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Conserved domains on  [gi|56119122|ref|NP_001007804|]
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ATP-dependent Clp protease ATP-binding subunit clpX-like, mitochondrial precursor [Rattus norvegicus]

Protein Classification

Zn-ribbon and AAA domain-containing protein( domain architecture ID 11641334)

Zn-ribbon and AAA domain-containing protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 172-605 0e+00

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


:

Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 551.96  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:COG1219  66 IKAFLDEYVIGQERAKKVLSVAVYNHYKRLNSG----------------------------------------------- 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 252 algasmqqqgsqqmpqekrggevlDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:COG1219  99 ------------------------SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGED 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGET 407
Cdd:COG1219 155 VENILLKLLQAADYDVEKAERGIIYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEF 232

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 408 VQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnlgkgrraaaaadlanrsgESNTHQDIEEKDrLLRHVEARDL 487
Cdd:COG1219 233 IQIDTTNILFICGGAFDGLEKIIERRLGKKSIGFGA---------------------EVKSKKEKDEGE-LLKQVEPEDL 290

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 488 IEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSI 567
Cdd:COG1219 291 IKFGLIPEFIGRLPVIATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSI 370

                       410       420       430
                ....*....|....*....|....*....|....*....
gi 56119122 568 MEKLLLEPMFEVPN-SDIVCVEVDKEVVEGKKEPGYIRA 605
Cdd:COG1219 371 LEEILLDVMYELPSrKDVKKVVITKEVVEGKAKPILVYK 409
Zn-ribbon super family cl02609
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 104-132 7.72e-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: 7.72e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 56119122 104 RCPKCGdlctHVETFV----------SSTRFVKCEKCHH 132
Cdd:cd00656   8 TCPKCG----HDEAYWwmlqtrsadePPTRFYKCTKCGH 42
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 172-605 0e+00

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 551.96  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:COG1219  66 IKAFLDEYVIGQERAKKVLSVAVYNHYKRLNSG----------------------------------------------- 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 252 algasmqqqgsqqmpqekrggevlDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:COG1219  99 ------------------------SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGED 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGET 407
Cdd:COG1219 155 VENILLKLLQAADYDVEKAERGIIYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEF 232

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 408 VQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnlgkgrraaaaadlanrsgESNTHQDIEEKDrLLRHVEARDL 487
Cdd:COG1219 233 IQIDTTNILFICGGAFDGLEKIIERRLGKKSIGFGA---------------------EVKSKKEKDEGE-LLKQVEPEDL 290

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 488 IEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSI 567
Cdd:COG1219 291 IKFGLIPEFIGRLPVIATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSI 370

                       410       420       430
                ....*....|....*....|....*....|....*....
gi 56119122 568 MEKLLLEPMFEVPN-SDIVCVEVDKEVVEGKKEPGYIRA 605
Cdd:COG1219 371 LEEILLDVMYELPSrKDVKKVVITKEVVEGKAKPILVYK 409
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
172-608 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 547.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:PRK05342  65 IKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHG----------------------------------------------- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  252 algasmqqqgsqqmpqekrggevlDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:PRK05342  98 ------------------------DKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGED 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGET 407
Cdd:PRK05342 154 VENILLKLLQAADYDVEKAQRGIVYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVASVPPQGGRKhPQQEF 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  408 VQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnlgkgrraaaaadlanrsgESNTHQDIEEKDRLLRHVEARDL 487
Cdd:PRK05342 232 IQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGA---------------------EVKSKKEKRTEGELLKQVEPEDL 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  488 IEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSI 567
Cdd:PRK05342 291 IKFGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSI 370

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|..
gi 56119122  568 MEKLLLEPMFEVPN-SDIVCVEVDKEVVEGKKEPGYIRAPSK 608
Cdd:PRK05342 371 LEEILLDVMFELPSrEDVEKVVITKEVVEGKAKPLLIYREKS 412
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 172-506 4.57e-141

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: 410.45  E-value: 4.57e-141
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:cd19497   6 IKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNN----------------------------------------------- 38

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 252 algasmqqqgsqqmpqekrggevLDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:cd19497  39 -----------------------LKQKDDDVELEKSNILLIGPTGSGKTLLAQTLAKILDVPFAIADATTLTEAGYVGED 95

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKIGSVPG-IHQLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGETVQ 409
Cdd:cd19497  96 VENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSEnPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEFIQ 175

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 410 VDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTPSNLgkgrraaaaadlanrsgesntHQDIEEKDRLLRHVEARDLIE 489
Cdd:cd19497 176 VDTTNILFICGGAFVGLEKIIARRLGKKSLGFGAETSS---------------------EKDEKERDELLSKVEPEDLIK 234

                       330
                ....*....|....*..
gi 56119122 490 FGMIPEFVGRLPVVVPL 506
Cdd:cd19497 235 FGLIPEFVGRLPVIVTL 251
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 102-600 1.31e-139

