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Conserved domains on  [gi|40806173|ref|NP_955399|]
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mitochondrial inner membrane m-AAA protease component paraplegin isoform 2 precursor [Homo sapiens]

Protein Classification

ATP-dependent metallopeptidase FtsH/Yme1/Tma family protein( domain architecture ID 1000290)

ATP-dependent metallopeptidase FtsH/Yme1/Tma family protein such as ATP-dependent zinc metalloprotease FtsH, which targets both cytoplasmic and membrane proteins and plays a role in quality control of integral membrane proteins

Gene Ontology:  GO:0016020
PubMed:  31988523|29097521|22498346|19656850|16966379|10788805

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HflB super family cl33892
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
147-442 3.66e-91

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


The actual alignment was detected with superfamily member COG0465:

Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 288.86  E-value: 3.66e-91
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 147 VIAVVMSLLNALSTSGGS---ISWNDFVhEMLAKGEVQRVQVVPesDVVEVYLHPGAvvfgrprlALMYRMQVANIDKFE 223
Cdd:COG0465   1 IALLLVLLFNLFSSSSSSvkeISYSEFL-QLVEAGKVKSVTIQG--DRITGTLKDGT--------KTRFTTYRVNDPELV 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 224 EKLRAAEDELNIEAKDRipvsykrTGFFGNALYSVGMTAVGLAILWYVFRlaGMTGREGGFSAFNQLKmARftIVDGKMG 303
Cdd:COG0465  70 DLLEEKGVEVTAKPPEE-------SSWLLSLLISLLPILLLIGLWIFFMR--RMQGGGGGAMSFGKSK-AK--LYDEDKP 137

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 304 KgVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIG 383
Cdd:COG0465 138 K-VTFDDVAGVDEAKEELQEIVDFLKDPEKFTRLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFV 216

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173 384 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:COG0465 217 GVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG-GHDEREQTLNQLLVEMDG 274
 
Name Accession Description Interval E-value
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
147-442 3.66e-91

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 288.86  E-value: 3.66e-91
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 147 VIAVVMSLLNALSTSGGS---ISWNDFVhEMLAKGEVQRVQVVPesDVVEVYLHPGAvvfgrprlALMYRMQVANIDKFE 223
Cdd:COG0465   1 IALLLVLLFNLFSSSSSSvkeISYSEFL-QLVEAGKVKSVTIQG--DRITGTLKDGT--------KTRFTTYRVNDPELV 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 224 EKLRAAEDELNIEAKDRipvsykrTGFFGNALYSVGMTAVGLAILWYVFRlaGMTGREGGFSAFNQLKmARftIVDGKMG 303
Cdd:COG0465  70 DLLEEKGVEVTAKPPEE-------SSWLLSLLISLLPILLLIGLWIFFMR--RMQGGGGGAMSFGKSK-AK--LYDEDKP 137

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 304 KgVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIG 383
Cdd:COG0465 138 K-VTFDDVAGVDEAKEELQEIVDFLKDPEKFTRLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFV 216

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173 384 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:COG0465 217 GVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG-GHDEREQTLNQLLVEMDG 274
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 306-442 9.32e-82

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: 250.61  E-value: 9.32e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 306 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGL 385
Cdd:cd19501   1 VTFKDVAGCEEAKEELKEVVEFLKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGV 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173 386 GAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:cd19501  81 GASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGG-GHDEREQTLNQLLVEMDG 136
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 265-442 2.26e-72

ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273520 [Multi-domain]  Cd Length: 495  Bit Score: 237.57  E-value: 2.26e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   265 LAILWYVFRLAgMTGreGGFSAFNQLKM-ARFTIvdgKMGKGVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPK 343
Cdd:TIGR01241  16 LVGVWFFFRRQ-MQG--GGGRAFSFGKSkAKLLN---EEKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPK 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   344 GALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSG 423
Cdd:TIGR01241  90 GVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG 169

                         170
                  ....*....|....*....
gi 40806173   424 fSNTEEEQTLNQLLVEMDG 442
Cdd:TIGR01241 170 -GNDEREQTLNQLLVEMDG 187
ftsH CHL00176
cell division protein; Validated
 265-442 2.62e-65

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 222.23  E-value: 2.62e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  265 LAILWYVFRLAGMTGREGGFSAFNQLKM-ARF-TIVDgkmgKGVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVP 342
Cdd:CHL00176 141 IGVLWFFFQRSSNFKGGPGQNLMNFGKSkARFqMEAD----TGITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIP 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  343 KGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMS 422
Cdd:CHL00176 217 KGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIG 296

                        170       180
                 ....*....|....*....|
gi 40806173  423 GfSNTEEEQTLNQLLVEMDG 442
Cdd:CHL00176 297 G-GNDEREQTLNQLLTEMDG 315
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 346-447 5.79e-35

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: 126.94  E-value: 5.79e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfs 425
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDS-- 79

                          90       100
                  ....*....|....*....|..
gi 40806173   426 ntEEEQTLNQLLVEMDGASLDQ 447
Cdd:pfam00004  80 --ESRRVVNQLLTELDGFTSSN 99
cell_div_CdvC NF041006
cell division protein CdvC;
306-442 9.70e-22

