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Conserved domains on  [gi|1308675207|gb|PKM47157|]
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ATP-dependent Clp protease ATP-binding subunit ClpX [Firmicutes bacterium HGW-Firmicutes-8]

Protein Classification

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

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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 4-407 0e+00

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


:

Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 875.14  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   4 FSDEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSE-DLGMEMGDLPKPKEIKEILDQYVIGQETAK 82
Cdd:COG1219     2 AGDSKKELKCSFCGKSQDEVRKLIAGPGVYICDECVELCNEIIEEELKEeEAEEELKKLPKPKEIKAFLDEYVIGQERAK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  83 KALAVAVYNHYKRINIGS-KIDDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDVENILLK 161
Cdd:COG1219    82 KVLSVAVYNHYKRLNSGSkDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLK 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 162 LIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQLDTTNIL 241
Cdd:COG1219   162 LLQAADYDVEKAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKHPQQEFIQIDTTNIL 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 242 FICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKKGKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEKALVRIL 321
Cdd:COG1219   242 FICGGAFDGLEKIIERRLGKKSIGFGAEVKSKKEKDEGELLKQVEPEDLIKFGLIPEFIGRLPVIATLEELDEEALVRIL 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 322 SEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITKEVVNKK 401
Cdd:COG1219   322 TEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMYELPSRKDVKKVVITKEVVEGK 401


                  ....*.
gi 1308675207 402 EQPILL 407
Cdd:COG1219   402 AKPILV 407
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 4-407 0e+00

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 875.14  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   4 FSDEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSE-DLGMEMGDLPKPKEIKEILDQYVIGQETAK 82
Cdd:COG1219     2 AGDSKKELKCSFCGKSQDEVRKLIAGPGVYICDECVELCNEIIEEELKEeEAEEELKKLPKPKEIKAFLDEYVIGQERAK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  83 KALAVAVYNHYKRINIGS-KIDDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDVENILLK 161
Cdd:COG1219    82 KVLSVAVYNHYKRLNSGSkDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLK 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 162 LIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQLDTTNIL 241
Cdd:COG1219   162 LLQAADYDVEKAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKHPQQEFIQIDTTNIL 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 242 FICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKKGKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEKALVRIL 321
Cdd:COG1219   242 FICGGAFDGLEKIIERRLGKKSIGFGAEVKSKKEKDEGELLKQVEPEDLIKFGLIPEFIGRLPVIATLEELDEEALVRIL 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 322 SEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITKEVVNKK 401
Cdd:COG1219   322 TEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMYELPSRKDVKKVVITKEVVEGK 401


                  ....*.
gi 1308675207 402 EQPILL 407
Cdd:COG1219   402 AKPILV 407
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
3-412 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 836.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   3 KFSDEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSEDlGMEMGDLPKPKEIKEILDQYVIGQETAK 82
Cdd:PRK05342    2 RGGDSKKLLYCSFCGKSQHEVRKLIAGPGVYICDECIELCNEIIREELKEE-AVELKELPTPKEIKAHLDQYVIGQERAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  83 KALAVAVYNHYKRINIGSKI-DDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDVENILLK 161
Cdd:PRK05342   81 KVLSVAVYNHYKRLRHGDKKdDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 162 LIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQLDTTNIL 241
Cdd:PRK05342  161 LLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNIL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 242 FICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKK-GKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEKALVRI 320
Cdd:PRK05342  241 FICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKeKRTEGELLKQVEPEDLIKFGLIPEFIGRLPVVATLEELDEEALVRI 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 321 LSEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITKEVVNK 400
Cdd:PRK05342  321 LTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMFELPSREDVEKVVITKEVVEG 400

                         410
                  ....*....|..
gi 1308675207 401 KEQPILLTVERK 412
Cdd:PRK05342  401 KAKPLLIYREKS 412
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 6-407 0e+00

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: 647.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   6 DEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSEDLGM-------EMGDLPKPKEIKEILDQYVIGQ 78
Cdd:TIGR00382   3 KKNETLYCSFCGKSQDEVRKLIAGPGVYICDECIELCHDILEEELGTRKESkeyeeefELSYLPTPKEIKAHLDEYVIGQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  79 ETAKKALAVAVYNHYKRINI--GSKIDD-VELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDV 155
Cdd:TIGR00382  83 EQAKKVLSVAVYNHYKRLNFekNKKSDNgVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDV 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 156 ENILLKLIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQL 235
Cdd:TIGR00382 163 ENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQI 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 236 DTTNILFICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKKgKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEK 315
Cdd:TIGR00382 243 DTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKS-KEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEE 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 316 ALVRILSEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITK 395
Cdd:TIGR00382 322 ALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVMFDLPSLEDLEKVVITK 401

                         410
                  ....*....|..
gi 1308675207 396 EVVNKKEQPILL 407
Cdd:TIGR00382 402 ETVLKQSEPLLI 413
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 62-309 5.58e-175

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: 488.65  E-value: 5.58e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  62 PKPKEIKEILDQYVIGQETAKKALAVAVYNHYKRINIGSKI--DDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAI 139
Cdd:cd19497     1 PTPKEIKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNNLKQkdDDVELEKSNILLIGPTGSGKTLLAQTLAKILDVPFAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 140 ADATSLTEAGYVGEDVENILLKLIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASV 219
Cdd:cd19497    81 ADATTLTEAGYVGEDVENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 220 PPQGGRKHPHQEFIQLDTTNILFICGGAFDGIEKIIQNRIGRKSLGFGAEIQS-KKGKNVSEVLKHILPEDLLKYGLIPE 298
Cdd:cd19497   161 PPQGGRKHPQQEFIQVDTTNILFICGGAFVGLEKIIARRLGKKSLGFGAETSSeKDEKERDELLSKVEPEDLIKFGLIPE 240

                         250
                  ....*....|.
gi 1308675207 299 FVGRLPVIVTL 309
Cdd:cd19497   241 FVGRLPVIVTL 251
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 109-306 1.04e-42

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: 147.73  E-value: 1.04e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 109 KSNIVMLGPTGSGKTLLAQTLARLLNV---PFAIADATSLTEagyvgedvENILLKLIQAADYDVEKAEKG--------- 176
Cdd:pfam07724   3 IGSFLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrrk 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 177 ---IVYIDEIDKIARksenpsitrdvsgeGVQQALLKILEGTVASvppqggrkhPHQEfIQLDTTNILFICGGAFDGIEK 253
Cdd:pfam07724  75 pysIVLIDEIEKAHP--------------GVQNDLLQILEGGTLT---------DKQG-RTVDFKNTLFIMTGNFGSEKI 130

