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Conserved domains on  [gi|1207180118|ref|XP_021333146|]
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caseinolytic mitochondrial matrix peptidase chaperone subunit Xa isoform X1 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ClpX super family cl34188
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 161-596 0e+00

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


The actual alignment was detected with superfamily member COG1219:

Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 537.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:COG1219    66 IKAFLDEYVIGQERAKKVLSVAVYNHYKRLNSG----------------------------------------------- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevlDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:COG1219    99 -------------------------SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGE 396
Cdd:COG1219   154 DVENILLKLLQAADYDVEKAERGIIYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQE 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 397 TVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnmgkgrraaaaadlanttggEVDAVAEIEEKDrLLKHVEAR 476
Cdd:COG1219   232 FIQIDTTNILFICGGAFDGLEKIIERRLGKKSIGFGA----------------------EVKSKKEKDEGE-LLKQVEPE 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 477 DLIEFGMIPEFVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLR 556
Cdd:COG1219   289 DLIKFGLIPEFIGRLPVIATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLR 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 1207180118 557 SIMEKLLLDPMFEVP-HSDIVSVDVSKDVVQGKAPPQYIRA 596
Cdd:COG1219   369 SILEEILLDVMYELPsRKDVKKVVITKEVVEGKAKPILVYK 409
DnaC super family cl43430
DNA replication protein DnaC [Replication, recombination and repair];
200-297 4.73e-04

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


The actual alignment was detected with superfamily member COG1484:

Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 42.08  E-value: 4.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 200 QQQVEVEKQASLTPREL-------ELRRREDEyRFTKLLQIAGIsPHGNALGA---SMQQQLNQQTPPEKRGGEVLDsth 269
Cdd:COG1484    23 DELLAQAACDELSYEEFlallleaEVAEREQR-RIERRLKAARF-PAAKTLEDfdfDAQPGLDRRQILELATLDFIE--- 97

                          90       100
                  ....*....|....*....|....*...
gi 1207180118 270 tdiklEKSNIVLLGPTGSGKTLLAQTLA 297
Cdd:COG1484    98 -----RGENLILLGPPGTGKTHLAIALG 120
Zn-ribbon super family cl02609
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 93-121 7.61e-03

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


The actual alignment was detected with superfamily member cd00656:

Pssm-ID: 445850  Cd Length: 45  Bit Score: 34.60  E-value: 7.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207180118  93 RCPKCGdpctHVETFV----------SSTRFVKCEKCHH 121
Cdd:cd00656     8 TCPKCG----HDEAYWwmlqtrsadePPTRFYKCTKCGH 42
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 161-596 0e+00

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 537.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:COG1219    66 IKAFLDEYVIGQERAKKVLSVAVYNHYKRLNSG----------------------------------------------- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevlDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:COG1219    99 -------------------------SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGE 396
Cdd:COG1219   154 DVENILLKLLQAADYDVEKAERGIIYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQE 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 397 TVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnmgkgrraaaaadlanttggEVDAVAEIEEKDrLLKHVEAR 476
Cdd:COG1219   232 FIQIDTTNILFICGGAFDGLEKIIERRLGKKSIGFGA----------------------EVKSKKEKDEGE-LLKQVEPE 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 477 DLIEFGMIPEFVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLR 556
Cdd:COG1219   289 DLIKFGLIPEFIGRLPVIATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLR 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 1207180118 557 SIMEKLLLDPMFEVP-HSDIVSVDVSKDVVQGKAPPQYIRA 596
Cdd:COG1219   369 SILEEILLDVMYELPsRKDVKKVVITKEVVEGKAKPILVYK 409
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
161-599 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 533.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:PRK05342   65 IKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHG----------------------------------------------- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevlDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:PRK05342   98 -------------------------DKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGE 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGE 396
Cdd:PRK05342  153 DVENILLKLLQAADYDVEKAQRGIVYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVASVPPQGGRKhPQQE 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 397 TVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnmgkgrraaaaadlanttggEVDAVAEIEEKDRLLKHVEAR 476
Cdd:PRK05342  231 FIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGA----------------------EVKSKKEKRTEGELLKQVEPE 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 477 DLIEFGMIPEFVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLR 556
Cdd:PRK05342  289 DLIKFGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLR 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....
gi 1207180118 557 SIMEKLLLDPMFEVP-HSDIVSVDVSKDVVQGKAPPQYIRAAAK 599
Cdd:PRK05342  369 SILEEILLDVMFELPsREDVEKVVITKEVVEGKAKPLLIYREKS 412
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 91-571 2.68e-137

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: 406.85  E-value: 2.68e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118  91 QLRCPKCGDPCTHVETFVSSTRFVKCEKChhffVVLSETDTKKSLSKDPESaaEAVKLAFQQKPPPPPKKIFAYLDKYVV 170
Cdd:TIGR00382   7 TLYCSFCGKSQDEVRKLIAGPGVYICDEC----IELCHDILEEELGTRKES--KEYEEEFELSYLPTPKEIKAHLDEYVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 171 GQDHAKKVLSVAVYNHYKRIynnmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphgnalgasmqqq 250
Cdd:TIGR00382  81 GQEQAKKVLSVAVYNHYKRL------------------------------------------------------------ 100

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 251 lnqqtppekrGGEVLDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLL 330
Cdd:TIGR00382 101 ----------NFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLL 170

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 331 QDANYVIEKAQQGIVFLDEVDKIGSV---PGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRKL-RGETVQVDTTNIL 406
Cdd:TIGR00382 171 QAADYDVEKAQKGIIYIDEIDKISRKsenPSI--TRDVSGEGVQQALLKIIEGTVANVPPQGGRKHpYQEFIQIDTSNIL 248