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 96.73  E-value: 9.70e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  306 VSFKDVAGMHEAKLEVREFVDY-LKSPERFlQLGAkvPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGG 384
Cdd:NF041006 100 VTFSDIVGLEDVKEALKEAIVYpSKRPDLF-PLGW--PRGILLYGPPGCGKTMLAAAVANEIDSEFIHVDAASIMSKWLG 176

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40806173  385 LGAARVRSLFKEARARA-----PCIVYIDEIDAVGKKRSTTMSGfsnteEEQTLNQLLVEMDG 442
Cdd:NF041006 177 EAEKNVAKIFKKAREKSkeegkPAIIFIDEIDALLGVYSSEVGG-----EVRVRNQFLKEMDG 234
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 342-418 1.07e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.00  E-value: 1.07e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173    342 PKGALLLGPPGCGKTLLAKAVATEAQVP---FLAMAGPEFVEVI--------------GGLGAARVRSLFKEARARAPCI 404
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVldqllliivggkkaSGSGELRLRLALALARKLKPDV 81

                           90
                   ....*....|....
gi 40806173    405 VYIDEIDAVGKKRS 418
Cdd:smart00382  82 LILDEITSLLDAEQ 95
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 346-410 4.04e-03

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 38.99  E-value: 4.04e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173  346 LLLGPPGCGKTLLAKAVATEAqvpflAMAG--------PEFVEViggLGAARV-RSLFKEAR--ARAPCIVyIDEI 410
Cdd:NF038214  94 LLLGPPGTGKTHLAIALGYAA-----CRQGyrvrfttaADLVEQ---LAQARAdGRLGRLLRrlARYDLLI-IDEL 160
 
Name Accession Description Interval E-value
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
147-442 3.66e-91

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 288.86  E-value: 3.66e-91
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 147 VIAVVMSLLNALSTSGGS---ISWNDFVhEMLAKGEVQRVQVVPesDVVEVYLHPGAvvfgrprlALMYRMQVANIDKFE 223
Cdd:COG0465   1 IALLLVLLFNLFSSSSSSvkeISYSEFL-QLVEAGKVKSVTIQG--DRITGTLKDGT--------KTRFTTYRVNDPELV 69

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 224 EKLRAAEDELNIEAKDRipvsykrTGFFGNALYSVGMTAVGLAILWYVFRlaGMTGREGGFSAFNQLKmARftIVDGKMG 303
Cdd:COG0465  70 DLLEEKGVEVTAKPPEE-------SSWLLSLLISLLPILLLIGLWIFFMR--RMQGGGGGAMSFGKSK-AK--LYDEDKP 137

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 304 KgVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIG 383
Cdd:COG0465 138 K-VTFDDVAGVDEAKEELQEIVDFLKDPEKFTRLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFV 216

                       250       260       270       280       290
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173 384 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:COG0465 217 GVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG-GHDEREQTLNQLLVEMDG 274
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 306-442 9.32e-82

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: 250.61  E-value: 9.32e-82
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 306 VSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGL 385
Cdd:cd19501   1 VTFKDVAGCEEAKEELKEVVEFLKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGV 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173 386 GAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:cd19501  81 GASRVRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGG-GHDEREQTLNQLLVEMDG 136
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 265-442 2.26e-72

ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH. [Cellular processes, Cell division, Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273520 [Multi-domain]  Cd Length: 495  Bit Score: 237.57  E-value: 2.26e-72
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   265 LAILWYVFRLAgMTGreGGFSAFNQLKM-ARFTIvdgKMGKGVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPK 343
Cdd:TIGR01241  16 LVGVWFFFRRQ-MQG--GGGRAFSFGKSkAKLLN---EEKPKVTFKDVAGIDEAKEELMEIVDFLKNPSKFTKLGAKIPK 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   344 GALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSG 423
Cdd:TIGR01241  90 GVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGG 169

                         170
                  ....*....|....*....
gi 40806173   424 fSNTEEEQTLNQLLVEMDG 442
Cdd:TIGR01241 170 -GNDEREQTLNQLLVEMDG 187
ftsH CHL00176
cell division protein; Validated
 265-442 2.62e-65

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 222.23  E-value: 2.62e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  265 LAILWYVFRLAGMTGREGGFSAFNQLKM-ARF-TIVDgkmgKGVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVP 342
Cdd:CHL00176 141 IGVLWFFFQRSSNFKGGPGQNLMNFGKSkARFqMEAD----TGITFRDIAGIEEAKEEFEEVVSFLKKPERFTAVGAKIP 216

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  343 KGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMS 422
Cdd:CHL00176 217 KGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRGAGIG 296

                        170       180
                 ....*....|....*....|
gi 40806173  423 GfSNTEEEQTLNQLLVEMDG 442
Cdd:CHL00176 297 G-GNDEREQTLNQLLTEMDG 315
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 305-442 5.60e-54

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 184.05  E-value: 5.60e-54
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 305 GVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIG 383
Cdd:COG1222  74 DVTFDDIGGLDEQIEEIREAVELpLKNPELFRKYGIEPPKGVLLYGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKYI 153