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: 413.01  E-value: 1.31e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   102 QLRCPKCGDLCTHVETFVSSTRFVKCEKCHHFFV-VLSEADSKKSIIKEPESAAEAVKLAFQQKpppppkkIYNYLDKYV 180
Cdd:TIGR00382   7 TLYCSFCGKSQDEVRKLIAGPGVYICDECIELCHdILEEELGTRKESKEYEEEFELSYLPTPKE-------IKAHLDEYV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   181 VGQSFAKKVLSVAVYNHYKRIynNIPANLRQQAEVEkqtsltpreleirrredeyrftkllqiagisphgnalgasmqqq 260
Cdd:TIGR00382  80 IGQEQAKKVLSVAVYNHYKRL--NFEKNKKSDNGVE-------------------------------------------- 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   261 gsqqmpqekrggevldsphddikLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLL 340
Cdd:TIGR00382 114 -----------------------LSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLL 170

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   341 QDANYNVEKAQQGIVFLDEVDKIGSV---PGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRKL-RGETVQVDTTNIL 416
Cdd:TIGR00382 171 QAADYDVEKAQKGIIYIDEIDKISRKsenPSI--TRDVSGEGVQQALLKIIEGTVANVPPQGGRKHpYQEFIQIDTSNIL 248

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   417 FVASGAFNGLDRIISRRKNEKYLGFGTPSNlgkgrraaaaadlanrsgesnthQDIEEKDRLLRHVEARDLIEFGMIPEF 496
Cdd:TIGR00382 249 FICGGAFVGLEKIIKKRTGKSSIGFGAEVK-----------------------KKSKEKADLLRQVEPEDLVKFGLIPEF 305

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   497 VGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPM 576
Cdd:TIGR00382 306 IGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVM 385

                         490       500
                  ....*....|....*....|....*
gi 56119122   577 FEVPN-SDIVCVEVDKEVVEGKKEP 600
Cdd:TIGR00382 386 FDLPSlEDLEKVVITKETVLKQSEP 410
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 285-503 9.12e-32

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: 121.15  E-value: 9.12e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   285 EKSNILLLGPTGSGKTLLAQTLAKCLDV---PFAICDCTTLTQagyvgediESVIAKLLQDANYNVEKAQQG-------- 353
Cdd:pfam07724   2 PIGSFLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrr 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   354 ----IVFLDEVDKIGSvpgihqlrdvggeGVQQGLLKLLEGTIVNVpeknsrklrGETVQVDTTNILFVASGAFNGLDRI 429
Cdd:pfam07724  74 kpysIVLIDEIEKAHP-------------GVQNDLLQILEGGTLTD---------KQGRTVDFKNTLFIMTGNFGSEKIS 131

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56119122   430 ISRRknekylgfgtpsnlgkgrraaaaadlanrsgesnthqDIEEKDRLLRHVEARDLIEFGMIPEFVGRLPVV 503
Cdd:pfam07724 132 DASR-------------------------------------LGDSPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 509-603 1.24e-19

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: 83.65  E-value: 1.24e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122    509 LDEKTLVQILTEPRNAVIPQYqalfSMDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPMFEVPNSDIVcVE 588
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELILSGEL-KD 75

                           90
                   ....*....|....*
gi 56119122    589 VDKEVVEGKKEPGYI 603
Cdd:smart01086  76 GDTVVVDVDDGELVF 90
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 104-132 7.72e-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: 7.72e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 56119122 104 RCPKCGdlctHVETFV----------SSTRFVKCEKCHH 132
Cdd:cd00656   8 TCPKCG----HDEAYWwmlqtrsadePPTRFYKCTKCGH 42
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 172-605 0e+00

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 551.96  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:COG1219  66 IKAFLDEYVIGQERAKKVLSVAVYNHYKRLNSG----------------------------------------------- 98

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 252 algasmqqqgsqqmpqekrggevlDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:COG1219  99 ------------------------SKDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGED 154

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGET 407
Cdd:COG1219 155 VENILLKLLQAADYDVEKAERGIIYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEF 232

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 408 VQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnlgkgrraaaaadlanrsgESNTHQDIEEKDrLLRHVEARDL 487
Cdd:COG1219 233 IQIDTTNILFICGGAFDGLEKIIERRLGKKSIGFGA---------------------EVKSKKEKDEGE-LLKQVEPEDL 290

                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 488 IEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSI 567
Cdd:COG1219 291 IKFGLIPEFIGRLPVIATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSI 370

                       410       420       430
                ....*....|....*....|....*....|....*....
gi 56119122 568 MEKLLLEPMFEVPN-SDIVCVEVDKEVVEGKKEPGYIRA 605
Cdd:COG1219 371 LEEILLDVMYELPSrKDVKKVVITKEVVEGKAKPILVYK 409
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
172-608 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 547.06  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:PRK05342  65 IKAHLDQYVIGQERAKKVLSVAVYNHYKRLRHG----------------------------------------------- 97

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  252 algasmqqqgsqqmpqekrggevlDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:PRK05342  98 ------------------------DKKDDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGED 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKI---GSVPGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGET 407
Cdd:PRK05342 154 VENILLKLLQAADYDVEKAQRGIVYIDEIDKIarkSENPSI--TRDVSGEGVQQALLKILEGTVASVPPQGGRKhPQQEF 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  408 VQVDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTpsnlgkgrraaaaadlanrsgESNTHQDIEEKDRLLRHVEARDL 487
Cdd:PRK05342 232 IQVDTTNILFICGGAFDGLEKIIKQRLGKKGIGFGA---------------------EVKSKKEKRTEGELLKQVEPEDL 290

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  488 IEFGMIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSI 567
Cdd:PRK05342 291 IKFGLIPEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSI 370