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 407 FVASGAFNGLDRIISRRKNEKYLGFGTPsNMGKgrraaaaadlanttggevdavaeIEEKDRLLKHVEARDLIEFGMIPE 486
Cdd:TIGR00382 249 FICGGAFVGLEKIIKKRTGKSSIGFGAE-VKKK-----------------------SKEKADLLRQVEPEDLVKFGLIPE 304

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 487 FVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLRSIMEKLLLDP 566
Cdd:TIGR00382 305 FIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDV 384


                  ....*
gi 1207180118 567 MFEVP 571
Cdd:TIGR00382 385 MFDLP 389
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 161-497 3.02e-137

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: 400.44  E-value: 3.02e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:cd19497     6 IKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNN----------------------------------------------- 38

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevLDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:cd19497    39 ------------------------LKQKDDDVELEKSNILLIGPTGSGKTLLAQTLAKILDVPFAIADATTLTEAGYVGE 94

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKIGSVPG-IHQLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGETV 398
Cdd:cd19497    95 DVENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSEnPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEFI 174

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 399 QVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTPSNmgkgrraaaaadlanttggevdAVAEIEEKDRLLKHVEARDL 478
Cdd:cd19497   175 QVDTTNILFICGGAFVGLEKIIARRLGKKSLGFGAETS----------------------SEKDEKERDELLSKVEPEDL 232

                         330
                  ....*....|....*....
gi 1207180118 479 IEFGMIPEFVGRLPVVVPL 497
Cdd:cd19497   233 IKFGLIPEFVGRLPVIVTL 251
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 275-494 1.22e-30

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: 117.68  E-value: 1.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 275 EKSNIVLLGPTGSGKTLLAQTLAKCLDV---PFAICDCTTLTQagyvgediESVIAKLLQDANYVIEKAQQG-------- 343
Cdd:pfam07724   2 PIGSFLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrr 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 344 ----IVFLDEVDKIGSvpgihqlrdvggeGVQQGLLKLLEGTIVNVpekntrklrGETVQVDTTNILFVASGAFNGLDRI 419
Cdd:pfam07724  74 kpysIVLIDEIEKAHP-------------GVQNDLLQILEGGTLTD---------KQGRTVDFKNTLFIMTGNFGSEKIS 131

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207180118 420 ISRRKNekylgfgtpsnmgkgrraaaaadlanttggevdavaeiEEKDRLLKHVEARDLIEFGMIPEFVGRLPVV 494
Cdd:pfam07724 132 DASRLG--------------------------------------DSPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 500-571 5.34e-20

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: 84.80  E-value: 5.34e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207180118  500 LDEETLVRILTEPRNAVVPQYqalfSMDKCELNMTPDALRAIARLALERKTGARGLRSIMEKLLLDPMFEVP 571
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELI 68
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
200-297 4.73e-04

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 42.08  E-value: 4.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 200 QQQVEVEKQASLTPREL-------ELRRREDEyRFTKLLQIAGIsPHGNALGA---SMQQQLNQQTPPEKRGGEVLDsth 269
Cdd:COG1484    23 DELLAQAACDELSYEEFlallleaEVAEREQR-RIERRLKAARF-PAAKTLEDfdfDAQPGLDRRQILELATLDFIE--- 97

                          90       100
                  ....*....|....*....|....*...
gi 1207180118 270 tdiklEKSNIVLLGPTGSGKTLLAQTLA 297
Cdd:COG1484    98 -----RGENLILLGPPGTGKTHLAIALG 120
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 93-121 7.61e-03

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


Pssm-ID: 259791  Cd Length: 45  Bit Score: 34.60  E-value: 7.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207180118  93 RCPKCGdpctHVETFV----------SSTRFVKCEKCHH 121
Cdd:cd00656     8 TCPKCG----HDEAYWwmlqtrsadePPTRFYKCTKCGH 42
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 196-299 7.88e-03

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 38.22  E-value: 7.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 196 AGSRQQQVEVEKQASLTPREL-------ELRRREDEyRFTKLLQIAGIsPHGNALGA---SMQQQLNQQTPPEKRGGEVL 265
Cdd:NF038214   10 ARALEELAEQAAREELSFEEFlallleaELAERENR-RIERRLKRARF-PAAKTLEDfdfTAAPGLDKAQIRELATLDFI 87

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1207180118 266 DsthtdiklEKSNIVLLGPTGSGKTLLAQTLAKC 299
Cdd:NF038214   88 E--------RAENVLLLGPPGTGKTHLAIALGYA 113
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 93-121 8.06e-03

DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441202 [Multi-domain]  Cd Length: 103  Bit Score: 36.46  E-value: 8.06e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207180118  93 RCPKCGdpctHVETFV----------SSTRFVKCEKCHH 121
Cdd:COG1594    64 ICPKCG----NDEAYWwlkqtrsadePETRFFRCTKCGH 98
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 161-596 0e+00

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 537.32  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:COG1219    66 IKAFLDEYVIGQERAKKVLSVAVYNHYKRLNSG----------------------------------------------- 98

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevlDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:COG1219    99 -------------------------SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGE 396
Cdd:COG1219   154 DVENILLKLLQAADYDVEKAERGIIYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQE 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 397 TVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnmgkgrraaaaadlanttggEVDAVAEIEEKDrLLKHVEAR 476
Cdd:COG1219   232 FIQIDTTNILFICGGAFDGLEKIIERRLGKKSIGFGA----------------------EVKSKKEKDEGE-LLKQVEPE 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 477 DLIEFGMIPEFVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLR 556
Cdd:COG1219   289 DLIKFGLIPEFIGRLPVIATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLR 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|.
gi 1207180118 557 SIMEKLLLDPMFEVP-HSDIVSVDVSKDVVQGKAPPQYIRA 596
Cdd:COG1219   369 SILEEILLDVMYELPsRKDVKKVVITKEVVEGKAKPILVYK 409
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
161-599 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 533.58  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:PRK05342   65 IKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHG----------------------------------------------- 97