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173 384 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSttmSGFSNTEEEQTLNQLLVEMDG 442
Cdd:COG1222 154 GEGARNVREVFELAREKAPSIIFIDEIDAIAARRT---DDGTSGEVQRTVNQLLAELDG 209
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
265-442 1.18e-52

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 188.32  E-value: 1.18e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  265 LAILWYVFRLAGMTGREG-GFSAFNQLKMARFTIVDGKmgkgVSFKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPK 343
Cdd:PRK10733 111 LLIGVWIFFMRQMQGGGGkGAMSFGKSKARMLTEDQIK----TTFADVAGCDEAKEEVAELVEYLREPSRFQKLGGKIPK 186

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  344 GALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSG 423
Cdd:PRK10733 187 GVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRGAGLGG 266

                        170
                 ....*....|....*....
gi 40806173  424 fSNTEEEQTLNQLLVEMDG 442
Cdd:PRK10733 267 -GHDEREQTLNQMLVEMDG 284
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 305-442 4.09e-45

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 162.31  E-value: 4.09e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  305 GVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIG 383
Cdd:PRK03992 127 NVTYEDIGGLEEQIREVREAVELpLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQKFI 206

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  384 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRstTMSGFSNTEEEQ-TLNQLLVEMDG 442
Cdd:PRK03992 207 GEGARLVRELFELAREKAPSIIFIDEIDAIAAKR--TDSGTSGDREVQrTLMQLLAEMDG 264
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 307-442 2.16e-41

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: 145.56  E-value: 2.16e-41
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 307 SFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGL 385
Cdd:cd19502   1 TYEDIGGLDEQIREIREVVELpLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKYIGE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173 386 GAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:cd19502  81 GARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTG-GDREVQRTMLELLNQLDG 136
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 317-442 1.60e-39

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: 140.11  E-value: 1.60e-39
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 317 AKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKE 396
Cdd:cd19481   1 LKASLREAVEAPRRGSRLRRYGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVGESEKNLRKIFER 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 40806173 397 ARARAPCIVYIDEIDAVGKKRSttmSGFSNTEEEQTLNQLLVEMDG 442
Cdd:cd19481  81 ARRLAPCILFIDEIDAIGRKRD---SSGESGELRRVLNQLLTELDG 123
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 317-444 2.48e-38

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: 137.03  E-value: 2.48e-38
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 317 AKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFK 395
Cdd:cd19511   1 VKRELKEAVEWpLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSKYVGESERAVREIFQ 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 40806173 396 EARARAPCIVYIDEIDAVGKKRSTTMSGfsnTEEEQTLNQLLVEMDGAS 444
Cdd:cd19511  81 KARQAAPCIIFFDEIDSLAPRRGQSDSS---GVTDRVVSQLLTELDGIE 126
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 310-442 1.67e-37

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: 135.22  E-value: 1.67e-37
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDYLKS-PERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAA 388
Cdd:cd19518   1 DIGGMDSTLKELCELLIHPILpPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGELKVPFLKISATEIVSGVSGESEE 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 40806173 389 RVRSLFKEARARAPCIVYIDEIDAVGKKRSTTmsgfSNTEEEQTLNQLLVEMDG 442
Cdd:cd19518  81 KIRELFDQAISNAPCIVFIDEIDAITPKRESA----QREMERRIVSQLLTCMDE 130
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 318-442 1.19e-36

second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP in metazoans is an ATP-dependent molecular chaperone which plays an essential role in many cellular processes, by segregating polyubiquitinated proteins from complexes or membranes. Cdc48/p97 consists of an N-terminal domain and two ATPase domains; this subfamily represents the second of the two ATPase domains. CDC48's roles include in the fragmentation of Golgi stacks during mitosis and for their reassembly after mitosis, and in the formation of the nuclear envelope, and of the transitional endoplasmic reticulum (tER). This RecA-like_cdc48_r2-like subfamily belongs to the RecA-like family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410936 [Multi-domain]  Cd Length: 161  Bit Score: 132.63  E-value: 1.19e-36
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 318 KLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKE 396
Cdd:cd19528   2 KRELQELVQYpVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFDK 81

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 40806173 397 ARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:cd19528  82 ARAAAPCVLFFDELDSIAKARGGNIGD-AGGAADRVINQILTEMDG 126
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 308-442 1.24e-35

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: 136.58  E-value: 1.24e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 308 FKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFV-EVIGGL 385
Cdd:COG0464 156 LDDLGGLEEVKEELRELVALpLKRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVsKYVGET 235

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173 386 gAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEeeqtLNQLLVEMDG 442
Cdd:COG0464 236 -EKNLREVFDKARGLAPCVLFIDEADALAGKRGEVGDGVGRRV----VNTLLTEMEE 287
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 306-442 5.59e-35

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: 138.89  E-value: 5.59e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   306 VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGG 384
Cdd:TIGR01243 450 VRWSDIGGLEEVKQELREAVEWpLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGPEILSKWVG 529

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 40806173   385 LGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTmsgFSNTEEEQTLNQLLVEMDG 442
Cdd:TIGR01243 530 ESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGAR---FDTSVTDRIVNQLLTEMDG 584
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 346-447 5.79e-35

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: 126.94  E-value: 5.79e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfs 425
Cdd:pfam00004   2 LLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDS-- 79