                        410       420       430       440
                 ....*....|....*....|....*....|....*....|..
gi 56119122  568 MEKLLLEPMFEVPN-SDIVCVEVDKEVVEGKKEPGYIRAPSK 608
Cdd:PRK05342 371 LEEILLDVMFELPSrEDVEKVVITKEVVEGKAKPLLIYREKS 412
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 172-506 4.57e-141

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: 410.45  E-value: 4.57e-141
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIYNNipanlrqqaevekqtsltpreleirrredeyrftkllqiagisphgn 251
Cdd:cd19497   6 IKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNN----------------------------------------------- 38

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 252 algasmqqqgsqqmpqekrggevLDSPHDDIKLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:cd19497  39 -----------------------LKQKDDDVELEKSNILLIGPTGSGKTLLAQTLAKILDVPFAIADATTLTEAGYVGED 95

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 332 IESVIAKLLQDANYNVEKAQQGIVFLDEVDKIGSVPG-IHQLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRK-LRGETVQ 409
Cdd:cd19497  96 VENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSEnPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKhPQQEFIQ 175

                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 410 VDTTNILFVASGAFNGLDRIISRRKNEKYLGFGTPSNLgkgrraaaaadlanrsgesntHQDIEEKDRLLRHVEARDLIE 489
Cdd:cd19497 176 VDTTNILFICGGAFVGLEKIIARRLGKKSLGFGAETSS---------------------EKDEKERDELLSKVEPEDLIK 234

                       330
                ....*....|....*..
gi 56119122 490 FGMIPEFVGRLPVVVPL 506
Cdd:cd19497 235 FGLIPEFVGRLPVIVTL 251
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 102-600 1.31e-139

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: 413.01  E-value: 1.31e-139
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   102 QLRCPKCGDLCTHVETFVSSTRFVKCEKCHHFFV-VLSEADSKKSIIKEPESAAEAVKLAFQQKpppppkkIYNYLDKYV 180
Cdd:TIGR00382   7 TLYCSFCGKSQDEVRKLIAGPGVYICDECIELCHdILEEELGTRKESKEYEEEFELSYLPTPKE-------IKAHLDEYV 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   181 VGQSFAKKVLSVAVYNHYKRIynNIPANLRQQAEVEkqtsltpreleirrredeyrftkllqiagisphgnalgasmqqq 260
Cdd:TIGR00382  80 IGQEQAKKVLSVAVYNHYKRL--NFEKNKKSDNGVE-------------------------------------------- 113

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   261 gsqqmpqekrggevldsphddikLEKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLL 340
Cdd:TIGR00382 114 -----------------------LSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLL 170

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   341 QDANYNVEKAQQGIVFLDEVDKIGSV---PGIhqLRDVGGEGVQQGLLKLLEGTIVNVPEKNSRKL-RGETVQVDTTNIL 416
Cdd:TIGR00382 171 QAADYDVEKAQKGIIYIDEIDKISRKsenPSI--TRDVSGEGVQQALLKIIEGTVANVPPQGGRKHpYQEFIQIDTSNIL 248

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   417 FVASGAFNGLDRIISRRKNEKYLGFGTPSNlgkgrraaaaadlanrsgesnthQDIEEKDRLLRHVEARDLIEFGMIPEF 496
Cdd:TIGR00382 249 FICGGAFVGLEKIIKKRTGKSSIGFGAEVK-----------------------KKSKEKADLLRQVEPEDLVKFGLIPEF 305

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   497 VGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPM 576
Cdd:TIGR00382 306 IGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVM 385

                         490       500
                  ....*....|....*....|....*
gi 56119122   577 FEVPN-SDIVCVEVDKEVVEGKKEP 600
Cdd:TIGR00382 386 FDLPSlEDLEKVVITKETVLKQSEP 410
hslU PRK05201
ATP-dependent protease ATPase subunit HslU;
172-597 5.31e-41

ATP-dependent protease ATPase subunit HslU;


Pssm-ID: 235364 [Multi-domain]  Cd Length: 443  Bit Score: 154.85  E-value: 5.31e-41
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRiyNNIPANLRQqaEVekqtslTPReleirrredeyrftkllqiagisphgn 251
Cdd:PRK05201   9 IVSELDKYIIGQDDAKRAVAIALRNRWRR--MQLPEELRD--EV------TPK--------------------------- 51

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  252 algasmqqqgsqqmpqekrggevldsphddikleksNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:PRK05201  52 ------------------------------------NILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRD 95

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  332 IESVI--------------------------------------------------------------------------- 336
Cdd:PRK05201  96 VESIIrdlveiavkmvreekrekvrekaeeaaeerildallppaknnwgeeeekeeisatrqkfrkklregelddkeiei 175

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  337 -------------------------------------------------------AKLL------QDANYNVEkaQQGIV 355
Cdd:PRK05201 176 evaeaapmmeimgppgmeemtiqlqdmfgnlgpkkkkkrklkvkearkilieeeaAKLIdmeeikQEAIERVE--QNGIV 253

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  356 FLDEVDKIGSVPGIHQlRDVGGEGVQQGLLKLLEGTIVNVpeknsrKLrGetvQVDTTNILFVASGAFNgldriISRrkn 435
Cdd:PRK05201 254 FIDEIDKIAARGGSSG-PDVSREGVQRDLLPLVEGSTVST------KY-G---MVKTDHILFIASGAFH-----VSK--- 314