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1308675207 254 IIQNRIGRkslgfgaeiqskkgkNVSEVLKHILPEDLLKYGLIPEFVGRLPVI 306
Cdd:pfam07724 131 SDASRLGD---------------SPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
zf-C4_ClpX smart00994
ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the ...
 11-49 2.69e-20

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


Pssm-ID: 198062 [Multi-domain]  Cd Length: 39  Bit Score: 83.39  E-value: 2.69e-20
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1308675207   11 LKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEE 49
Cdd:smart00994   1 LRCSFCGKSESEVRKLIAGPGVYICDECVELCYEILEEE 39
 
Name Accession Description Interval E-value
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 4-407 0e+00

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 875.14  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   4 FSDEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSE-DLGMEMGDLPKPKEIKEILDQYVIGQETAK 82
Cdd:COG1219     2 AGDSKKELKCSFCGKSQDEVRKLIAGPGVYICDECVELCNEIIEEELKEeEAEEELKKLPKPKEIKAFLDEYVIGQERAK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  83 KALAVAVYNHYKRINIGS-KIDDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDVENILLK 161
Cdd:COG1219    82 KVLSVAVYNHYKRLNSGSkDDDDVELEKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLK 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 162 LIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQLDTTNIL 241
Cdd:COG1219   162 LLQAADYDVEKAERGIIYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANVPPQGGRKHPQQEFIQIDTTNIL 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 242 FICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKKGKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEKALVRIL 321
Cdd:COG1219   242 FICGGAFDGLEKIIERRLGKKSIGFGAEVKSKKEKDEGELLKQVEPEDLIKFGLIPEFIGRLPVIATLEELDEEALVRIL 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 322 SEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITKEVVNKK 401
Cdd:COG1219   322 TEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMYELPSRKDVKKVVITKEVVEGK 401


                  ....*.
gi 1308675207 402 EQPILL 407
Cdd:COG1219   402 AKPILV 407
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
3-412 0e+00

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 836.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   3 KFSDEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSEDlGMEMGDLPKPKEIKEILDQYVIGQETAK 82
Cdd:PRK05342    2 RGGDSKKLLYCSFCGKSQHEVRKLIAGPGVYICDECIELCNEIIREELKEE-AVELKELPTPKEIKAHLDQYVIGQERAK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  83 KALAVAVYNHYKRINIGSKI-DDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDVENILLK 161
Cdd:PRK05342   81 KVLSVAVYNHYKRLRHGDKKdDDVELQKSNILLIGPTGSGKTLLAQTLARILDVPFAIADATTLTEAGYVGEDVENILLK 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 162 LIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQLDTTNIL 241
Cdd:PRK05342  161 LLQAADYDVEKAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPQQEFIQVDTTNIL 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 242 FICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKK-GKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEKALVRI 320
Cdd:PRK05342  241 FICGGAFDGLEKIIKQRLGKKGIGFGAEVKSKKeKRTEGELLKQVEPEDLIKFGLIPEFIGRLPVVATLEELDEEALVRI 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 321 LSEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITKEVVNK 400
Cdd:PRK05342  321 LTEPKNALVKQYQKLFEMDGVELEFTDEALEAIAKKAIERKTGARGLRSILEEILLDVMFELPSREDVEKVVITKEVVEG 400

                         410
                  ....*....|..
gi 1308675207 401 KEQPILLTVERK 412
Cdd:PRK05342  401 KAKPLLIYREKS 412
clpX TIGR00382
endopeptidase Clp ATP-binding regulatory subunit (clpX); A member of the ATP-dependent ...
 6-407 0e+00

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: 647.21  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207   6 DEKGQLKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEELSEDLGM-------EMGDLPKPKEIKEILDQYVIGQ 78
Cdd:TIGR00382   3 KKNETLYCSFCGKSQDEVRKLIAGPGVYICDECIELCHDILEEELGTRKESkeyeeefELSYLPTPKEIKAHLDEYVIGQ 82

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  79 ETAKKALAVAVYNHYKRINI--GSKIDD-VELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGEDV 155
Cdd:TIGR00382  83 EQAKKVLSVAVYNHYKRLNFekNKKSDNgVELSKSNILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDV 162

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 156 ENILLKLIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASVPPQGGRKHPHQEFIQL 235
Cdd:TIGR00382 163 ENILLKLLQAADYDVEKAQKGIIYIDEIDKISRKSENPSITRDVSGEGVQQALLKIIEGTVANVPPQGGRKHPYQEFIQI 242

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 236 DTTNILFICGGAFDGIEKIIQNRIGRKSLGFGAEIQSKKgKNVSEVLKHILPEDLLKYGLIPEFVGRLPVIVTLEALDEK 315
Cdd:TIGR00382 243 DTSNILFICGGAFVGLEKIIKKRTGKSSIGFGAEVKKKS-KEKADLLRQVEPEDLVKFGLIPEFIGRLPVIATLEKLDEE 321

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 316 ALVRILSEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITKCTITK 395
Cdd:TIGR00382 322 ALIAILTKPKNALVKQYQALFKMDNVELDFEEEALKAIAKKALERKTGARGLRSIVEGLLLDVMFDLPSLEDLEKVVITK 401

                         410
                  ....*....|..
gi 1308675207 396 EVVNKKEQPILL 407
Cdd:TIGR00382 402 ETVLKQSEPLLI 413
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 62-309 5.58e-175

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: 488.65  E-value: 5.58e-175
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  62 PKPKEIKEILDQYVIGQETAKKALAVAVYNHYKRINIGSKI--DDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAI 139
Cdd:cd19497     1 PTPKEIKEHLDKYVIGQERAKKVLSVAVYNHYKRIRNNLKQkdDDVELEKSNILLIGPTGSGKTLLAQTLAKILDVPFAI 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 140 ADATSLTEAGYVGEDVENILLKLIQAADYDVEKAEKGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVASV 219
Cdd:cd19497    81 ADATTLTEAGYVGEDVENILLKLLQAADYDVERAQRGIVYIDEIDKIARKSENPSITRDVSGEGVQQALLKILEGTVANV 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 220 PPQGGRKHPHQEFIQLDTTNILFICGGAFDGIEKIIQNRIGRKSLGFGAEIQS-KKGKNVSEVLKHILPEDLLKYGLIPE 298
Cdd:cd19497   161 PPQGGRKHPQQEFIQVDTTNILFICGGAFVGLEKIIARRLGKKSLGFGAETSSeKDEKERDELLSKVEPEDLIKFGLIPE 240

