: 40.21  E-value: 2.46e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 111 KSNIIIVGETGTGKTLLARTIA-RMLE--VPFAIADATI--------LTEAGYVGeDVESILSRLLQasdyNVAAAEKGI 179
Cdd:PRK11034  207 KNNPLLVGESGVGKTAIAEGLAwRIVQgdVPEVMADCTIysldigslLAGTKYRG-DFEKRFKALLK----QLEQDTNSI 281


                  ....*....
gi 1176162545 180 VFIDEIDKI 188
Cdd:PRK11034  282 LFIDEIHTI 290
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 114-190 2.96e-03

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: 38.17  E-value: 2.96e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYvGEdvesilSRLLQASDYNVAAA-EKGIVFIDEIDKISR 190
Cdd:cd19520    38 VLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWY-GE------SQKLVAAVFSLASKlQPSIIFIDEIDSFLR 108
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 114-181 3.59e-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: 36.81  E-value: 3.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTEA-------GYVGEDV--------------ESILSRLLQASDYNV 172
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARALLKKLGLPKDSVYSRNpdddfwdGYTGQPVviiddfgqnpdgpdEAELIRLVSSTPYPP 80

                          90
                  ....*....|..
gi 1176162545 173 ---AAAEKGIVF 181
Cdd:pfam00910  81 pmaALEEKGTPF 92
RocR COG3829
RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis ...
 112-131 3.66e-03

RocR-type transcriptional regulator, contains PAS, AAA-type ATPase, and DNA-binding Fis domains [Transcription, Signal transduction mechanisms];


Pssm-ID: 443041 [Multi-domain]  Cd Length: 448  Bit Score: 39.37  E-value: 3.66e-03
                          10        20
                  ....*....|....*....|
gi 1176162545 112 SNIIIVGETGTGKTLLARTI 131
Cdd:COG3829   162 STVLILGESGTGKELFARAI 181
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 114-204 3.67e-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: 37.91  E-value: 3.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTeAGYVGEDvESILSRLLQASdynvAAAEKGIVFIDEIDKI--SRK 191
Cdd:cd19524    36 LLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT-SKYVGEG-EKLVRALFAVA----RELQPSIIFIDEVDSLlsERS 109

                          90
                  ....*....|...
gi 1176162545 192 SDNPSITRDVSGE 204
Cdd:cd19524   110 EGEHEASRRLKTE 122
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 114-213 4.31e-03

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


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 37.86  E-value: 4.31e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVGEDVESIlsRLLQASDYNVAAAekgIVFIDEIDKIS--R 190
Cdd:cd19529    30 ILLYGPPGTGKTLLAKAVATESNANFiSVKGPELLSK--WVGESEKAI--REIFRKARQVAPC---VIFFDEIDSIAprR 102

                          90       100
                  ....*....|....*....|...
gi 1176162545 191 KSDNPSitrDVSGEGVQQALLKL 213
Cdd:cd19529   103 GTTGDS---GVTERVVNQLLTEL 122
PRK14021 PRK14021
bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional
 115-151 4.49e-03

bifunctional shikimate kinase/3-dehydroquinate synthase; Provisional


Pssm-ID: 184458 [Multi-domain]  Cd Length: 542  Bit Score: 39.07  E-value: 4.49e-03
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1176162545 115 IIVGETGTGKTLLARTIARMLEVPFAIADATILTEAG 151
Cdd:PRK14021   10 VIIGMMGAGKTRVGKEVAQMMRLPFADADVEIEREIG 46
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 43-191 5.97e-03

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 38.73  E-value: 5.97e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545  43 EELSAKQPDKYKQFKLLKPAEIKSYIDQY-------VIGQEDAKRILSVAVynhykRISQKGKSIDKKkddIEIEK-SNI 114
Cdd:TIGR01243 419 KELKVTMKDFMEALKMVEPSAIREVLVEVpnvrwsdIGGLEEVKQELREAV-----EWPLKHPEIFEK---MGIRPpKGV 490