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevlDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:PRK05342   98 -------------------------DKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGE 152

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGE 396
Cdd:PRK05342  153 DVENILLKLLQAADYDVEKAQRGIVYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVASVPPQGGRKhPQQE 230

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 397 TVQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnmgkgrraaaaadlanttggEVDAVAEIEEKDRLLKHVEAR 476
Cdd:PRK05342  231 FIQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGA----------------------EVKSKKEKRTEGELLKQVEPE 288

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 477 DLIEFGMIPEFVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLR 556
Cdd:PRK05342  289 DLIKFGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLR 368

                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....
gi 1207180118 557 SIMEKLLLDPMFEVP-HSDIVSVDVSKDVVQGKAPPQYIRAAAK 599
Cdd:PRK05342  369 SILEEILLDVMFELPsREDVEKVVITKEVVEGKAKPLLIYREKS 412
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 91-571 2.68e-137

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: 406.85  E-value: 2.68e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118  91 QLRCPKCGDPCTHVETFVSSTRFVKCEKChhffVVLSETDTKKSLSKDPESaaEAVKLAFQQKPPPPPKKIFAYLDKYVV 170
Cdd:TIGR00382   7 TLYCSFCGKSQDEVRKLIAGPGVYICDEC----IELCHDILEEELGTRKES--KEYEEEFELSYLPTPKEIKAHLDEYVI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 171 GQDHAKKVLSVAVYNHYKRIynnmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphgnalgasmqqq 250
Cdd:TIGR00382  81 GQEQAKKVLSVAVYNHYKRL------------------------------------------------------------ 100

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 251 lnqqtppekrGGEVLDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLL 330
Cdd:TIGR00382 101 ----------NFEKNKKSDNGVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLL 170

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 331 QDANYVIEKAQQGIVFLDEVDKIGSV---PGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRKL-RGETVQVDTTNIL 406
Cdd:TIGR00382 171 QAADYDVEKAQKGIIYIDEIDKISRKsenPSI--TRDVSGEGVQQALLKIIEGTVANVPPQGGRKHpYQEFIQIDTSNIL 248

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 407 FVASGAFNGLDRIISRRKNEKYLGFGTPsNMGKgrraaaaadlanttggevdavaeIEEKDRLLKHVEARDLIEFGMIPE 486
Cdd:TIGR00382 249 FICGGAFVGLEKIIKKRTGKSSIGFGAE-VKKK-----------------------SKEKADLLRQVEPEDLVKFGLIPE 304

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 487 FVGRLPVVVPLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALERKTGARGLRSIMEKLLLDP 566
Cdd:TIGR00382 305 FIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDV 384


                  ....*
gi 1207180118 567 MFEVP 571
Cdd:TIGR00382 385 MFDLP 389
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 161-497 3.02e-137

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: 400.44  E-value: 3.02e-137
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIYNNmpagsrqqqvevekqasltprelelrrredeyrftkllqiagisphg 240
Cdd:cd19497     6 IKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNN----------------------------------------------- 38

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevLDSTHTDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:cd19497    39 ------------------------LKQKDDDVELEKSNILLIGPTGSGKTLLAQTLAKILDVPFAIADATTLTEAGYVGE 94

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDANYVIEKAQQGIVFLDEVDKIGSVPG-IHQLRDVGGEGVQQGLLKLLEGTIVNVPEKNTRK-LRGETV 398
Cdd:cd19497    95 DVENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSEnPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEFI 174

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 399 QVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTPSNmgkgrraaaaadlanttggevdAVAEIEEKDRLLKHVEARDL 478
Cdd:cd19497   175 QVDTTNILFICGGAFVGLEKIIARRLGKKSLGFGAETS----------------------SEKDEKERDELLSKVEPEDL 232

                         330
                  ....*....|....*....
gi 1207180118 479 IEFGMIPEFVGRLPVVVPL 497
Cdd:cd19497   233 IKFGLIPEFVGRLPVIVTL 251
hslU PRK05201
ATP-dependent protease ATPase subunit HslU;
161-571 2.54e-40

ATP-dependent protease ATPase subunit HslU;


Pssm-ID: 235364 [Multi-domain]  Cd Length: 443  Bit Score: 152.92  E-value: 2.54e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRiynnmpagsrqQQVEvekqasltpreLELRrreDEyrftkllqiagISPhg 240
Cdd:PRK05201    9 IVSELDKYIIGQDDAKRAVAIALRNRWRR-----------MQLP-----------EELR---DE-----------VTP-- 50

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevldsthtdikleKsNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:PRK05201   51 -----------------------------------K-NILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGR 94

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVI-------------------------------------------------------------------------- 326
Cdd:PRK05201   95 DVESIIrdlveiavkmvreekrekvrekaeeaaeerildallppaknnwgeeeekeeisatrqkfrkklregelddkeie 174

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 327 --------------------------------------------------------AKLL------QDAnyvIEKAQQ-G 343
Cdd:PRK05201  175 ievaeaapmmeimgppgmeemtiqlqdmfgnlgpkkkkkrklkvkearkilieeeaAKLIdmeeikQEA---IERVEQnG 251

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 344 IVFLDEVDKIGSVPGIHQlRDVGGEGVQQGLLKLLEGTIVNvpeknTRklRGetvQVDTTNILFVASGAFNgldriISRr 423
Cdd:PRK05201  252 IVFIDEIDKIAARGGSSG-PDVSREGVQRDLLPLVEGSTVS-----TK--YG---MVKTDHILFIASGAFH-----VSK- 314