                         250
                  ....*....|.
gi 1308675207 299 FVGRLPVIVTL 309
Cdd:cd19497   241 FVGRLPVIVTL 251
hslU PRK05201
ATP-dependent protease ATPase subunit HslU;
64-401 2.45e-58

ATP-dependent protease ATPase subunit HslU;


Pssm-ID: 235364 [Multi-domain]  Cd Length: 443  Bit Score: 196.84  E-value: 2.45e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  64 PKEIKEILDQYVIGQETAKKALAVAVYNHYKRINIGSKIDDvELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADAT 143
Cdd:PRK05201    6 PREIVSELDKYIIGQDDAKRAVAIALRNRWRRMQLPEELRD-EVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEAT 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 144 SLTEAGYVGEDVENI-----------------------------------LL---------------------------- 160
Cdd:PRK05201   85 KFTEVGYVGRDVESIirdlveiavkmvreekrekvrekaeeaaeerildaLLppaknnwgeeeekeeisatrqkfrkklr 164

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 161 -------------------------------------------------------------------KLIqaaDYD---- 169
Cdd:PRK05201  165 egelddkeieievaeaapmmeimgppgmeemtiqlqdmfgnlgpkkkkkrklkvkearkilieeeaaKLI---DMEeikq 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 170 --VEKAEK-GIVYIDEIDKIARKSENPSitRDVSGEGVQQALLKILEGTVASVppqggrKHPhqefiQLDTTNILFICGG 246
Cdd:PRK05201  242 eaIERVEQnGIVFIDEIDKIAARGGSSG--PDVSREGVQRDLLPLVEGSTVST------KYG-----MVKTDHILFIASG 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 247 AFdgiekiiqnrigrkslgfgaeiqskkgkNVSEvlkhilPEDLlkyglIPEFVGRLPVIVTLEALDEKALVRILSEPKN 326
Cdd:PRK05201  309 AF----------------------------HVSK------PSDL-----IPELQGRFPIRVELDALTEEDFVRILTEPKA 349

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 327 ALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNT-----GARGLRSIIEDIMMDVMYEIPSRDDiTKCTITKEVVNKK 401
Cdd:PRK05201  350 SLIKQYQALLATEGVTLEFTDDAIRRIAEIAYQVNEkteniGARRLHTVMEKLLEDISFEAPDMSG-ETVTIDAAYVDEK 428
HslU COG1220
ATP-dependent protease HslVU (ClpYQ), ATPase subunit HslU [Posttranslational modification, ...
 64-405 1.11e-54

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


Pssm-ID: 440833 [Multi-domain]  Cd Length: 454  Bit Score: 187.56  E-value: 1.11e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  64 PKEIKEILDQYVIGQETAKKALAVAVYNHYKRinigSKIDDvELQK----SNIVMLGPTGSGKTLLAQTLARLLNVPFAI 139
Cdd:COG1220     6 PREIVAELDKYIIGQDEAKRAVAIALRNRWRR----QQLPE-ELRDeitpKNILMIGPTGVGKTEIARRLAKLANAPFIK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 140 ADATSLTEAGYVGEDVE-----------------------------------NILL------------------------ 160
Cdd:COG1220    81 VEATKFTEVGYVGRDVEsmirdlveiavkmvreekmekvrekaeeaaeerilDLLLpppkkkagsnnpfeeeeeeeeeee 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207     --------------------------------------------------------------------------------
Cdd:COG1220   161 eisrtrekfrkklregelddreieieveessspgveimgppgmeemgmnlqdmfgnlmpkkkkkrkvkvkearkiltqee 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 161 --KLIqaaDYD------VEKAEK-GIVYIDEIDKIARKSENPSItrDVSGEGVQQALLKILEGTVASVppqggrKHPhqe 231
Cdd:COG1220   241 aaKLI---DMDevkqeaIERAEQnGIIFIDEIDKIASRGGGSGP--DVSREGVQRDLLPIVEGSTVNT------KYG--- 306

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 232 fiQLDTTNILFICGGAFdgiekiiqnrigrkslgfgaeiqskkgkNVSEvlkhilPEDLlkyglIPEFVGRLPVIVTLEA 311
Cdd:COG1220   307 --MVKTDHILFIAAGAF----------------------------HVSK------PSDL-----IPELQGRFPIRVELDS 345

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 312 LDEKALVRILSEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNT-----GARGLRSIIEDIMMDVMYEIPSRD 386
Cdd:COG1220   346 LTEEDFVRILTEPKNALTKQYQALLATEGVELEFTDDAIREIAEIAFEVNErteniGARRLHTVMEKLLEDISFEAPDLS 425

                         490
                  ....*....|....*....
gi 1308675207 387 DiTKCTITKEVVNKKEQPI 405
Cdd:COG1220   426 G-KTVVIDAAYVDEKLGDI 443
hslU TIGR00390
ATP-dependent protease HslVU, ATPase subunit; This model represents the ATPase subunit of ...
 64-401 4.32e-49

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: 172.69  E-value: 4.32e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  64 PKEIKEILDQYVIGQETAKKALAVAVYNHYKRINIGSKIDDvELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADAT 143
Cdd:TIGR00390   3 PREIVAELDKYIIGQDNAKKSVAIALRNRYRRSQLNEELKD-EVTPKNILMIGPTGVGKTEIARRLAKLANAPFIKVEAT 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 144 SLTEAGYVGEDVENILLKLIQAA--------------------------------------------------------- 166
Cdd:TIGR00390  82 KFTEVGYVGRDVESMVRDLTDAAvklvkeeaiekvrdraeelaeerivdvllppaknqwgqteqqqepesareafrkklr 161

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 167 -----DYDVE---------------------------------------------------------------------- 171
Cdd:TIGR00390 162 egeldDKEIEidvsakmpsgieimappgmeemtmqlqslfqnlggqkkkkrklkikdakkaliaeeaaklvdpeeikqea 241