                          90       100
                  ....*....|....*....|..
gi 40806173   426 ntEEEQTLNQLLVEMDGASLDQ 447
Cdd:pfam00004  80 --ESRRVVNQLLTELDGFTSSN 99
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 317-442 7.30e-34

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: 125.30  E-value: 7.30e-34
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 317 AKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFK 395
Cdd:cd19529   1 VKQELKEAVEWpLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATESNANFISVKGPELLSKWVGESEKAIREIFR 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*...
gi 40806173 396 EARARAPCIVYIDEIDAVGKKR-STTMSGFSnteeEQTLNQLLVEMDG 442
Cdd:cd19529  81 KARQVAPCVIFFDEIDSIAPRRgTTGDSGVT----ERVVNQLLTELDG 124
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 310-444 1.11e-33

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: 124.71  E-value: 1.11e-33
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAA 388
Cdd:cd19503   1 DIGGLDEQIASLKELIELpLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSIVSKYLGESEK 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173 389 RVRSLFKEARARAPCIVYIDEIDAVGKKRSTTmsgfSNTEEEQTLNQLLVEMDGAS 444
Cdd:cd19503  81 NLREIFEEARSHAPSIIFIDEIDALAPKREED----QREVERRVVAQLLTLMDGMS 132
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 310-442 2.30e-32

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: 121.39  E-value: 2.30e-32
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAA 388
Cdd:cd19519   1 DIGGCRKQLAQIREMVELpLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESES 80

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 40806173 389 RVRSLFKEARARAPCIVYIDEIDAVGKKRSTTmsgfSNTEEEQTLNQLLVEMDG 442
Cdd:cd19519  81 NLRKAFEEAEKNAPAIIFIDEIDAIAPKREKT----HGEVERRIVSQLLTLMDG 130
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 306-447 3.35e-31

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 124.49  E-value: 3.35e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  306 VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGG 384
Cdd:PTZ00454 142 VTYSDIGGLDIQKQEIREAVELpLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFIRVVGSEFVQKYLG 221

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40806173  385 LGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDGasLDQ 447
Cdd:PTZ00454 222 EGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTG-ADREVQRILLELLNQMDG--FDQ 281
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 306-442 5.49e-31

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: 126.95  E-value: 5.49e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   306 VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGG 384
Cdd:TIGR01243 175 VTYEDIGGLKEAKEKIREMVELpMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAYFISINGPEIMSKYYG 254

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 40806173   385 LGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTmsgfSNTEEEQTLNQLLVEMDG 442
Cdd:TIGR01243 255 ESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEV----TGEVEKRVVAQLLTLMDG 308
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 328-444 7.61e-31

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


Pssm-ID: 410938 [Multi-domain]  Cd Length: 161  Bit Score: 116.82  E-value: 7.61e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 328 LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYI 407
Cdd:cd19530  16 IKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANESGANFISVKGPELLNKYVGESERAVRQVFQRARASAPCVIFF 95

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 40806173 408 DEIDAVGKKRSTTMSGFSnteeEQTLNQLLVEMDGAS 444
Cdd:cd19530  96 DEVDALVPKRGDGGSWAS----ERVVNQLLTEMDGLE 128
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 307-442 1.06e-30

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 123.73  E-value: 1.06e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  307 SFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGL 385
Cdd:PTZ00361 181 SYADIGGLEQQIQEIKEAVELpLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGD 260

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173  386 GAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGfSNTEEEQTLNQLLVEMDG 442
Cdd:PTZ00361 261 GPKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSG-GEKEIQRTMLELLNQLDG 316
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
308-442 1.30e-30

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 118.83  E-value: 1.30e-30
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 308 FKDVAGMHEAKLEVREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMagpEFVEVIG---G 384
Cdd:COG1223   1 LDDVVGQEEAKKKLKLIIKELRRRENLRKFGLWPPRKILFYGPPGTGKTMLAEALAGELKLPLLTV---RLDSLIGsylG 77

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 385 LGAARVRSLFKEARaRAPCIVYIDEIDAVGKKRsttmsGFSNTEEE--QTLNQLLVEMDG 442
Cdd:COG1223  78 ETARNLRKLFDFAR-RAPCVIFFDEFDAIAKDR-----GDQNDVGEvkRVVNALLQELDG 131
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 311-442 2.08e-27

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: 107.44  E-value: 2.08e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 311 VAGMHEAKLEVREFVDY-LKSPERFlQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAAR 389
Cdd:cd19509   1 IAGLDDAKEALKEAVILpSLRPDLF-PGLRGPPRGILLYGPPGTGKTLLARAVASESGSTFFSISASSLVSKWVGESEKI 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|...
gi 40806173 390 VRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEeqtlNQLLVEMDG 442
Cdd:cd19509  80 VRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVK----TEFLVQMDG 128
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 329-443 1.83e-25

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: 102.12  E-value: 1.83e-25
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 329 KSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYID 408
Cdd:cd19526  14 KYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFSRAQSAKPCILFFD 93