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  436 ekylgfgtPSNLgkgrraaaaadlanrsgesnthqdieekdrllrhveardliefgmIPEFVGRLPVVVPLHSLDEKTLV 515
Cdd:PRK05201 315 --------PSDL---------------------------------------------IPELQGRFPIRVELDALTEEDFV 341

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  516 QILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALE--RKT---GARGLRSIMEKLLLEPMFEVPNSDIVCVEVD 590
Cdd:PRK05201 342 RILTEPKASLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQvnEKTeniGARRLHTVMEKLLEDISFEAPDMSGETVTID 421


                 ....*..
gi 56119122  591 KEVVEGK 597
Cdd:PRK05201 422 AAYVDEK 428
HslU COG1220
ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, ...
 331-597 5.96e-38

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


Pssm-ID: 440833 [Multi-domain]  Cd Length: 454  Bit Score: 146.35  E-value: 5.96e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 331 DIESVIakllQDANYNVEkaQQGIVFLDEVDKIGSvPGIHQLRDVGGEGVQQGLLKLLEGTivnvpeknsrklrgeTVQ- 409
Cdd:COG1220 246 DMDEVK----QEAIERAE--QNGIIFIDEIDKIAS-RGGGSGPDVSREGVQRDLLPIVEGS---------------TVNt 303

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 410 ----VDTTNILFVASGAFNgldriISRrknekylgfgtPSNLgkgrraaaaadlanrsgesnthqdieekdrllrhvear 485
Cdd:COG1220 304 kygmVKTDHILFIAAGAFH-----VSK-----------PSDL-------------------------------------- 329

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 486 dliefgmIPEFVGRLPVVVPLHSLDEKTLVQILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLALE--RKT---G 560
Cdd:COG1220 330 -------IPELQGRFPIRVELDSLTEEDFVRILTEPKNALTKQYQALLATEGVELEFTDDAIREIAEIAFEvnERTeniG 402

                       250       260       270
                ....*....|....*....|....*....|....*..
gi 56119122 561 ARGLRSIMEKLLLEPMFEVPNSDIVCVEVDKEVVEGK 597
Cdd:COG1220 403 ARRLHTVMEKLLEDISFEAPDLSGKTVVIDAAYVDEK 439
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 285-503 9.12e-32

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: 121.15  E-value: 9.12e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   285 EKSNILLLGPTGSGKTLLAQTLAKCLDV---PFAICDCTTLTQagyvgediESVIAKLLQDANYNVEKAQQG-------- 353
Cdd:pfam07724   2 PIGSFLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrr 73

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   354 ----IVFLDEVDKIGSvpgihqlrdvggeGVQQGLLKLLEGTIVNVpeknsrklrGETVQVDTTNILFVASGAFNGLDRI 429
Cdd:pfam07724  74 kpysIVLIDEIEKAHP-------------GVQNDLLQILEGGTLTD---------KQGRTVDFKNTLFIMTGNFGSEKIS 131

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56119122   430 ISRRknekylgfgtpsnlgkgrraaaaadlanrsgesnthqDIEEKDRLLRHVEARDLIEFGMIPEFVGRLPVV 503
Cdd:pfam07724 132 DASR-------------------------------------LGDSPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
RecA-like_HslU cd19498
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ...
 172-424 3.58e-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: 119.79  E-value: 3.58e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRiynnipanlrQQAEVEKQTSLTPReleirrredeyrftkllqiagisphgn 251
Cdd:cd19498   5 IVSELDKYIIGQDEAKRAVAIALRNRWRR----------MQLPEELRDEVTPK--------------------------- 47

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 252 algasmqqqgsqqmpqekrggevldsphddikleksNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:cd19498  48 ------------------------------------NILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEVGYVGRD 91

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 332 IESVIAKLLqdanynvekaqQGIVFLDEVDKIGSVPGIHQlRDVGGEGVQQGLLKLLEGTIVNVpeknsrklrgETVQVD 411
Cdd:cd19498  92 VESIIRDLV-----------EGIVFIDEIDKIAKRGGSSG-PDVSREGVQRDLLPIVEGSTVST----------KYGPVK 149

                       250
                ....*....|...
gi 56119122 412 TTNILFVASGAFN 424
Cdd:cd19498 150 TDHILFIAAGAFH 162
hslU TIGR00390
ATP-dependent protease HslVU, ATPase subunit; This model represents the ATPase subunit of ...
 172-597 5.70e-31

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: 126.08  E-value: 5.70e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   172 IYNYLDKYVVGQSFAKKVLSVAVYNHYKRIynnipanlrqQAEVEKQTSLTPReleirrredeyrftkllqiagisphgn 251
Cdd:TIGR00390   6 IVAELDKYIIGQDNAKKSVAIALRNRYRRS----------QLNEELKDEVTPK--------------------------- 48

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   252 algasmqqqgsqqmpqekrggevldsphddikleksNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGED 331
Cdd:TIGR00390  49 ------------------------------------NILMIGPTGVGKTEIARRLAKLANAPFIKVEATKFTEVGYVGRD 92

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   332 IESVI----------------AKLLQDANYNVEK---------------------------------------------- 349
Cdd:TIGR00390  93 VESMVrdltdaavklvkeeaiEKVRDRAEELAEErivdvllppaknqwgqteqqqepesareafrkklregelddkeiei 172