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 172 --KAEK-GIVYIDEIDKIARKSENPSitRDVSGEGVQQALLKILEGTVASVppqggrKHPhqefiQLDTTNILFICGGAF 248
Cdd:TIGR00390 242 idAVEQsGIIFIDEIDKIAKKGESSG--ADVSREGVQRDLLPIVEGSTVNT------KYG-----MVKTDHILFIAAGAF 308

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 249 dgiekiiqnrigrkslgfgaeiqskkgkNVSEvlkhilPEDLlkyglIPEFVGRLPVIVTLEALDEKALVRILSEPKNAL 328
Cdd:TIGR00390 309 ----------------------------QLAK------PSDL-----IPELQGRFPIRVELQALTTDDFERILTEPKNSL 349

                         410       420       430       440       450       460       470
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1308675207 329 IKQYQKFFEMDGINLEFKEDALETISKEAMK-----RNTGARGLRSIIEDIMMDVMYEIPSRdDITKCTITKEVVNKK 401
Cdd:TIGR00390 350 IKQYKALMKTEGVNIEFSDEAIKRIAELAYNvnektENIGARRLHTVLERLLEDISFEAPDL-SGQNITIDADYVSKK 426
RecA-like_HslU cd19498
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ...
 63-309 9.83e-48

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: 161.39  E-value: 9.83e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  63 KPKEIKEILDQYVIGQETAKKALAVAVYNHYKRINIGSKIDDvELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADA 142
Cdd:cd19498     1 TPREIVSELDKYIIGQDEAKRAVAIALRNRWRRMQLPEELRD-EVTPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEA 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 143 TSLTEAGYVGEDVENILLKLIqaadydvekaeKGIVYIDEIDKIARKSEnpSITRDVSGEGVQQALLKILEGTVASVppq 222
Cdd:cd19498    80 TKFTEVGYVGRDVESIIRDLV-----------EGIVFIDEIDKIAKRGG--SSGPDVSREGVQRDLLPIVEGSTVST--- 143

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 223 ggrkhphqEFIQLDTTNILFICGGAFdgiekiiqnrigrkslgfgaeiqskkgkNVSEvlkhilPEDllkygLIPEFVGR 302
Cdd:cd19498   144 --------KYGPVKTDHILFIAAGAF----------------------------HVAK------PSD-----LIPELQGR 176


                  ....*..
gi 1308675207 303 LPVIVTL 309
Cdd:cd19498   177 FPIRVEL 183
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 109-306 1.04e-42

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: 147.73  E-value: 1.04e-42
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 109 KSNIVMLGPTGSGKTLLAQTLARLLNV---PFAIADATSLTEagyvgedvENILLKLIQAADYDVEKAEKG--------- 176
Cdd:pfam07724   3 IGSFLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYME--------EHSVSRLIGAPPGYVGYEEGGqlteavrrk 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 177 ---IVYIDEIDKIARksenpsitrdvsgeGVQQALLKILEGTVASvppqggrkhPHQEfIQLDTTNILFICGGAFDGIEK 253
Cdd:pfam07724  75 pysIVLIDEIEKAHP--------------GVQNDLLQILEGGTLT---------DKQG-RTVDFKNTLFIMTGNFGSEKI 130

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1308675207 254 IIQNRIGRkslgfgaeiqskkgkNVSEVLKHILPEDLLKYGLIPEFVGRLPVI 306
Cdd:pfam07724 131 SDASRLGD---------------SPDYELLKEEVMDLLKKGFIPEFLGRLPII 168
zf-C4_ClpX smart00994
ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the ...
 11-49 2.69e-20

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


Pssm-ID: 198062 [Multi-domain]  Cd Length: 39  Bit Score: 83.39  E-value: 2.69e-20
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1308675207   11 LKCSFCGKLQDQVKKLVAGPGVYICDECIELCNEIIEEE 49
Cdd:smart00994   1 LRCSFCGKSESEVRKLIAGPGVYICDECVELCYEILEEE 39
zf-C4_ClpX pfam06689
ClpX C4-type zinc finger; The ClpX heat shock protein of Escherichia coli is a member of the ...
 11-48 4.26e-20

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


Pssm-ID: 461988 [Multi-domain]  Cd Length: 39  Bit Score: 82.58  E-value: 4.26e-20
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1308675207  11 LKCSFCGKLQDQVKKLVAGP-GVYICDECIELCNEIIEE 48
Cdd:pfam06689   1 LRCSFCGKSEDEVKKLIAGPnGVYICDECVELCYEILEE 39
ClpB_D2-small smart01086
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 312-396 1.12e-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: 82.88  E-value: 1.12e-19
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  312 LDEKALVRILSEPKNALIKQYqkffEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDI--- 388
Cdd:smart01086   1 LDKEDLVRIVDLPLNALQKRL----AEKGITLEFTDEALDWLAEKGYDPKYGARPLRRIIQRELEDPLAELILSGELkdg 76


                   ....*...
gi 1308675207  389 TKCTITKE 396
Cdd:smart01086  77 DTVVVDVD 84
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 81-214 8.40e-19

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: 82.72  E-value: 8.40e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  81 AKKALAVAVYNHYKRiniGSKIDDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAgYVGEDVENiLL 160
Cdd:cd19481     1 LKASLREAVEAPRRG---SRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSK-YVGESEKN-LR 75

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1308675207 161 KLIQAAdydvEKAEKGIVYIDEIDKIARKSENPSITRDVSgeGVQQALLKILEG 214
Cdd:cd19481    76 KIFERA----RRLAPCILFIDEIDAIGRKRDSSGESGELR--RVLNQLLTELDG 123
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 76-261 6.49e-14

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 68.71  E-value: 6.49e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  76 IGQETAKKALAVAVYNHykrinigskiddvelQKSNIVMLGPTGSGKTLLAQTLARLL---NVPFAIADATSLTEAGYVG 152
Cdd:cd00009     1 VGQEEAIEALREALELP---------------PPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEGLVVA 65

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 153 EDVENILLKLIQAAdydVEKAEKGIVYIDEIDKIARksenpsitrdvsgeGVQQALLKILEGTVASVPpqggrkhphqef 232
Cdd:cd00009    66 ELFGHFLVRLLFEL---AEKAKPGVLFIDEIDSLSR--------------GAQNALLRVLETLNDLRI------------ 116