                        90       100       110
                ....*....|....*....|....*....|....*
gi 40806173 409 EIDAVGKKRSTTMSGFSnteeEQTLNQLLVEMDGA 443
Cdd:cd19526  94 EFDSIAPKRGHDSTGVT----DRVVNQLLTQLDGV 124
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 328-444 2.70e-24

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: 98.74  E-value: 2.70e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 328 LKSPERFlQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAARVRSLFKEARARAPCIVYI 407
Cdd:cd19527  13 LEHPELF-SSGLRKRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINMYIGESEANVREVFQKARDAKPCVIFF 91

                        90       100       110
                ....*....|....*....|....*....|....*..
gi 40806173 408 DEIDAVGKKRSTtmSGFSNTEEEQTLNQLLVEMDGAS 444
Cdd:cd19527  92 DELDSLAPSRGN--SGDSGGVMDRVVSQLLAELDGMS 126
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 310-444 2.22e-23

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: 96.59  E-value: 2.22e-23
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLqlGAKVP-KGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGA 387
Cdd:cd19522   1 DIADLEEAKKLLEEAVVLpMWMPEFFK--GIRRPwKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKYRGESE 78

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173 388 ARVRSLFKEARARAPCIVYIDEIDAVGKKRSTtmsGFSNTEEEQTLNQLLVEMDGAS 444
Cdd:cd19522  79 KLVRLLFEMARFYAPTTIFIDEIDSICSRRGT---SEEHEASRRVKSELLVQMDGVG 132
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 303-444 9.26e-22

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: 92.74  E-value: 9.26e-22
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 303 GKGVSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKvPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEV 381
Cdd:cd19525  16 GPPINWADIAGLEFAKKTIKEIVVWpMLRPDIFTGLRGP-PKGILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSK 94

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40806173 382 IGGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTmsgfSNTEEEQTLNQLLVEMDGAS 444
Cdd:cd19525  95 WVGEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEG----EHESSRRIKTEFLVQLDGAT 153
cell_div_CdvC NF041006
cell division protein CdvC;
306-442 9.70e-22

cell division protein CdvC;


Pssm-ID: 468935 [Multi-domain]  Cd Length: 371  Bit Score: 96.73  E-value: 9.70e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  306 VSFKDVAGMHEAKLEVREFVDY-LKSPERFlQLGAkvPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGG 384
Cdd:NF041006 100 VTFSDIVGLEDVKEALKEAIVYpSKRPDLF-PLGW--PRGILLYGPPGCGKTMLAAAVANEIDSEFIHVDAASIMSKWLG 176

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40806173  385 LGAARVRSLFKEARARA-----PCIVYIDEIDAVGKKRSTTMSGfsnteEEQTLNQLLVEMDG 442
Cdd:NF041006 177 EAEKNVAKIFKKAREKSkeegkPAIIFIDEIDALLGVYSSEVGG-----EVRVRNQFLKEMDG 234
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 306-446 2.61e-21

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


Pssm-ID: 410929 [Multi-domain]  Cd Length: 170  Bit Score: 90.69  E-value: 2.61e-21
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 306 VSFKDVAGMHEAKLEVREFVDYlksPERFLQL--GAKVP-KGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVI 382
Cdd:cd19521   4 VKWEDVAGLEGAKEALKEAVIL---PVKFPHLftGNRKPwSGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKW 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40806173 383 GGLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSnteeEQTLNQLLVEMDGASLD 446
Cdd:cd19521  81 MGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEAS----RRIKTELLVQMNGVGND 140
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 306-446 1.16e-20

proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 200312 [Multi-domain]  Cd Length: 512  Bit Score: 94.78  E-value: 1.16e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   306 VSFKDVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATE-AQVP---------FLAMA 374
Cdd:TIGR03689 179 VTYADIGGLGSQIEQIRDAVELpFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVANSlAARIgaegggksyFLNIK 258

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173   375 GPEFVEVIGGLGAARVRSLFKEARARA----PCIVYIDEIDAVGKKRSttmSGFSNTEEEQTLNQLLVEMDGA-SLD 446
Cdd:TIGR03689 259 GPELLNKYVGETERQIRLIFQRAREKAsegrPVIVFFDEMDSLFRTRG---SGVSSDVETTVVPQLLAEIDGVeSLD 332
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 310-443 2.41e-20

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: 87.98  E-value: 2.41e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLQLGAKvPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAA 388
Cdd:cd19524   1 DIAGQDLAKQALQEMVILpSLRPELFTGLRAP-ARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEK 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173 389 RVRSLFKEARARAPCIVYIDEIDAVGKKRSTtmsgfSNTEEEQTL-NQLLVEMDGA 443
Cdd:cd19524  80 LVRALFAVARELQPSIIFIDEVDSLLSERSE-----GEHEASRRLkTEFLIEFDGV 130
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 310-420 1.81e-19

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: 85.55  E-value: 1.81e-19
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLQLG-AKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGA 387
Cdd:cd19520   1 DIGGLDEVITELKELVILpLQRPELFDNSRlLQPPKGVLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWYGESQ 80

                        90       100       110
                ....*....|....*....|....*....|...
gi 40806173 388 ARVRSLFKEARARAPCIVYIDEIDAVGKKRSTT 420
Cdd:cd19520  81 KLVAAVFSLASKLQPSIIFIDEIDSFLRQRSST 113
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 322-448 1.68e-16