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 424 knekylgfgtPSnmgkgrraaaaadlanttggevdavaeieekdrllkhvearDLIefgmiPEFVGRLPVVVPLHSLDEE 503
Cdd:PRK05201  315 ----------PS-----------------------------------------DLI-----PELQGRFPIRVELDALTEE 338

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207180118 504 TLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALE--RKT---GARGLRSIMEKLLLDPMFEVP 571
Cdd:PRK05201  339 DFVRILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQvnEKTeniGARRLHTVMEKLLEDISFEAP 411
HslU COG1220
ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, ...
 337-571 6.71e-38

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


Pssm-ID: 440833 [Multi-domain]  Cd Length: 454  Bit Score: 145.96  E-value: 6.71e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 337 IEKAQQ-GIVFLDEVDKIGSvPGIHQLRDVGGEGVQQGLLKLLEGTIVNvpeknTRklRGetvQVDTTNILFVASGAFNg 415
Cdd:COG1220   255 IERAEQnGIIFIDEIDKIAS-RGGGSGPDVSREGVQRDLLPIVEGSTVN-----TK--YG---MVKTDHILFIAAGAFH- 322

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 416 ldriISRrknekylgfgtPSnmgkgrraaaaaDLanttggevdavaeieekdrllkhveardliefgmIPEFVGRLPVVV 495
Cdd:COG1220   323 ----VSK-----------PS------------DL----------------------------------IPELQGRFPIRV 341

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 496 PLHSLDEETLVRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLALE--RKT---GARGLRSIMEKLLLDPMFEV 570
Cdd:COG1220   342 ELDSLTEEDFVRILTEPKNALTKQYQALLATEGVELEFTDDAIREIAEIAFEvnERTeniGARRLHTVMEKLLEDISFEA 421


                  .
gi 1207180118 571 P 571
Cdd:COG1220   422 P 422
RecA-like_HslU cd19498
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ...
 161-414 1.02e-31

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: 121.33  E-value: 1.02e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRiynnmpagsrqQQVEVEKQASLTPRelelrrredeyrftkllqiagisphg 240
Cdd:cd19498     5 IVSELDKYIIGQDEAKRAVAIALRNRWRR-----------MQLPEELRDEVTPK-------------------------- 47

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevldsthtdikleksNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:cd19498    48 -------------------------------------NILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEVGYVGR 90

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLqdanyviekaqQGIVFLDEVDKIGSVPGIHQlRDVGGEGVQQGLLKLLEGTIVNVpekntrklrgETVQV 400
Cdd:cd19498    91 DVESIIRDLV-----------EGIVFIDEIDKIAKRGGSSG-PDVSREGVQRDLLPIVEGSTVST----------KYGPV 148

                         250
                  ....*....|....
gi 1207180118 401 DTTNILFVASGAFN 414
Cdd:cd19498   149 KTDHILFIAAGAFH 162
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 275-494 1.22e-30

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: 117.68  E-value: 1.22e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 275 EKSNIVLLGPTGSGKTLLAQTLAKCLDV---PFAICDCTTLTQagyvgediESVIAKLLQDANYVIEKAQQG-------- 343
Cdd:pfam07724   2 PIGSFLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrr 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 344 ----IVFLDEVDKIGSvpgihqlrdvggeGVQQGLLKLLEGTIVNVpekntrklrGETVQVDTTNILFVASGAFNGLDRI 419
Cdd:pfam07724  74 kpysIVLIDEIEKAHP-------------GVQNDLLQILEGGTLTD---------KQGRTVDFKNTLFIMTGNFGSEKIS 131

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207180118 420 ISRRKNekylgfgtpsnmgkgrraaaaadlanttggevdavaeiEEKDRLLKHVEARDLIEFGMIPEFVGRLPVV 494
Cdd:pfam07724 132 DASRLG--------------------------------------DSPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
hslU TIGR00390
ATP-dependent protease HslVU, ATPase subunit; This model represents the ATPase subunit of ...
 161-571 6.21e-29

ATP-dependent protease HslVU, ATPase subunit; This model represents the ATPase subunit of HslVU, while the proteasome-related peptidase subunit is HslV. Residues 54-61 of the model contain a P-loop ATP-binding motif. Cys-287 of E. coli (position 308 in the seed alignment) is Ser in other members of the seed alignment. [Protein fate, Protein folding and stabilization]


Pssm-ID: 273052 [Multi-domain]  Cd Length: 441  Bit Score: 119.92  E-value: 6.21e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 161 IFAYLDKYVVGQDHAKKVLSVAVYNHYKRIynnmpagsrqqQVEVEKQASLTPRelelrrredeyrftkllqiagisphg 240
Cdd:TIGR00390   6 IVAELDKYIIGQDNAKKSVAIALRNRYRRS-----------QLNEELKDEVTPK-------------------------- 48

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 241 nalgasmqqqlnqqtppekrggevldsthtdikleksNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGE 320
Cdd:TIGR00390  49 -------------------------------------NILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGR 91

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 321 DIESVIAKLLQDA--------------------------------------------------------------NYVIE 338
Cdd:TIGR00390  92 DVESMVRDLTDAAvklvkeeaiekvrdraeelaeerivdvllppaknqwgqteqqqepesareafrkklregeldDKEIE 171

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 339 ------------------------------------------------------------------------KAQQ-GIV 345
Cdd:TIGR00390 172 idvsakmpsgieimappgmeemtmqlqslfqnlggqkkkkrklkikdakkaliaeeaaklvdpeeikqeaidAVEQsGII 251