                         170       180
                  ....*....|....*....|....*....
gi 1308675207 233 iqlDTTNILFICGGAFDGIEKIIQNRIGR 261
Cdd:cd00009   117 ---DRENVRVIGATNRPLLGDLDRALYDR 142
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 112-214 4.14e-13

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


Pssm-ID: 459627 [Multi-domain]  Cd Length: 130  Bit Score: 66.08  E-value: 4.14e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEaGYVGEDVENIlLKLIQAAdydvEKAEKGIVYIDEIDKIARKSE 191
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS-KYVGESEKRL-RELFEAA----KKLAPCVIFIDEIDALAGSRG 74

                          90       100
                  ....*....|....*....|...
gi 1308675207 192 NPSitrDVSGEGVQQALLKILEG 214
Cdd:pfam00004  75 SGG---DSESRRVVNQLLTELDG 94
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 47-214 2.61e-12

AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms];


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 68.01  E-value: 2.61e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  47 EEELSEDLGMEMGDLPKPKEIKEILDQYVIGQETAKKAlavavynhYKRINIGskiddvelQKSNIVMLGPTGSGKTLLA 126
Cdd:COG0464   145 EEELLELREAILDDLGGLEEVKEELRELVALPLKRPEL--------REEYGLP--------PPRGLLLYGPPGTGKTLLA 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 127 QTLARLLNVPFAIADATSLTeAGYVGEDVENIlLKLIQAAdydvEKAEKGIVYIDEIDKIARKSENpsiTRDVSGEGVQQ 206
Cdd:COG0464   209 RALAGELGLPLIEVDLSDLV-SKYVGETEKNL-REVFDKA----RGLAPCVLFIDEADALAGKRGE---VGDGVGRRVVN 279


                  ....*...
gi 1308675207 207 ALLKILEG 214
Cdd:COG0464   280 TLLTEMEE 287
ClpB_D2-small pfam10431
C-terminal, D2-small domain, of ClpB protein; This is the C-terminal domain of ClpB protein, ...
 312-390 3.33e-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: 58.96  E-value: 3.33e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308675207 312 LDEKALVRILsepKNALIKQYQKFFEmDGINLEFKEDALETISKEAMKRNTGARGLRSIIEDIMMDVMYEIPSRDDITK 390
Cdd:pfam10431   1 LSKEELRKIV---DLQLKELQKRLAE-RGITLELTDAAKDWLAEKGYDPEYGARPLRRAIQREIEDPLAEEILSGELKE 75
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 112-214 6.31e-09

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: 6.31e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDVENiLLKLIQAAdydvEKAEKGIVYIDEIDKIARKSE 191
Cdd:cd19503    37 VLLHGPPGTGKTLLARAVANEAGANFLSISGPSIV-SKYLGESEKN-LREIFEEA----RSHAPSIIFIDEIDALAPKRE 110

                          90       100
                  ....*....|....*....|...
gi 1308675207 192 npSITRDVSGEGVQQaLLKILEG 214
Cdd:cd19503   111 --EDQREVERRVVAQ-LLTLMDG 130
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 112-208 2.17e-08

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: 53.18  E-value: 2.17e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDVENILLKLIQAADYdvekaEKGIVYIDEIDKIARKSE 191
Cdd:cd19518    37 VLLHGPPGCGKTMLANAIAGELKVPFLKISATEIV-SGVSGESEEKIRELFDQAISN-----APCIVFIDEIDAITPKRE 110

                          90
                  ....*....|....*..
gi 1308675207 192 NPSitRDVSGEGVQQAL 208
Cdd:cd19518   111 SAQ--REMERRIVSQLL 125
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 75-189 3.46e-07

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


Pssm-ID: 410909 [Multi-domain]  Cd Length: 171  Bit Score: 49.92  E-value: 3.46e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  75 VIGQETAKKALAVAV---YNHYKRINIGSKIddvelqKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAgYV 151
Cdd:cd19501     6 VAGCEEAKEELKEVVeflKNPEKFTKLGAKI------PKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEM-FV 78

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1308675207 152 GEDVENIlLKLIQAAdydvEKAEKGIVYIDEIDKIARK 189
Cdd:cd19501    79 GVGASRV-RDLFEQA----KKNAPCIVFIDEIDAVGRK 111
clpA PRK11034
ATP-dependent Clp protease ATP-binding subunit; Provisional
 65-373 3.55e-07

ATP-dependent Clp protease ATP-binding subunit; Provisional


Pssm-ID: 236828 [Multi-domain]  Cd Length: 758  Bit Score: 52.53  E-value: 3.55e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  65 KEIKEILDQYVIGQETAKKALAVAVynHYKRINIGSKIDDVelqkSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATS 144
Cdd:PRK11034  450 KNLGDRLKMLVFGQDKAIEALTEAI--KMSRAGLGHEHKPV----GSFLFAGPTGVGKTEVTVQLSKALGIELLRFDMSE 523

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 145 LTE-----------AGYVGEDVENILLKLiqaadydVEKAEKGIVYIDEIDKiarksENPSITrdvsgegvqQALLKILE 213
Cdd:PRK11034  524 YMErhtvsrligapPGYVGFDQGGLLTDA-------VIKHPHAVLLLDEIEK-----AHPDVF---------NLLLQVMD 582

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 214 -GTVASvppQGGRKHPHQEFIQLDTTNIlficggafdGIEKIIqnrigRKSLGFgaeIQSKKGKNVSEVLKHIlpedllk 292
Cdd:PRK11034  583 nGTLTD---NNGRKADFRNVVLVMTTNA---------GVRETE-----RKSIGL---IHQDNSTDAMEEIKKI------- 635

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 293 ygLIPEFVGRLPVIVTLEALDEkalvRILSEPKNALIKQYQKFFEMDGINLEFKEDALETISKEAMKRNTGARGLRSIIE 372
Cdd:PRK11034  636 --FTPEFRNRLDNIIWFDHLST----DVIHQVVDKFIVELQAQLDQKGVSLEVSQEARDWLAEKGYDRAMGARPMARVIQ 709


                  .
gi 1308675207 373 D 373
Cdd:PRK11034  710 D 710
YifB COG0606
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ...
 75-133 5.39e-07

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: 51.58  E-value: 5.39e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  75 VIGQETAKKALAVAVY-NHykrinigskiddvelqksNIVMLGPTGSGKTLLAQTLARLL 133
Cdd:COG0606   194 VKGQEQAKRALEIAAAgGH------------------NLLMIGPPGSGKTMLARRLPGIL 235
clpC CHL00095
Clp protease ATP binding subunit
 63-414 1.00e-06