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: 77.14  E-value: 1.68e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 322 REFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVAT--EAQVPFLaMAGPEFVEVIGGLGAARVRSLFKEA-- 397
Cdd:cd19504  15 RAFASRVFPPEIVEQLGCKHVKGILLYGPPGTGKTLMARQIGKmlNAREPKI-VNGPEILNKYVGESEANIRKLFADAee 93

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 40806173 398 --RARAPC----IVYIDEIDAVGKKRSTTMSGfsNTEEEQTLNQLLVEMDGasLDQL 448
Cdd:cd19504  94 eqRRLGANsglhIIIFDEIDAICKQRGSMAGS--TGVHDTVVNQLLSKIDG--VEQL 146
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 312-430 7.79e-16

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 74.49  E-value: 7.79e-16
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 312 AGMHEAKLEVREFVDYlksperflqlgaKVPKGALLLGPPGCGKTLLAKAVATEA---QVPFLAMAGPEFVE---VIGGL 385
Cdd:cd00009   1 VGQEEAIEALREALEL------------PPPKNLLLYGPPGTGKTTLARAIANELfrpGAPFLYLNASDLLEglvVAELF 68

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*
gi 40806173 386 GAARVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEE 430
Cdd:cd00009  69 GHFLVRLLFELAEKAKPGVLFIDEIDSLSRGAQNALLRVLETLND 113
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 310-411 4.71e-15

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: 72.79  E-value: 4.71e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAK--LEVREfVDYLKSPERFlqlGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGA 387
Cdd:cd19507   1 DVGGLDNLKdwLKKRK-AAFSKQASAY---GLPTPKGLLLVGIQGTGKSLTAKAIAGVWQLPLLRLDMGRLFGGLVGESE 76

                        90       100
                ....*....|....*....|....
gi 40806173 388 ARVRSLFKEARARAPCIVYIDEID 411
Cdd:cd19507  77 SRLRQMIQTAEAIAPCVLWIDEIE 100
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 310-442 4.94e-15

ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces cerevisiae Yta7 is a chromatin-associated AAA-ATPase involved in regulation of chromatin dynamics. Its human ortholog ANCCA/ATAD2 transcriptionally activates pathways of malignancy in a broad range of cancers. The RecA-like_Yta7 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: 410925 [Multi-domain]  Cd Length: 170  Bit Score: 72.93  E-value: 4.94e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEA-----QVPFLAMAGPEFVEVIG 383
Cdd:cd19517   1 DIGGLSHYINQLKEMVFFpLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECskggqKVSFFMRKGADCLSKWV 80

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 40806173 384 GLGAARVRSLFKEARARAPCIVYIDEIDAVGKKRSttmsgfsnTEEEQT----LNQLLVEMDG 442
Cdd:cd19517  81 GEAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRS--------SKQEQIhasiVSTLLALMDG 135
ycf46 CHL00195
Ycf46; Provisional
 306-426 1.52e-12

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 69.66  E-value: 1.52e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  306 VSFKDVAGMHEAKlevrefvDYLKS-----PERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAM-AGPEFV 379
Cdd:CHL00195 225 EKISDIGGLDNLK-------DWLKKrstsfSKQASNYGLPTPRGLLLVGIQGTGKSLTAKAIANDWQLPLLRLdVGKLFG 297

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 40806173  380 EVIGGlGAARVRSLFKEARARAPCIVYIDEID-AVGKKRSTTMSGFSN 426
Cdd:CHL00195 298 GIVGE-SESRMRQMIRIAEALSPCILWIDEIDkAFSNSESKGDSGTTN 344
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 310-442 4.55e-11

ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent 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: 410931 [Multi-domain]  Cd Length: 163  Bit Score: 61.44  E-value: 4.55e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 310 DVAGMHEAKLEVREFVDY-LKSPERFLQLgAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVIGGLGAA 388
Cdd:cd19523   1 DIAGLGALKAAIKEEVLWpLLRPDAFSGL-LRLPRSILLFGPRGTGKTLLGRCLASQLGATFLRLRGSTLVAKWAGEGEK 79

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|....
gi 40806173 389 RVRSLFKEARARAPCIVYIDEIDAVGKKRSTTMSGFSNTEEEqtlnqLLVEMDG 442
Cdd:cd19523  80 ILQASFLAARCRQPSVLFISDLDALLSSQDDEASPVGRLQVE-----LLAQLDG 128
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 342-418 1.07e-09

ATPases associated with a variety of cellular activities; AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 57.00  E-value: 1.07e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173    342 PKGALLLGPPGCGKTLLAKAVATEAQVP---FLAMAGPEFVEVI--------------GGLGAARVRSLFKEARARAPCI 404
Cdd:smart00382   2 GEVILIVGPPGSGKTTLARALARELGPPgggVIYIDGEDILEEVldqllliivggkkaSGSGELRLRLALALARKLKPDV 81

                           90
                   ....*....|....
gi 40806173    405 VYIDEIDAVGKKRS 418
Cdd:smart00382  82 LILDEITSLLDAEQ 95
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 346-440 9.05e-08