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 346 FLDEVDKIgSVPGIHQLRDVGGEGVQQGLLKLLEGTIVNVPEKntrklrgetvQVDTTNILFVASGAFNgldriISRrkn 425
Cdd:TIGR00390 252 FIDEIDKI-AKKGESSGADVSREGVQRDLLPIVEGSTVNTKYG----------MVKTDHILFIAAGAFQ-----LAK--- 312

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 426 ekylgfgtPSNMgkgrraaaaadlanttggevdavaeieekdrllkhveardliefgmIPEFVGRLPVVVPLHSLDEETL 505
Cdd:TIGR00390 313 --------PSDL----------------------------------------------IPELQGRFPIRVELQALTTDDF 338

                         490       500       510       520       530       540       550
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1207180118 506 VRILTEPRNAVVPQYQALFSMDKCELNMTPDALRAIARLA--LERKT---GARGLRSIMEKLLLDPMFEVP 571
Cdd:TIGR00390 339 ERILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAynVNEKTeniGARRLHTVLERLLEDISFEAP 409
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 500-571 5.34e-20

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: 84.80  E-value: 5.34e-20
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207180118  500 LDEETLVRILTEPRNAVVPQYqalfSMDKCELNMTPDALRAIARLALERKTGARGLRSIMEKLLLDPMFEVP 571
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELI 68
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 276-422 1.09e-15

The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 74.49  E-value: 1.09e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 276 KSNIVLLGPTGSGKTLLAQTLAKCL---DVPFAICDCTTLTQAGYVGEDIESVIAKLLQDANyviEKAQQGIVFLDEVDK 352
Cdd:cd00009    19 PKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELA---EKAKPGVLFIDEIDS 95

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 353 IgsvpgihqlrdvgGEGVQQGLLKLLEGtivnvpEKNTRKLRGETVQVDTTNILFVASGAFNGLDRIISR 422
Cdd:cd00009    96 L-------------SRGAQNALLRVLET------LNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIR 146
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 276-380 4.17e-15

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: 73.09  E-value: 4.17e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 276 KSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEdIESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGS 355
Cdd:cd19481    26 PKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLL-SKYVGE-SEKNLRKIFERA----RRLAPCILFIDEIDAIGR 99

                          90       100
                  ....*....|....*....|....*
gi 1207180118 356 VPGIHQLRDVGGEGVQQgLLKLLEG 380
Cdd:cd19481   100 KRDSSGESGELRRVLNQ-LLTELDG 123
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 279-380 2.34e-11

ATPase family associated with various cellular activities (AAA); AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 61.46  E-value: 2.34e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQaGYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGSVPG 358
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVGES-EKRLRELFEAA----KKLAPCVIFIDEIDALAGSRG 74

                          90       100
                  ....*....|....*....|..
gi 1207180118 359 IHQLRDvgGEGVQQGLLKLLEG 380
Cdd:pfam00004  75 SGGDSE--SRRVVNQLLTELDG 94
ClpB_D2-small pfam10431
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 500-571 4.08e-11

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: 59.34  E-value: 4.08e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1207180118 500 LDEETLVRILTEprnAVVPQYQALFSmDKCELNMTPDALRAIARLALERKTGARGLRSIMEKLLLDPMFEVP 571
Cdd:pfam10431   1 LSKEELRKIVDL---QLKELQKRLAE-RGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREIEDPLAEEI 68
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 279-380 1.65e-10

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: 63.39  E-value: 1.65e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEdIESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGsvPG 358
Cdd:COG0464   194 LLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLV-SKYVGE-TEKNLREVFDKA----RGLAPCVLFIDEADALA--GK 265

                          90       100
                  ....*....|....*....|..
gi 1207180118 359 IHQLRDVGGEGVQQGLLKLLEG 380
Cdd:COG0464   266 RGEVGDGVGRRVVNTLLTEMEE 287
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 276-383 1.27e-08

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: 54.30  E-value: 1.27e-08
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118  276 KSNIVLLGPTGSGKTLLAQTLAKCLDVP---FAICDCTTLTQAGYVGEDIESVI--------AKLLQDANYVIEKAQQGI 344
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVLDQLLLIIVGgkkasgsgELRLRLALALARKLKPDV 81

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 1207180118  345 VFLDEVDKIGSVPGIHQLRDVGGEGVQQGLLKLLEGTIV 383
Cdd:smart00382  82 LILDEITSLLDAEQEALLLLLEELRLLLLLKSEKNLTVI 120
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 279-380 6.46e-08

first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and p97 or VCP metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the first of the two ATPase domains. This subfamily also includes the first of the two ATPase domains of NVL (nuclear VCP-like protein) 2, an isoform of NVL mainly present in the nucleolus, which is involved in ribosome biogenesis, in telomerase assembly and the regulation of telomerase activity, and in pre-rRNA processing. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 52.68  E-value: 6.46e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLtQAGYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGSVPG 358
Cdd:cd19503    37 VLLHGPPGTGKTLLARAVANEAGANFLSISGPSI-VSKYLGES-EKNLREIFEEA----RSHAPSIIFIDEIDALAPKRE 110

                          90       100
                  ....*....|....*....|..
gi 1207180118 359 IHQlRDVGGEGVQQgLLKLLEG 380
Cdd:cd19503   111 EDQ-REVERRVVAQ-LLTLMDG 130
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 485-567 2.79e-06

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


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 50.47  E-value: 2.79e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 485 PEFVGRLPVVVPLHSLDEETLVRI----LTEPRNAVVPQyqalfsmdKCELNMTPDALRAIARLALERKTGARGLRSIME 560
Cdd:COG0542   733 PEFLNRIDEIIVFHPLSKEELRKIvdlqLKRLRKRLAER--------GITLELTDAAKDFLAEKGYDPEYGARPLKRAIQ 804


                  ....*..
gi 1207180118 561 KLLLDPM 567
Cdd:COG0542   805 RELEDPL 811
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 279-378 3.23e-06