Clp protease ATP binding subunit


Pssm-ID: 214361 [Multi-domain]  Cd Length: 821  Bit Score: 51.21  E-value: 1.00e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  63 KPKEIKEILDQYVIGQETAKKALAVAVYNHY---KRIN--IGSKIddvelqksnivMLGPTGSGKTLLAQTLARLLnvpF 137
Cdd:CHL00095  499 KLLHMEETLHKRIIGQDEAVVAVSKAIRRARvglKNPNrpIASFL-----------FSGPTGVGKTELTKALASYF---F 564

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 138 AIADAT---SLTE--------------AGYVGEDVENILLKLIQAADYDVekaekgiVYIDEIDKiARKSenpsitrdvs 200
Cdd:CHL00095  565 GSEDAMirlDMSEymekhtvskligspPGYVGYNEGGQLTEAVRKKPYTV-------VLFDEIEK-AHPD---------- 626

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 201 gegVQQALLKILEGtvasvppqgGR----KHPHQEF---IQLDTTNIlficgGAfdgieKIIQNRIGrkSLGFGAEiQSK 273
Cdd:CHL00095  627 ---IFNLLLQILDD---------GRltdsKGRTIDFkntLIIMTSNL-----GS-----KVIETNSG--GLGFELS-ENQ 681

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 274 KGKNVSEVLKHILPEDLLKYgLIPEFVGRLPVIVTLEALDEKALVRILsepkNALIKQYQKFFEMDGINLEFKEDALETI 353
Cdd:CHL00095  682 LSEKQYKRLSNLVNEELKQF-FRPEFLNRLDEIIVFRQLTKNDVWEIA----EIMLKNLFKRLNEQGIQLEVTERIKTLL 756

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1308675207 354 SKEAMKRNTGARGLRSIIEDIMMDvmyeipsrdditkcTITKEVVNKKEQP---ILLTVERKKK 414
Cdd:CHL00095  757 IEEGYNPLYGARPLRRAIMRLLED--------------PLAEEVLSFKIKPgdiIIVDVNDEKE 806
Mg_chelatase pfam01078
Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that ...
 75-133 1.40e-06

Magnesium chelatase, subunit ChlI; Magnesium-chelatase is a three-component enzyme that catalyzes the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.


Pssm-ID: 426032 [Multi-domain]  Cd Length: 207  Bit Score: 48.69  E-value: 1.40e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  75 VIGQETAKKALAVAVY-NHykrinigskiddvelqksNIVMLGPTGSGKTLLAQTLARLL 133
Cdd:pfam01078   5 VKGQEQAKRALEIAAAgGH------------------NLLMIGPPGSGKTMLAKRLPGIL 46
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 75-218 1.82e-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: 47.73  E-value: 1.82e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  75 VIGQETAKKALAVAVYNHYKRINIGSkiDDVELQKSnIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGED 154
Cdd:cd19509     1 IAGLDDAKEALKEAVILPSLRPDLFP--GLRGPPRG-ILLYGPPGTGKTLLARAVASESGSTFFSISASSLV-SKWVGES 76

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1308675207 155 vENILLKLIQAAdydvEKAEKGIVYIDEIDKI--ARKSENPSITRDVSGEgvqqaLLKILEGTVAS 218
Cdd:cd19509    77 -EKIVRALFALA----RELQPSIIFIDEIDSLlsERGSGEHEASRRVKTE-----FLVQMDGVLNK 132
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
112-189 2.32e-06

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 49.65  E-value: 2.32e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAgYVGEDVENILLKLIQAadydvEKAEKGIVYIDEIDKIARK 189
Cdd:PRK10733  188 VLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEM-FVGVGASRVRDMFEQA-----KKAAPCIIFIDEIDAVGRQ 259
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 63-185 3.59e-06

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: 47.17  E-value: 3.59e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  63 KPKEIKEILDQYVIGQETAKKALAVAVYNHykRINIGSKiddvelQKSNIVML--GPTGSGKTLLAQTLARLL---NVPF 137
Cdd:cd19499     1 KLLNLEERLHERVVGQDEAVKAVSDAIRRA--RAGLSDP------NRPIGSFLflGPTGVGKTELAKALAELLfgdEDNL 72

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 138 AIADATSLTEAGYVGedvenillKLIQAADYDVEKAEKG------------IVYIDEIDK 185
Cdd:cd19499    73 IRIDMSEYMEKHSVS--------RLIGAPPGYVGYTEGGqlteavrrkpysVVLLDEIEK 124
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 75-202 4.45e-06

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: 46.38  E-value: 4.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  75 VIGQETAKKALAVAVYNHYKRINIgskIDDVELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGED 154
Cdd:cd19524     2 IAGQDLAKQALQEMVILPSLRPEL---FTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLT-SKYVGEG 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 1308675207 155 vENILLKLIQAAdydvEKAEKGIVYIDEIDKI--ARKSENPSITRDVSGE 202
Cdd:cd19524    78 -EKLVRALFAVA----RELQPSIIFIDEVDSLlsERSEGEHEASRRLKTE 122
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 112-214 4.64e-06

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 48.75  E-value: 4.64e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDVENiLLKLIQAAdydvEKAEKGIVYIDEIDKIARKSE 191
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIM-SKYYGESEER-LREIFKEA----EENAPSIIFIDEIDAIAPKRE 288

                          90       100
                  ....*....|....*....|...
gi 1308675207 192 npSITRDVSGEGVQQaLLKILEG 214
Cdd:TIGR01243 289 --EVTGEVEKRVVAQ-LLTLMDG 308
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 111-225 8.68e-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: 44.98  E-value: 8.68e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 111 NIVMLGPTGSGKTLLAQTLARLLN--VPFAIADATSLTEAGYVGE-DVENILLKLIQAADYDVEKaEKGIVYIDEIDKIA 187
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSnrPVFYVQLTRDTTEEDLFGRrNIDPGGASWVDGPLVRAAR-EGEIAVLDEINRAN 79

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 1308675207 188 RKsenpsitrdvsgegVQQALLKILEGTVASVPPQGGR 225
Cdd:pfam07728  80 PD--------------VLNSLLSLLDERRLLLPDGGEL 103
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 108-192 9.30e-06