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   350 -------------------------------------------------------------------------AQQGIVF 356
Cdd:TIGR00390 173 dvsakmpsgieimappgmeemtmqlqslfqnlggqkkkkrklkikdakkaliaeeaaklvdpeeikqeaidavEQSGIIF 252

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   357 LDEVDKIgSVPGIHQLRDVGGEGVQQGLLKLLEGTIVNVPEKnsrklrgetvQVDTTNILFVASGAFNgldriISRrkne 436
Cdd:TIGR00390 253 IDEIDKI-AKKGESSGADVSREGVQRDLLPIVEGSTVNTKYG----------MVKTDHILFIAAGAFQ-----LAK---- 312

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   437 kylgfgtPSNLgkgrraaaaadlanrsgesnthqdieekdrllrhveardliefgmIPEFVGRLPVVVPLHSLDEKTLVQ 516
Cdd:TIGR00390 313 -------PSDL---------------------------------------------IPELQGRFPIRVELQALTTDDFER 340

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   517 ILTEPRNAVIPQYQALFSMDKCELNVTEDALKAIARLA--LERKT---GARGLRSIMEKLLLEPMFEVPNSDIVCVEVDK 591
Cdd:TIGR00390 341 ILTEPKNSLIKQYKALMKTEGVNIEFSDEAIKRIAELAynVNEKTeniGARRLHTVLERLLEDISFEAPDLSGQNITIDA 420


                  ....*.
gi 56119122   592 EVVEGK 597
Cdd:TIGR00390 421 DYVSKK 426
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 509-603 1.24e-19

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: 83.65  E-value: 1.24e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122    509 LDEKTLVQILTEPRNAVIPQYqalfSMDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPMFEVPNSDIVcVE 588
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELILSGEL-KD 75

                           90
                   ....*....|....*
gi 56119122    589 VDKEVVEGKKEPGYI 603
Cdd:smart01086  76 GDTVVVDVDDGELVF 90
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 286-432 5.84e-16

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: 75.26  E-value: 5.84e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 286 KSNILLLGPTGSGKTLLAQTLAKCL---DVPFAICDCTTLTQAGYVGEDIESVIAKLLQDAnynVEKAQQGIVFLDEVDK 362
Cdd:cd00009  19 PKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVAELFGHFLVRLLFEL---AEKAKPGVLFIDEIDS 95

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 363 IgsvpgihqlrdvgGEGVQQGLLKLLEGtivnvpEKNSRKLRGETVQVDTTNILFVASGAFNGLDRIISR 432
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 ...
 286-390 6.10e-16

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: 75.40  E-value: 6.10e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 286 KSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEdIESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGS 365
Cdd:cd19481  26 PKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLL-SKYVGE-SEKNLRKIFERA----RRLAPCILFIDEIDAIGR 99

                        90       100
                ....*....|....*....|....*
gi 56119122 366 VPGIHQLRDVGGEGVQQgLLKLLEG 390
Cdd:cd19481 100 KRDSSGESGELRRVLNQ-LLTELDG 123
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 289-390 4.33e-12

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: 63.77  E-value: 4.33e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQaGYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGSVPG 368
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVGES-EKRLRELFEAA----KKLAPCVIFIDEIDALAGSRG 74

                          90       100
                  ....*....|....*....|..
gi 56119122   369 IHQLRDvgGEGVQQGLLKLLEG 390
Cdd:pfam00004  75 SGGDSE--SRRVVNQLLTELDG 94
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 289-390 4.89e-11

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: 64.93  E-value: 4.89e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEdIESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGsvPG 368
Cdd:COG0464 194 LLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLV-SKYVGE-TEKNLREVFDKA----RGLAPCVLFIDEADALA--GK 265

                        90       100
                ....*....|....*....|..
gi 56119122 369 IHQLRDVGGEGVQQGLLKLLEG 390
Cdd:COG0464 266 RGEVGDGVGRRVVNTLLTEMEE 287
ClpB_D2-small pfam10431
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 509-580 7.68e-10

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: 55.49  E-value: 7.68e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 56119122   509 LDEKTLVQILTEprnAVIPQYQALFSmDKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPMFEVP 580
Cdd:pfam10431   1 LSKEELRKIVDL---QLKELQKRLAE-RGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREIEDPLAEEI 68
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 286-393 8.77e-09

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: 54.69  E-value: 8.77e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122    286 KSNILLLGPTGSGKTLLAQTLAKCLDVP---FAICDCTTLTQAGYVGEDIESVI--------AKLLQDANYNVEKAQQGI 354
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVLDQLLLIIVGgkkasgsgELRLRLALALARKLKPDV 81

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 56119122    355 VFLDEVDKIGSVPGIHQLRDVGGEGVQQGLLKLLEGTIV 393
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 ...
 289-390 1.04e-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: 54.99  E-value: 1.04e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLtQAGYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGSVPG 368
Cdd:cd19503  37 VLLHGPPGTGKTLLARAVANEAGANFLSISGPSI-VSKYLGES-EKNLREIFEEA----RSHAPSIIFIDEIDALAPKRE 110

                        90       100
                ....*....|....*....|..
gi 56119122 369 IHQlRDVGGEGVQQgLLKLLEG 390
Cdd:cd19503 111 EDQ-REVERRVVAQ-LLTLMDG 130
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 289-365 3.36e-07

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 52.70  E-value: 3.36e-07
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGS 365
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 ...
 288-432 6.39e-07