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: 47.72  E-value: 3.23e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiesviAKLLQDANYVIEKAQQGIVFLDEVDKIGSvpg 358
Cdd:cd19502    40 VLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQK-YIGEG-----ARLVRELFEMAREKAPSIIFIDEIDAIGA--- 110

                          90       100
                  ....*....|....*....|...
gi 1207180118 359 ihQLRDVGGEG---VQQGLLKLL 378
Cdd:cd19502   111 --KRFDSGTGGdreVQRTMLELL 131
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 279-355 3.35e-06

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 49.62  E-value: 3.35e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGS 355
Cdd:COG1222   115 VLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSK-YIGEG-ARNVREVFELA----REKAPSIIFIDEIDAIAA 185
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 278-422 4.07e-06

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: 46.52  E-value: 4.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 278 NIVLLGPTGSGKTLLAQTLAKcldvpfAICDCTTLTQAGYVG---EDIE-----SVIAKLLQDANYViEKAQQG-IVFLD 348
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAA------ALSNRPVFYVQLTRDtteEDLFgrrniDPGGASWVDGPLV-RAAREGeIAVLD 73

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1207180118 349 EVDKIGSVpgihqlrdvggegVQQGLLKLLEGTIVNVPEkntrklRGETVQVDTTNILFVASGafNGLDRIISR 422
Cdd:pfam07728  74 EINRANPD-------------VLNSLLSLLDERRLLLPD------GGELVKAAPDGFRLIATM--NPLDRGLNE 126
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 279-355 4.18e-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: 47.35  E-value: 4.18e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLLQDANyvieKAQQGIVFLDEVDKIGS 355
Cdd:cd19509    35 ILLYGPPGTGKTLLARAVASESGSTFFSISASSLV-SKWVGES-EKIVRALFALAR----ELQPSIIFIDEIDSLLS 105
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 279-355 1.35e-05

first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL exists in two forms with N-terminal extensions of different lengths in mammalian cells. NVL has two alternatively spliced isoforms, a short form, NVL1, and a long form, NVL2. NVL2, the major species, is mainly present in the nucleolus, whereas NVL1 is nucleoplasmic. Each has an N-terminal domain, followed by two tandem ATPase domains; this subfamily includes the first of the two ATPase domains. NVL2 is involved in the biogenesis of the 60S ribosome subunit by associating specifically with ribosome protein L5 and modulating the function of DOB1. NVL2 is also required for telomerase assembly and the regulation of telomerase activity, and is involved in pre-rRNA processing. The role of NVL1 is unclear. This RecA-like_NVL_r1-like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 45.86  E-value: 1.35e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDIESViakllqdaNYVIEKAQQG---IVFLDEVDKIGS 355
Cdd:cd19518    37 VLLHGPPGCGKTMLANAIAGELKVPFLKISATEIV-SGVSGESEEKI--------RELFDQAISNapcIVFIDEIDAITP 107
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
279-358 5.55e-05

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 46.18  E-value: 5.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFaicdcTTLTQAGYVgEDIESVIAKLLQDANYVIEKAQQGIVFLDEVDKIGSVPG 358
Cdd:PRK10733  188 VLMVGPPGTGKTLLAKAIAGEAKVPF-----FTISGSDFV-EMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG 261
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 279-353 2.01e-04

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: 42.14  E-value: 2.01e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLLQdanyVIEKAQQGIVFLDEVDKI 353
Cdd:cd19524    36 LLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT-SKYVGEG-EKLVRALFA----VARELQPSIIFIDEVDSL 104
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 279-355 2.86e-04

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 41.89  E-value: 2.86e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGS 355
Cdd:cd19511    30 VLLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSK-YVGES-ERAVREIFQKA----RQAAPCIIFFDEIDSLAP 100
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 279-354 3.31e-04

ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc metallopeptidase for both cytoplasmic and membrane proteins. It is anchored to the cytoplasmic membrane such that the amino- and carboxy-termini are exposed to the cytoplasm. It presents a membrane-bound hexameric structure that is able to unfold and degrade protein substrates. It is comprised of an N-terminal transmembrane region and the larger C-terminal cytoplasmic region, which consists of an ATPase domain and a protease domain. This RecA-Like FTsH subfamily represents the ATPase domain, and belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 41.83  E-value: 3.31e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFaicdcttLTQAG------YVGediesVIAKLLQDanyVIEKAQQG---IVFLDE 349
Cdd:cd19501    40 VLLVGPPGTGKTLLAKAVAGEAGVPF-------FSISGsdfvemFVG-----VGASRVRD---LFEQAKKNapcIVFIDE 104


                  ....*
gi 1207180118 350 VDKIG 354
Cdd:cd19501   105 IDAVG 109
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 279-351 3.87e-04

ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ATPase family AAA domain-containing protein 1 (ATAD1, also known as Thorase) is an ATPase that plays a critical role in regulating the surface expression of alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors, thereby regulating synaptic plasticity, learning and memory. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 41.64  E-value: 3.87e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYvGEDiESVIAKLLQDANyvieKAQQGIVFLDEVD 351
Cdd:cd19520    38 VLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWY-GES-QKLVAAVFSLAS----KLQPSIIFIDEID 104
aroK PRK00131
shikimate kinase; Reviewed
 274-304 4.25e-04

shikimate kinase; Reviewed


Pssm-ID: 234654 [Multi-domain]  Cd Length: 175  Bit Score: 41.33  E-value: 4.25e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1207180118 274 LEKSNIVLLGPTGSGKTLLAQTLAKCLDVPF 304
Cdd:PRK00131    2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDF 32
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 279-378 4.47e-04