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: 45.44  E-value: 9.30e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  108 QKSNIVMLGPTGSGKTLLAQTLARLLNVP---FAIADATSLTEAGYVGEDVENILL--------KLIQAADYDVEKAEKG 176
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVLDQLLLIIVGGkkasgsgeLRLRLALALARKLKPD 80

                           90
                   ....*....|....*.
gi 1308675207  177 IVYIDEIDKIARKSEN 192
Cdd:smart00382  81 VLILDEITSLLDAEQE 96
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 112-214 1.58e-05

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


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 45.12  E-value: 1.58e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDVENiLLKLIQAAdydvEKAEKGIVYIDEIDKIARKSE 191
Cdd:cd19519    37 ILLYGPPGTGKTLIARAVANETGAFFFLINGPEIM-SKLAGESESN-LRKAFEEA----EKNAPAIIFIDEIDAIAPKRE 110

                          90       100
                  ....*....|....*....|...
gi 1308675207 192 NpsITRDVSGEGVQQaLLKILEG 214
Cdd:cd19519   111 K--THGEVERRIVSQ-LLTLMDG 130
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 75-186 2.98e-05

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: 44.59  E-value: 2.98e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  75 VIGQETAKKALAVAVYNHYKRINIGSKIddvELQKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGED 154
Cdd:cd19525    24 IAGLEFAKKTIKEIVVWPMLRPDIFTGL---RGPPKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLT-SKWVGEG 99

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1308675207 155 VenillKLIQAADYDVEKAEKGIVYIDEIDKI 186
Cdd:cd19525   100 E-----KMVRALFSVARCKQPAVIFIDEIDSL 126
ClpA COG0542
ATP-dependent Clp protease, ATP-binding subunit ClpA [Posttranslational modification, protein ...
 297-372 1.15e-04

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


Pssm-ID: 440308 [Multi-domain]  Cd Length: 836  Bit Score: 44.30  E-value: 1.15e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 297 PEFVGRLPVIVTLEALDEKALVRI----LSEPKNALIKQyqkffemdGINLEFKEDALETISKEAMKRNTGARGLRSIIE 372
Cdd:COG0542   733 PEFLNRIDEIIVFHPLSKEELRKIvdlqLKRLRKRLAER--------GITLELTDAAKDFLAEKGYDPEYGARPLKRAIQ 804
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 108-214 1.38e-04

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


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 42.12  E-value: 1.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 108 QKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAgYVGEDVENILLKLIQAADydvekAEKGIVYIDEIDKIA 187
Cdd:cd19527    25 KRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINM-YIGESEANVREVFQKARD-----AKPCVIFFDELDSLA 98

                          90       100
                  ....*....|....*....|....*..
gi 1308675207 188 RKSENPSITRDVSGEGVQQaLLKILEG 214
Cdd:cd19527    99 PSRGNSGDSGGVMDRVVSQ-LLAELDG 124
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 112-211 1.65e-04

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: 42.09  E-value: 1.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNV--PFAIADATSLTEagYVGEDVENIlLKLIqaADYDVEKAEKG------IVYIDEI 183
Cdd:cd19504    38 ILLYGPPGTGKTLMARQIGKMLNArePKIVNGPEILNK--YVGESEANI-RKLF--ADAEEEQRRLGansglhIIIFDEI 112

                          90       100       110
                  ....*....|....*....|....*....|.
gi 1308675207 184 DKIARKSENpsiTRDVSGEG---VQQALLKI 211
Cdd:cd19504   113 DAICKQRGS---MAGSTGVHdtvVNQLLSKI 140
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 112-202 1.98e-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: 41.89  E-value: 1.98e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDvENILLKLIQAADYDVEKAekgiVYIDEIDKIARK-- 189
Cdd:cd19522    36 VLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLT-SKYRGES-EKLVRLLFEMARFYAPTT----IFIDEIDSICSRrg 109

                          90
                  ....*....|....
gi 1308675207 190 -SENPSITRDVSGE 202
Cdd:cd19522   110 tSEEHEASRRVKSE 123
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 108-214 2.04e-04

second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as Peroxin-1)/PEX6 is a protein unfoldase; PEX1 and PEX6 form a heterohexameric Type-2 AAA-ATPase complex and are essential for peroxisome biogenesis as they are required for the import of folded proteins into the peroxisomal matrix. PEX-1 is required for stability of PEX5. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410934 [Multi-domain]  Cd Length: 158  Bit Score: 41.65  E-value: 2.04e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 108 QKSNIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDVENILLKLIQAAdydveKAEKGIVYIDEIDKIA 187
Cdd:cd19526    26 LRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELL-NKYIGASEQNVRDLFSRAQ-----SAKPCILFFDEFDSIA 99

                          90       100
                  ....*....|....*....|....*....
gi 1308675207 188 --RKSENPSITRDVsgegVQQaLLKILEG 214
Cdd:cd19526   100 pkRGHDSTGVTDRV----VNQ-LLTQLDG 123
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 109-244 2.60e-04

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


Pssm-ID: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 41.78  E-value: 2.60e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 109 KSNIVML-GPTGSGKTLLAQTLARLLNVPFA------IADatsltEA-------GYVGEDVENILLKLIQAadydveKAE 174
Cdd:cd19500    36 KGPILCLvGPPGVGKTSLGKSIARALGRKFVrislggVRD-----EAeirghrrTYVGAMPGRIIQALKKA------GTN 104

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1308675207 175 KGIVYIDEIDKIARKSE-NPSitrdvsgegvqQALLKILEgtvasvPPQGGRKHPHQEFIQLDTTNILFIC 244
Cdd:cd19500   105 NPVFLLDEIDKIGSSFRgDPA-----------SALLEVLD------PEQNSTFSDHYLDVPFDLSKVLFIA 158
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 112-194 2.65e-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: 41.26  E-value: 2.65e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYvGEDVenillKLIQAADYDVEKAEKGIVYIDEIDKIARkSE 191
Cdd:cd19520    38 VLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWY-GESQ-----KLVAAVFSLASKLQPSIIFIDEIDSFLR-QR 110