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


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 48.83  E-value: 6.39e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   288 NILLLGPTGSGKTLLAQTLAKcldvpfAICDCTTLTQAGYvgEDIESviAKLLQDANYN-----------VEKAQQG-IV 355
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAA------ALSNRPVFYVQLT--RDTTE--EDLFGRRNIDpggaswvdgplVRAAREGeIA 70

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56119122   356 FLDEVDKIGSVpgihqlrdvggegVQQGLLKLLEGTIVNVPEknsrklRGETVQVDTTNILFVASGafNGLDRIISR 432
Cdd:pfam07728  71 VLDEINRANPD-------------VLNSLLSLLDERRLLLPD------GGELVKAAPDGFRLIATM--NPLDRGLNE 126
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 445-592 1.11e-06

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


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 52.01  E-value: 1.11e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 445 SNLGkgrraaaAADLANRSGESNTHQDIEEK--DRLLRHVEardliefgmiPEFVGRLPVVVPLHSLDEKTLVQI----L 518
Cdd:COG0542 699 SNIG-------SELILDLAEDEPDYEEMKEAvmEELKKHFR----------PEFLNRIDEIIVFHPLSKEELRKIvdlqL 761

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 519 TEPRNAVIPQyqalfsmdKCELNVTEDALKAIARLALERKTGARGLRSIMEKLLLEPM------FEVPNSDIVCVEVDKE 592
Cdd:COG0542 762 KRLRKRLAER--------GITLELTDAAKDFLAEKGYDPEYGARPLKRAIQRELEDPLaeeilaGEIKEGDTITVDVDDG 833
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 289-365 1.55e-06

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: 48.55  E-value: 1.55e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLLQDANYNVEkaqqGIVFLDEVDKIGS 365
Cdd:cd19518  37 VLLHGPPGCGKTMLANAIAGELKVPFLKISATEIV-SGVSGES-EEKIRELFDQAISNAP----CIVFIDEIDAITP 107
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 289-388 2.08e-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: 48.10  E-value: 2.08e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiesviAKLLQDANYNVEKAQQGIVFLDEVDKIGSvpg 368
Cdd:cd19502  40 VLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQK-YIGEG-----ARLVRELFEMAREKAPSIIFIDEIDAIGA--- 110

                        90       100
                ....*....|....*....|...
gi 56119122 369 ihQLRDVGGEG---VQQGLLKLL 388
Cdd:cd19502 111 --KRFDSGTGGdreVQRTMLELL 131
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 289-365 2.14e-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: 48.12  E-value: 2.14e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLLQDANynveKAQQGIVFLDEVDKIGS 365
Cdd:cd19509  35 ILLYGPPGTGKTLLARAVASESGSTFFSISASSLV-SKWVGES-EKIVRALFALAR----ELQPSIIFIDEIDSLLS 105
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
289-368 6.01e-06

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 49.26  E-value: 6.01e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  289 ILLLGPTGSGKTLLAQTLAKCLDVPFaicdcTTLTQAGYVgEDIESVIAKLLQDANYNVEKAQQGIVFLDEVDKIGSVPG 368
Cdd:PRK10733 188 VLMVGPPGTGKTLLAKAIAGEAKVPF-----FTISGSDFV-EMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG 261
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 289-364 1.23e-05

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: 46.07  E-value: 1.23e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFaicdcttLTQAG------YVGediesVIAKLLQDANYNVEKAQQGIVFLDEVDK 362
Cdd:cd19501  40 VLLVGPPGTGKTLLAKAVAGEAGVPF-------FSISGsdfvemFVG-----VGASRVRDLFEQAKKNAPCIVFIDEIDA 107


                ..
gi 56119122 363 IG 364
Cdd:cd19501 108 VG 109
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 289-365 4.01e-05

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 44.20  E-value: 4.01e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGS 365
Cdd:cd19511  30 VLLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSK-YVGES-ERAVREIFQKA----RQAAPCIIFFDEIDSLAP 100
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 289-361 4.89e-05

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: 44.34  E-value: 4.89e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYvGEdiesviAKLLQDANYNV-EKAQQGIVFLDEVD 361
Cdd:cd19520  38 VLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWY-GE------SQKLVAAVFSLaSKLQPSIIFIDEID 104
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 289-363 1.02e-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: 43.30  E-value: 1.02e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKI 363
Cdd:cd19524  36 LLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT-SKYVGEG-EKLVRALFAVA----RELQPSIIFIDEVDSL 104
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 287-393 2.67e-04

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 43.92  E-value: 2.67e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  287 SNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTltqAGyVgEDIESVIAKllqdANYNVEKAQQGIVFLDEvdkigsv 366
Cdd:PRK13342  37 SSMILWGPPGTGKTTLARIIAGATDAPFEALSAVT---SG-V-KDLREVIEE----ARQRRSAGRRTILFIDE------- 100

                         90       100       110
                 ....*....|....*....|....*....|...
gi 56119122  367 pgIH-----QlrdvggegvQQGLLKLLE-GTIV 393
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 ...
 289-363 3.33e-04

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: 41.65  E-value: 3.33e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLtQAGYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKI 363
Cdd:cd19519  37 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEI-MSKLAGES-ESNLRKAFEEA----EKNAPAIIFIDEIDAI 105
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 289-414 5.10e-04