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1176162545 115 IIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVGEDVESILSRLLQASDynvaaAEKGIVFIDEIDKISRK 191
Cdd:TIGR01243 491 LLFGPPGTGKTLLAKAVATESGANFiAVRGPEILSK--WVGESEKAIREIFRKARQ-----AAPAIIFFDEIDAIAPA 561
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 113-200 6.83e-03

ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase domains; ATPase AAA-domain protein 3 (ATAD3) is a ubiquitously expressed mitochondrial protein involved in mitochondrial dynamics, DNA-nucleoid structural organization, cholesterol transport and steroidogenesis. The ATAD3 gene family in human comprises three paralog genes: ATAD3A, ATAD3B and ATAD3C. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 37.12  E-value: 6.83e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 113 NIIIVGETGTGKTLLARTIARMLEVPFAIADATILTEAGYVGedvesiLSRLLQASDYNVAAAEKGIVFIDEIDKISRKS 192
Cdd:cd19512    24 NILFYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREG------VTAIHKVFDWANTSRRGLLLFVDEADAFLRKR 97


                  ....*...
gi 1176162545 193 DNPSITRD 200
Cdd:cd19512    98 STEKISED 105
TIGR02928 TIGR02928
orc1/cdc6 family replication initiation protein; Members of this protein family are found ...
 112-193 7.89e-03

orc1/cdc6 family replication initiation protein; Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 274354 [Multi-domain]  Cd Length: 365  Bit Score: 38.00  E-value: 7.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 112 SNIIIVGETGTGKTLLARTIARMLE-------VPFAI-------------ADATILTEAGYVGEDV-ESILS-----RLL 165
Cdd:TIGR02928  41 SNVFIYGKTGTGKTAVTKYVMKELEeaaedrdVRVVTvyvncqildtlyqVLVELANQLRGSGEEVpTTGLStsevfRRL 120

                          90       100       110
                  ....*....|....*....|....*....|
gi 1176162545 166 qasdYNVAAAEKGIVFI--DEIDKISRKSD 193
Cdd:TIGR02928 121 ----YKELNERGDSLIIvlDEIDYLVGDDD 146
ABC_NikE_OppD_transporters cd03257
ATP-binding cassette domain of nickel/oligopeptides specific transporters; The ABC transporter ...
 106-166 8.29e-03

ATP-binding cassette domain of nickel/oligopeptides specific transporters; The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.


Pssm-ID: 213224 [Multi-domain]  Cd Length: 228  Bit Score: 37.49  E-value: 8.29e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1176162545 106 DIEIEKSNII-IVGETGTGKTLLARTIARMLevpfAIADATILteagYVGEDVESILSRLLQ 166
Cdd:cd03257    25 SFSIKKGETLgLVGESGSGKSTLARAILGLL----KPTSGSII----FDGKDLLKLSRRLRK 78
ycf46 CHL00195
Ycf46; Provisional
 114-194 8.32e-03

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 38.46  E-value: 8.32e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 114 IIIVGETGTGKTLLARTIARMLEVPFAIADATILTeAGYVGEDvESILSRLLQASDynvaAAEKGIVFIDEIDKISRKSD 193
Cdd:CHL00195  262 LLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLF-GGIVGES-ESRMRQMIRIAE----ALSPCILWIDEIDKAFSNSE 335


                  .
gi 1176162545 194 N 194
Cdd:CHL00195  336 S 336
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 112-196 8.37e-03

ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein sorting-associated protein 4 (Vps4) is believed to be involved in intracellular protein transport out of a prevacuolar endosomal compartment. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 37.15  E-value: 8.37e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1176162545 112 SNIIIVGETGTGKTLLARTIARMLEVPF-AIADATILTEagYVGEDvESILSRLLQASDYNvaaaEKGIVFIDEIDKI-S 189
Cdd:cd19521    41 SGILLYGPPGTGKSYLAKAVATEANSTFfSVSSSDLVSK--WMGES-EKLVKQLFAMAREN----KPSIIFIDEVDSLcG 113


                  ....*..
gi 1176162545 190 RKSDNPS 196
Cdd:cd19521   114 TRGEGES 120
 
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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