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: 51.37  E-value: 9.05e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEfVEVIGGLGAARVRSLFKEA-RARAPCIVYIDEIDAVGKKRSTT-MSg 423
Cdd:cd19512  26 LFYGPPGTGKTLFAKKLALHSGMDYAIMTGGD-VAPMGREGVTAIHKVFDWAnTSRRGLLLFVDEADAFLRKRSTEkIS- 103

                        90
                ....*....|....*..
gi 40806173 424 fsnTEEEQTLNQLLVEM 440
Cdd:cd19512 104 ---EDLRAALNAFLYRT 117
ClpX COG1219
ATP-dependent protease Clp, ATPase subunit ClpX [Posttranslational modification, protein ...
 346-416 9.23e-08

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


Pssm-ID: 440832 [Multi-domain]  Cd Length: 409  Bit Score: 54.28  E-value: 9.23e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 346 LLLGPPGCGKTLLAKAVATEAQVPFlAMA-----------GpEFVEVIgglgaarVRSLFKEA---RARAPC-IVYIDEI 410
Cdd:COG1219 113 LLIGPTGSGKTLLAQTLARILDVPF-AIAdattlteagyvG-EDVENI-------LLKLLQAAdydVEKAERgIIYIDEI 183


                ....*.
gi 40806173 411 DAVGKK 416
Cdd:COG1219 184 DKIARK 189
RecA-like_ClpX cd19497
ATP-dependent Clp protease ATP-binding subunit ClpX; ClpX is a component of the ATP-dependent ...
 346-416 1.16e-07

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: 52.99  E-value: 1.16e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 346 LLLGPPGCGKTLLAKAVATEAQVPF-------LAMAG--PEFVEVIgglgaarVRSLFKEAR---ARAP-CIVYIDEIDA 412
Cdd:cd19497  54 LLIGPTGSGKTLLAQTLAKILDVPFaiadattLTEAGyvGEDVENI-------LLKLLQAADydvERAQrGIVYIDEIDK 126


                ....
gi 40806173 413 VGKK 416
Cdd:cd19497 127 IARK 130
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 346-411 2.69e-07

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


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 49.60  E-value: 2.69e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173   346 LLLGPPGCGKTLLAKAVAtEA--QVPFLAMAGPEFVEV--------IGGLGAARVRSLFKEArARAPCIVYIDEID 411
Cdd:pfam07728   3 LLVGPPGTGKTELAERLA-AAlsNRPVFYVQLTRDTTEedlfgrrnIDPGGASWVDGPLVRA-AREGEIAVLDEIN 76
clpX PRK05342
ATP-dependent Clp protease ATP-binding subunit ClpX;
346-416 3.11e-07

ATP-dependent Clp protease ATP-binding subunit ClpX;


Pssm-ID: 235422 [Multi-domain]  Cd Length: 412  Bit Score: 52.47  E-value: 3.11e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  346 LLLGPPGCGKTLLAKAVATEAQVPFlAMA-----------GpEFVEVIgglgaarVRSLFKEA-----RA-RApcIVYID 408
Cdd:PRK05342 112 LLIGPTGSGKTLLAQTLARILDVPF-AIAdattlteagyvG-EDVENI-------LLKLLQAAdydveKAqRG--IVYID 180


                 ....*...
gi 40806173  409 EIDAVGKK 416
Cdd:PRK05342 181 EIDKIARK 188
PRK04195 PRK04195
replication factor C large subunit; Provisional
 307-411 7.00e-07

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 51.46  E-value: 7.00e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173  307 SFKDVAGMHEAKLEVREFVdylkspERFLQlgaKVPKGALLL-GPPGCGKTLLAKAVATEaqvpflamAGPEFVE----- 380
Cdd:PRK04195  12 TLSDVVGNEKAKEQLREWI------ESWLK---GKPKKALLLyGPPGVGKTSLAHALAND--------YGWEVIElnasd 74

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 40806173  381 ---------VIGglGAARVRSLFKEARArapcIVYIDEID 411
Cdd:PRK04195  75 qrtadvierVAG--EAATSGSLFGARRK----LILLDEVD 108
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 346-410 1.29e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 50.47  E-value: 1.29e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173  346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGpefveVIGGLgaARVRSLFKEARARA----PCIVYIDEI 410
Cdd:PRK13342  40 ILWGPPGTGKTTLARIIAGATDAPFEALSA-----VTSGV--KDLREVIEEARQRRsagrRTILFIDEI 101
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 335-427 1.41e-06

ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; however, its function remains unclear. The gene encoding YCF2 is the largest known plastid gene in angiosperms and has been used to predict phylogenetic relationships. 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: 410913 [Multi-domain]  Cd Length: 161  Bit Score: 48.14  E-value: 1.41e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 335 LQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMA-------GPEFVEVIGGLGAA-------RVRSLFKEARAR 400
Cdd:cd19505   5 LRLGLSPSKGILLIGSIETGRSYLIKSLAANSYVPLIRISlnkllynKPDFGNDDWIDGMLilkeslhRLNLQFELAKAM 84

                        90       100
                ....*....|....*....|....*..
gi 40806173 401 APCIVYIDEIDAVGKKRSTTMSGFSNT 427
Cdd:cd19505  85 SPCIIWIPNIHELNVNRSTQNLEEDPK 111
RecA-like_HslU cd19498
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ...
 341-416 1.80e-06