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 43.22  E-value: 4.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiesviAKLLQDANYVIEKAQQGIVFLDEVDKIGSVpg 358
Cdd:PTZ00361  220 VILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQK-YLGDG-----PKLVRELFRVAEENAPSIVFIDEIDAIGTK-- 291

                          90       100
                  ....*....|....*....|.
gi 1207180118 359 iHQLRDVGGEG-VQQGLLKLL 378
Cdd:PTZ00361  292 -RYDATSGGEKeIQRTMLELL 311
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
200-297 4.73e-04

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 42.08  E-value: 4.73e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 200 QQQVEVEKQASLTPREL-------ELRRREDEyRFTKLLQIAGIsPHGNALGA---SMQQQLNQQTPPEKRGGEVLDsth 269
Cdd:COG1484    23 DELLAQAACDELSYEEFlallleaEVAEREQR-RIERRLKAARF-PAAKTLEDfdfDAQPGLDRRQILELATLDFIE--- 97

                          90       100
                  ....*....|....*....|....*...
gi 1207180118 270 tdiklEKSNIVLLGPTGSGKTLLAQTLA 297
Cdd:COG1484    98 -----RGENLILLGPPGTGKTHLAIALG 120
ftsH CHL00176
cell division protein; Validated
 279-354 4.90e-04

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 43.11  E-value: 4.90e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFaicdcttLTQAG--YVgEDIESVIAKLLQDanyVIEKAQQG---IVFLDEVDKI 353
Cdd:CHL00176  219 VLLVGPPGTGKTLLAKAIAGEAEVPF-------FSISGseFV-EMFVGVGAARVRD---LFKKAKENspcIVFIDEIDAV 287


                  .
gi 1207180118 354 G 354
Cdd:CHL00176  288 G 288
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 277-383 5.93e-04

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 42.76  E-value: 5.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 277 SNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTltqAGyVgEDIESVIAKLLQDANYviekAQQGIVFLDEvdkigsv 356
Cdd:PRK13342   37 SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVT---SG-V-KDLREVIEEARQRRSA----GRRTILFIDE------- 100

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1207180118 357 pgIH-----QlrdvggegvQQGLLKLLE-GTIV 383
Cdd:PRK13342  101 --IHrfnkaQ---------QDALLPHVEdGTIT 122
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 279-353 1.23e-03

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: 40.11  E-value: 1.23e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLtQAGYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKI 353
Cdd:cd19519    37 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-MSKLAGES-ESNLRKAFEEA----EKNAPAIIFIDEIDAI 105
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 279-404 1.72e-03

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 41.43  E-value: 1.72e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLtQAGYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKIGSvpg 358
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEI-MSKYYGES-EERLREIFKEA----EENAPSIIFIDEIDAIAP--- 285

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 1207180118 359 ihQLRDVGGE---GVQQGLLKLLEGTivnvpekntrKLRGETVQVDTTN 404
Cdd:TIGR01243 286 --KREEVTGEvekRVVAQLLTLMDGL----------KGRGRVIVIGATN 322
FlhF COG1419
Flagellar biosynthesis GTPase FlhF [Cell motility];
199-298 2.16e-03

Flagellar biosynthesis GTPase FlhF [Cell motility];


Pssm-ID: 441029 [Multi-domain]  Cd Length: 361  Bit Score: 40.62  E-value: 2.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 199 RQQQVEVEKQASLTPRELELRRRedeyrftklLQIAGISPhgnALGASMQQQLNQQTPPEKRGGEV-------LDSTHTD 271
Cdd:COG1419    92 EQLSGLAGESARLPPELAELLER---------LLEAGVSP---ELARELLEKLPEDLSAEEAWRALlealarrLPVAEDP 159

                          90       100
                  ....*....|....*....|....*..
gi 1207180118 272 IKLEKSNIVLLGPTGSGKTLlaqTLAK 298
Cdd:COG1419   160 LLDEGGVIALVGPTGVGKTT---TIAK 183
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 270-355 2.43e-03

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: 39.59  E-value: 2.43e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 270 TDIKLEKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiesviAKLLQDANYVIEKAQQGIVFLDE 349
Cdd:cd19525    49 TGLRGPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLT-SKWVGEG-----EKMVRALFSVARCKQPAVIFIDE 122


                  ....*.
gi 1207180118 350 VDKIGS 355
Cdd:cd19525   123 IDSLLS 128
NACHT pfam05729
NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in ...
 279-382 2.95e-03

NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in MHC transcription activation. This family is closely related to pfam00931.


Pssm-ID: 428606 [Multi-domain]  Cd Length: 166  Bit Score: 38.83  E-value: 2.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLA---------KCLDVPFAICdCTTLTQAG--------------YVGEDIESVIAKLLqdany 335
Cdd:pfam05729   3 VILQGEAGSGKTTLLQKLAllwaqgklpQGFDFVFFLP-CRELSRSGnarsladllfsqwpEPAAPVSEVWAVIL----- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1207180118 336 viEKAQQGIVFLDEVDKIGSVPGIHQlrdvGGEGVQQGLLKLLEGTI 382
Cdd:pfam05729  77 --ELPERLLLILDGLDELVSDLGQLD----GPCPVLTLLSSLLRKKL 117
MCM8 cd17759
DNA helicase Mcm8; Mcm8 plays an important role homologous recombination repair. It forms a ...
 275-386 3.52e-03

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: 39.82  E-value: 3.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 275 EKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLLQDANYVIeKAQQGIVFLDEVDKIG 354
Cdd:cd17759    42 GDPHVLIVGDPGLGKSQMLQAACNIAPRGVYVCGNTTTTSGLTVTLTKDGRSGDFALEAGALV-LGDQGICGIDEFDKMG 120

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1207180118 355 SvpgihqlrdvggegVQQGLLKLLEGTIVNVP 386
Cdd:cd17759   121 S--------------QHQALLEAMEQQSVSLA 138
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 280-310 3.74e-03

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: 39.77  E-value: 3.74e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1207180118 280 VLL-GPTGSGKTLLAQTLAKCLDVPFAICDCT 310
Cdd:COG0714    34 LLLeGVPGVGKTTLAKALARALGLPFIRIQFT 65
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 274-357 4.39e-03

DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression.