                  ...
gi 1308675207 192 NPS 194
Cdd:cd19520   111 SST 113
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 112-212 3.11e-04

proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily contains ATPase subunits of the eukaryotic 26S proteasome, and of the archaeal proteasome which carry out ATP-dependent degradation of substrates of the ubiquitin-proteasome pathway. The eukaryotic 26S proteasome consists of a proteolytic 20S core particle (CP), and a 19S regulatory particle (RP) which provides the ATP-dependence and the specificity for ubiquitinated proteins. In the archaea the RP is a homohexameric complex of proteasome-activating nucleotidase (PAN). This subfamily also includes various eukaryotic 26S subunits including, proteasome 26S subunit, ATPase 2 (PSMC2, also known as S7 and MSS1) which is a member of the 19S RP and has a chaperone like activity; and proteasome 20S subunit alpha 6 (PSMA6, also known as IOTA, p27K, and PROS27) which is a member of the 20S CP. This RecA-like_PAN subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 41.17  E-value: 3.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAgYVGEDVEnILLKLIQAADydvEKAeKGIVYIDEIDKIARKSE 191
Cdd:cd19502    40 VLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQK-YIGEGAR-LVRELFEMAR---EKA-PSIIFIDEIDAIGAKRF 113

                          90       100
                  ....*....|....*....|.
gi 1308675207 192 NPSITRDvsgEGVQQALLKIL 212
Cdd:cd19502   114 DSGTGGD---REVQRTMLELL 131
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 111-198 4.26e-04

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: 40.59  E-value: 4.26e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 111 NIVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGYVGedveniLLKLIQAADYdVEKAEKG-IVYIDEIDKIARK 189
Cdd:cd19512    24 NILFYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREG------VTAIHKVFDW-ANTSRRGlLLFVDEADAFLRK 96


                  ....*....
gi 1308675207 190 SENPSITRD 198
Cdd:cd19512    97 RSTEKISED 105
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 112-185 5.87e-04

ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of photosynthesis in cyanobacteria, especially in CO2 uptake and utilization. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410915 [Multi-domain]  Cd Length: 161  Bit Score: 40.43  E-value: 5.87e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGEDVENiLLKLIQAAdydvEKAEKGIVYIDEIDK 185
Cdd:cd19507    34 LLLVGIQGTGKSLTAKAIAGVWQLPLLRLDMGRLF-GGLVGESESR-LRQMIQTA----EAIAPCVLWIDEIEK 101
NadR3 COG3172
Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase ...
 112-181 1.12e-03

Nicotinamide riboside kinase [Coenzyme transport and metabolism]; Nicotinamide riboside kinase is part of the Pathway/BioSystem: NAD biosynthesis


Pssm-ID: 442405 [Multi-domain]  Cd Length: 178  Bit Score: 39.80  E-value: 1.12e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAiadatslTEAG----------YVGEDVENILLKLIQAADYDVEKAEKgIVYID 181
Cdd:COG3172    11 IVLLGAESTGKTTLARALAAHYNTPWV-------PEYGreyleekgraLTYDDLLAIARGQLALEDAAAKRANK-LLFCD 82
aroK PRK00131
shikimate kinase; Reviewed
 107-137 1.41e-03

shikimate kinase; Reviewed


Pssm-ID: 234654 [Multi-domain]  Cd Length: 175  Bit Score: 39.40  E-value: 1.41e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1308675207 107 LQKSNIVMLGPTGSGKTLLAQTLARLLNVPF 137
Cdd:PRK00131    2 LKGPNIVLIGFMGAGKSTIGRLLAKRLGYDF 32
GntK cd02021
Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting ...
 112-142 1.47e-03

Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.


Pssm-ID: 238979 [Multi-domain]  Cd Length: 150  Bit Score: 38.77  E-value: 1.47e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADA 142
Cdd:cd02021     2 IVVMGVSGSGKSTVGKALAERLGAPFIDGDD 32
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
71-191 2.61e-03

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 39.73  E-value: 2.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207  71 LDQYvIGQETAKKALAVAVYNHYKRiniGSKIDDVELQksnivmlGPTGSGKTLLAQTLARLLNVPFAIADATSLTEAGy 150
Cdd:PRK00080   24 LDEF-IGQEKVKENLKIFIEAAKKR---GEALDHVLLY-------GPPGLGKTTLANIIANEMGVNIRITSGPALEKPG- 91

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|..
gi 1308675207 151 vgeDVENILLKLiqaadydvekaEKG-IVYIDEIDKIARKSE 191
Cdd:PRK00080   92 ---DLAAILTNL-----------EEGdVLFIDEIHRLSPVVE 119
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 116-216 3.19e-03

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 39.68  E-value: 3.19e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 116 GPTGSGKTLLAQTLARLLNVPFAIADATSlteAGyVGEdveniLLKLIQAADYDVEKAEKGIVYIDEIDkiaR--KSEnp 193
Cdd:PRK13342   43 GPPGTGKTTLARIIAGATDAPFEALSAVT---SG-VKD-----LREVIEEARQRRSAGRRTILFIDEIH---RfnKAQ-- 108

                          90       100
                  ....*....|....*....|....
gi 1308675207 194 sitrdvsgegvQQALLKILE-GTV 216
Cdd:PRK13342  109 -----------QDALLPHVEdGTI 121
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 112-187 4.54e-03

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


Pssm-ID: 410937 [Multi-domain]  Cd Length: 159  Bit Score: 37.48  E-value: 4.54e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPFAIADATSLTeAGYVGED---VENILLKLIQAAdydvekaeKGIVYIDEIDKIA 187
Cdd:cd19529    30 ILLYGPPGTGKTLLAKAVATESNANFISVKGPELL-SKWVGESekaIREIFRKARQVA--------PCVIFFDEIDSIA 99
SK cd00464
Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic ...
 111-137 5.05e-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: 5.05e-03
                          10        20
                  ....*....|....*....|....*..
gi 1308675207 111 NIVMLGPTGSGKTLLAQTLARLLNVPF 137
Cdd:cd00464     1 NIVLIGMMGAGKTTVGRLLAKALGLPF 27
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 112-194 5.67e-03

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: 37.26  E-value: 5.67e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1308675207 112 IVMLGPTGSGKTLLAQTLARLLNVPF-AIADATSLTEagYVGEDvENILLKLIQAAdydvEKAEKGIVYIDEIDKIA-RK 189
Cdd:cd19511    30 VLLYGPPGCGKTLLAKALASEAGLNFiSVKGPELFSK--YVGES-ERAVREIFQKA----RQAAPCIIFFDEIDSLApRR 102


                  ....*
gi 1308675207 190 SENPS 194
Cdd:cd19511   103 GQSDS 107
 
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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