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 43.36  E-value: 5.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLtQAGYVGEDiESVIAKLLQDANYNVEkaqqGIVFLDEVDKIGSvpg 368
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEI-MSKYYGES-EERLREIFKEAEENAP----SIIFIDEIDAIAP--- 285

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*....
gi 56119122   369 ihQLRDVGGE---GVQQGLLKLLEGTivnvpeknsrKLRGETVQVDTTN 414
Cdd:TIGR01243 286 --KREEVTGEvekRVVAQLLTLMDGL----------KGRGRVIVIGATN 322
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 290-362 7.58e-04

Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and eukaryotic Heat shock protein 104 (Hsp104) are ATP-dependent molecular chaperones and essential proteins of the heat-shock response. ClpB/Hsp104 ATPases, in concert with the DnaK/Hsp70 chaperone system, disaggregate and reactivate aggregated proteins. This RecA-like_ClpB_Hsp104_like subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 41.01  E-value: 7.58e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 290 LLLGPTGSGKTLLAQTLAK----------CLDVPFAIC--DCTTLTQA--GYVGEDIESVIAKLLQDANYNVekaqqgiV 355
Cdd:cd19499  45 LFLGPTGVGKTELAKALAEllfgdednliRIDMSEYMEkhSVSRLIGAppGYVGYTEGGQLTEAVRRKPYSV-------V 117


                ....*..
gi 56119122 356 FLDEVDK 362
Cdd:cd19499 118 LLDEIEK 124
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 289-368 8.20e-04

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


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 40.74  E-value: 8.20e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLLQDANYNVEKAqqgiVFLDEVDKIGSVPG 368
Cdd:cd19522  36 VLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLT-SKYRGES-EKLVRLLFEMARFYAPTT----IFIDEIDSICSRRG 109
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 289-365 1.06e-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: 40.74  E-value: 1.06e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTqAGYVGEDiESVIAKLlqdanYNVEKAQQ-GIVFLDEVDKIGS 365
Cdd:cd19525  58 ILLFGPPGTGKTLIGKCIASQSGATFFSISASSLT-SKWVGEG-EKMVRAL-----FSVARCKQpAVIFIDEIDSLLS 128
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 289-411 1.25e-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: 40.17  E-value: 1.25e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDV--PFAICDCTTLTQagYVGEDiESVIAKLLQDA--NYNVEKAQQG--IVFLDEVDK 362
Cdd:cd19504  38 ILLYGPPGTGKTLMARQIGKMLNArePKIVNGPEILNK--YVGES-EANIRKLFADAeeEQRRLGANSGlhIIIFDEIDA 114

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 56119122 363 IGSVPGIHQlrdvGGEGVQQGLLKLLEGTIVNVPEKNSRKLRGETVQVD 411
Cdd:cd19504 115 ICKQRGSMA----GSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKD 159
MCM8 cd17759
DNA helicase Mcm8; Mcm8 plays an important role homologous recombination repair. It forms a ...
 285-396 1.28e-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: 41.36  E-value: 1.28e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 285 EKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAGYVGEDIESVIAKLLQDANYNVeKAQQGIVFLDEVDKIG 364
Cdd:cd17759  42 GDPHVLIVGDPGLGKSQMLQAACNIAPRGVYVCGNTTTTSGLTVTLTKDGRSGDFALEAGALV-LGDQGICGIDEFDKMG 120

                        90       100       110
                ....*....|....*....|....*....|..
gi 56119122 365 SvpgihqlrdvggegVQQGLLKLLEGTIVNVP 396
Cdd:cd17759 121 S--------------QHQALLEAMEQQSVSLA 138
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 285-363 1.73e-03

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


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 39.42  E-value: 1.73e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 56119122 285 EKSNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKI 363
Cdd:cd19527  25 KRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINM-YIGES-EANVREVFQKA----RDAKPCVIFFDELDSL 97
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 289-320 1.83e-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: 40.54  E-value: 1.83e-03
                        10        20        30
                ....*....|....*....|....*....|..
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCT 320
Cdd:COG0714  34 LLLEGVPGVGKTTLAKALARALGLPFIRIQFT 65
DEAD pfam00270
DEAD/DEAH box helicase; Members of this family include the DEAD and DEAH box helicases. ...
 284-367 1.90e-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: 39.53  E-value: 1.90e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   284 LEKSNILLLGPTGSGKTL-----LAQTLAKCLDVPFAICDCTT--LTQagyvgeDIESVIAKLLQDANYNVEKAQQGIVF 356
Cdd:pfam00270  12 LEGRDVLVQAPTGSGKTLafllpALEALDKLDNGPQALVLAPTreLAE------QIYEELKKLGKGLGLKVASLLGGDSR 85

                          90
                  ....*....|.
gi 56119122   357 LDEVDKIGSVP 367
Cdd:pfam00270  86 KEQLEKLKGPD 96
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 288-361 3.36e-03

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


Pssm-ID: 410920 [Multi-domain]  Cd Length: 150  Bit Score: 38.66  E-value: 3.36e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 56119122 288 NILLLGPTGSGKTLLAQTLAKCLDVPFAIcdcTTLTQAGYVGEDIESVIAKLLQDANynveKAQQG-IVFLDEVD 361
Cdd:cd19512  24 NILFYGPPGTGKTLFAKKLALHSGMDYAI---MTGGDVAPMGREGVTAIHKVFDWAN----TSRRGlLLFVDEAD 91
aroK PRK00131
shikimate kinase; Reviewed
 284-314 3.89e-03

shikimate kinase; Reviewed


Pssm-ID: 234654 [Multi-domain]  Cd Length: 175  Bit Score: 38.63  E-value: 3.89e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 56119122  284 LEKSNILLLGPTGSGKTLLAQTLAKCLDVPF 314
Cdd:PRK00131   2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDF 32
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 289-390 4.64e-03