Pssm-ID: 425570 [Multi-domain]  Cd Length: 165  Bit Score: 38.38  E-value: 4.39e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 274 LEKSNIVLLGPTGSGKTL-----LAQTLAKCLDVPFAICDCTT--LTQagyvgeDIESVIAKLLQDANYVIEKAQQGIVF 346
Cdd:pfam00270  12 LEGRDVLVQAPTGSGKTLafllpALEALDKLDNGPQALVLAPTreLAE------QIYEELKKLGKGLGLKVASLLGGDSR 85

                          90
                  ....*....|.
gi 1207180118 347 LDEVDKIGSVP 357
Cdd:pfam00270  86 KEQLEKLKGPD 96
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 279-358 5.07e-03

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: 38.24  E-value: 5.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 279 IVLLGPTGSGKTLLAQTLAKCLDV--PFAICDCTTLTQagYVGEDiESVIAKLLQDANyvIEKAQQG------IVFLDEV 350
Cdd:cd19504    38 ILLYGPPGTGKTLMARQIGKMLNArePKIVNGPEILNK--YVGES-EANIRKLFADAE--EEQRRLGansglhIIIFDEI 112

                          90
                  ....*....|..
gi 1207180118 351 DKI----GSVPG 358
Cdd:cd19504   113 DAIckqrGSMAG 124
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 275-353 6.00e-03

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


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 37.88  E-value: 6.00e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1207180118 275 EKSNIVLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiESVIAKLLQDAnyviEKAQQGIVFLDEVDKI 353
Cdd:cd19527    25 KRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINM-YIGES-EANVREVFQKA----RDAKPCVIFFDELDSL 97
SK cd00464
Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic ...
 278-304 6.90e-03

Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.


Pssm-ID: 238260 [Multi-domain]  Cd Length: 154  Bit Score: 37.54  E-value: 6.90e-03
                          10        20
                  ....*....|....*....|....*..
gi 1207180118 278 NIVLLGPTGSGKTLLAQTLAKCLDVPF 304
Cdd:cd00464     1 NIVLIGMMGAGKTTVGRLLAKALGLPF 27
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 93-121 7.61e-03

C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The homologous C-terminal zinc ribbon domains of subunits A12.2, Rpb9, and C11 in RNA Polymerases (Pol) I, II, and III, respectively are required for intrinsic transcript cleavage. TFS is a related archaeal protein that is involved in RNA cleavage by archaeal polymerase. These proteins have two zinc-binding beta-ribbon domains, N-terminal zinc ribbon (N-ribbon) and C-terminal zinc ribbon (C-ribbon). Transcription Factor IIS (TFIIS) domain III is homologous to the C-ribbon domain that stimulates the weak cleavage activity of Rpb9 for Pol II.


Pssm-ID: 259791  Cd Length: 45  Bit Score: 34.60  E-value: 7.61e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207180118  93 RCPKCGdpctHVETFV----------SSTRFVKCEKCHH 121
Cdd:cd00656     8 TCPKCG----HDEAYWwmlqtrsadePPTRFYKCTKCGH 42
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 196-299 7.88e-03

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 38.22  E-value: 7.88e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 196 AGSRQQQVEVEKQASLTPREL-------ELRRREDEyRFTKLLQIAGIsPHGNALGA---SMQQQLNQQTPPEKRGGEVL 265
Cdd:NF038214   10 ARALEELAEQAAREELSFEEFlallleaELAERENR-RIERRLKRARF-PAAKTLEDfdfTAAPGLDKAQIRELATLDFI 87

                          90       100       110
                  ....*....|....*....|....*....|....
gi 1207180118 266 DsthtdiklEKSNIVLLGPTGSGKTLLAQTLAKC 299
Cdd:NF038214   88 E--------RAENVLLLGPPGTGKTHLAIALGYA 113
RPB9 COG1594
DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; ...
 93-121 8.06e-03

DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]; DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS is part of the Pathway/BioSystem: RNA polymerase


Pssm-ID: 441202 [Multi-domain]  Cd Length: 103  Bit Score: 36.46  E-value: 8.06e-03
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1207180118  93 RCPKCGdpctHVETFV----------SSTRFVKCEKCHH 121
Cdd:COG1594    64 ICPKCG----NDEAYWwlkqtrsadePETRFFRCTKCGH 98
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 280-352 8.10e-03

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: 37.93  E-value: 8.10e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 280 VLLGPTGSGKTLLAQTLAK----------CLDVPFAIC--DCTTLTQA--GYVGEDIESVIAKLLQDANYviekaqqGIV 345
Cdd:cd19499    45 LFLGPTGVGKTELAKALAEllfgdednliRIDMSEYMEkhSVSRLIGAppGYVGYTEGGQLTEAVRRKPY-------SVV 117


                  ....*..
gi 1207180118 346 FLDEVDK 352
Cdd:cd19499   118 LLDEIEK 124
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 280-355 9.59e-03

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 38.66  E-value: 9.59e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1207180118 280 VLL-GPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiesviAKLLQDanyVIEKAQQ---GIVFLDEVDKIGS 355
Cdd:PRK03992  168 VLLyGPPGTGKTLLAKAVAHETNATFIRVVGSELVQK-FIGEG-----ARLVRE---LFELAREkapSIIFIDEIDAIAA 238
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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