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


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 38.25  E-value: 4.64e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 289 ILLLGPTGSGKTLLAQTLAKCLDVPF-AICDCTTLTQagYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGSVP 367
Cdd:cd19529  30 ILLYGPPGTGKTLLAKAVATESNANFiSVKGPELLSK--WVGES-EKAIREIFRKA----RQVAPCVIFFDEIDSIAPRR 102

                        90       100
                ....*....|....*....|...
gi 56119122 368 GIHQLRDVGGEGVQQgLLKLLEG 390
Cdd:cd19529 103 GTTGDSGVTERVVNQ-LLTELDG 124
CDC6 COG1474
Cdc6-related protein, AAA superfamily ATPase [Replication, recombination and repair];
287-368 5.35e-03

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


Pssm-ID: 441083 [Multi-domain]  Cd Length: 389  Bit Score: 39.45  E-value: 5.35e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122 287 SNILLLGPTGSGKTLLAQTLAKCL-------DVPFAIC--DC---TTLTQagyvgediesVIAKLLQDANYNVEKAQQG- 353
Cdd:COG1474  52 SNVLIYGPTGTGKTAVAKYVLEELeeeaeerGVDVRVVyvNCrqaSTRYR----------VLSRILEELGSGEDIPSTGl 121

                        90       100       110
                ....*....|....*....|....*....|....*
gi 56119122 354 --------------------IVFLDEVDKIGSVPG 368
Cdd:COG1474 122 stdelfdrlyealderdgvlVVVLDEIDYLVDDEG 156
NACHT pfam05729
NACHT domain; This NTPase domain is found in apoptosis proteins as well as those involved in ...
 289-392 5.57e-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: 38.05  E-value: 5.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   289 ILLLGPTGSGKTLLAQTLA---------KCLDVPFAICdCTTLTQAG--------------YVGEDIESVIAKLLqdany 345
Cdd:pfam05729   3 VILQGEAGSGKTTLLQKLAllwaqgklpQGFDFVFFLP-CRELSRSGnarsladllfsqwpEPAAPVSEVWAVIL----- 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 56119122   346 nvEKAQQGIVFLDEVDKIGSVPGIHQlrdvGGEGVQQGLLKLLEGTI 392
Cdd:pfam05729  77 --ELPERLLLILDGLDELVSDLGQLD----GPCPVLTLLSSLLRKKL 117
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 289-388 6.34e-03

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 39.37  E-value: 6.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  289 ILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiesviAKLLQDANYNVEKAQQGIVFLDEVDKIGSVpg 368
Cdd:PTZ00361 220 VILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQK-YLGDG-----PKLVRELFRVAEENAPSIVFIDEIDAIGTK-- 291

                         90       100
                 ....*....|....*....|.
gi 56119122  369 iHQLRDVGGEG-VQQGLLKLL 388
Cdd:PTZ00361 292 -RYDATSGGEKeIQRTMLELL 311
Zn-ribbon cd00656
C-terminal zinc ribbon domain of RNA polymerase intrinsic transcript cleavage subunit; The ...
 104-132 7.72e-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: 7.72e-03
                        10        20        30
                ....*....|....*....|....*....|....*....
gi 56119122 104 RCPKCGdlctHVETFV----------SSTRFVKCEKCHH 132
Cdd:cd00656   8 TCPKCG----HDEAYWwmlqtrsadePPTRFYKCTKCGH 42
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 287-365 7.86e-03

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 39.05  E-value: 7.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122  287 SNILLLGPTGSGKTLLAQTLAKCLDVPFAICDCTTLTQAgYVGEDiesviAKLLQDA-NYNVEKAqQGIVFLDEVDKIGS 365
Cdd:PRK03992 166 KGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQK-FIGEG-----ARLVRELfELAREKA-PSIIFIDEIDAIAA 238
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 289-390 8.68e-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: 39.12  E-value: 8.68e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 56119122   289 ILLLGPTGSGKTLLAQTLAKCLDVPF-AICDCTTLTQagYVGEDiESVIAKLLQDAnynvEKAQQGIVFLDEVDKIGSVP 367
Cdd:TIGR01243 490 VLLFGPPGTGKTLLAKAVATESGANFiAVRGPEILSK--WVGES-EKAIREIFRKA----RQAAPAIIFFDEIDAIAPAR 562

                          90       100
                  ....*....|....*....|...
gi 56119122   368 GIHQLRDVGGEGVQQgLLKLLEG 390
Cdd:TIGR01243 563 GARFDTSVTDRIVNQ-LLTEMDG 584
YifB COG0606
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ...
 288-306 9.44e-03

Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440371 [Multi-domain]  Cd Length: 502  Bit Score: 38.87  E-value: 9.44e-03
                        10
                ....*....|....*....
gi 56119122 288 NILLLGPTGSGKTLLAQTL 306
Cdd:COG0606 213 NLLMIGPPGSGKTMLARRL 231
 
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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