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: 48.14  E-value: 1.80e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173 341 VPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFVEVigGLGAARVRSLFKEArarAPCIVYIDEIDAVGKK 416
Cdd:cd19498  45 TPKNILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTEV--GYVGRDVESIIRDL---VEGIVFIDEIDKIAKR 115
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 346-410 2.45e-06

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 49.67  E-value: 2.45e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173 346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGpefveVIGGLgaARVRSLFKEARARA----PCIVYIDEI 410
Cdd:COG2256  53 ILWGPPGTGKTTLARLIANATDAEFVALSA-----VTSGV--KDIREVIEEARERRaygrRTILFVDEI 114
FtsH_ext pfam06480
FtsH Extracellular; This domain is found in the FtsH family of proteins. FtsH is the only ...
 145-242 3.92e-06

FtsH Extracellular; This domain is found in the FtsH family of proteins. FtsH is the only membrane-bound ATP-dependent protease universally conserved in prokaryotes. It only efficiently degrades proteins that have a low thermodynamic stability - e.g. it lacks robust unfoldase activity. This feature may be key and implies that this could be a criterion for degrading a protein. In Oenococcus oeni FtsH is involved in protection against environmental stress, and shows increased expression under heat or osmotic stress. These two lines of evidence suggest that it is a fundamental prokaryotic self-protection mechanism that checks if proteins are correctly folded (personal obs: Yeats C). The precise function of this N-terminal region is unclear.


Pssm-ID: 377663 [Multi-domain]  Cd Length: 103  Bit Score: 45.67  E-value: 3.92e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   145 LLVIAVVMSLLNALSTSGGS----ISWNDFVhEMLAKGEVQRVQVVPESDVVEVYLHPGAVVfGRPRLAlMYRMQVANID 220
Cdd:pfam06480   5 LLILLVLLLLFLLFLLSSSSstkeISYSEFL-EYLEAGKVKKVVVQDDEILPTGVVEGTLKD-GSKFTT-YFIPSLPNVD 81

                          90       100
                  ....*....|....*....|..
gi 40806173   221 KFEEKLRAAEDELNIEAKDRIP 242
Cdd:pfam06480  82 SLLEKLEDALEEKGVKVSVKPP 103
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 321-442 3.01e-05

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


Pssm-ID: 410918 [Multi-domain]  Cd Length: 153  Bit Score: 44.26  E-value: 3.01e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 321 VREFVDYLKSPERFLQLGAKVPKGALLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEfveviGGLGAARVRSLFKEARAR 400
Cdd:cd19510   2 IDDLKDFIKNEDWYNDRGIPYRRGYLLYGPPGTGKSSFIAALAGELDYDICDLNLSE-----VVLTDDRLNHLLNTAPKQ 76

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....
gi 40806173 401 ApcIVYIDEIDAVGKKRSTTMSGFSNTEEEQ--TLNQLLVEMDG 442
Cdd:cd19510  77 S--IILLEDIDAAFESREHNKKNPSAYGGLSrvTFSGLLNALDG 118
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
343-378 7.30e-05

DNA helicase TIP49, TBP-interacting protein [Transcription];


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 44.96  E-value: 7.30e-05
                        10        20        30
                ....*....|....*....|....*....|....*...
gi 40806173 343 KGALLLGPPGCGKTLLAKAVATE--AQVPFLAMAGPEF 378
Cdd:COG1224  65 KGILIVGPPGTGKTALAVAIARElgEDTPFVAISGSEI 102
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 309-415 1.56e-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: 42.55  E-value: 1.56e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 309 KDVAGMHEAKLEVREFVDYLKsperflqLGAKVpKGALLL--GPPGCGKTLLAKAVATeaqvpflAMaGPEFVEV-IGGL 385
Cdd:cd19500  10 ADHYGLEDVKERILEYLAVRK-------LKGSM-KGPILClvGPPGVGKTSLGKSIAR-------AL-GRKFVRIsLGGV 73

                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*.
gi 40806173 386 --------------GA--ARVRSLFKEARARAPCIVyIDEIDAVGK 415
Cdd:cd19500  74 rdeaeirghrrtyvGAmpGRIIQALKKAGTNNPVFL-LDEIDKIGS 118
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 313-441 2.63e-04

type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the actinobacterial flavor of type VII secretion systems. Species such as Mycobacterium tuberculosis have several instances of this system per genome, designated EccA1, EccA2, etc. [Protein fate, Protein and peptide secretion and trafficking]


Pssm-ID: 188437 [Multi-domain]  Cd Length: 557  Bit Score: 43.68  E-value: 2.63e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   313 GMHEAKLEVREFVDYLKSPERFLQLGAKVPKGA---LLLGPPGCGKTLLAKAVATeaqvpFLAMAG----PEFVEV---- 381
Cdd:TIGR03922 280 GLERVKRQVAALKSSTAMALARAERGLPVAQTSnhmLFAGPPGTGKTTIARVVAK-----IYCGLGvlrkPLVREVsrad 354

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 40806173   382 -IG---GLGAARVRSLFKEARARapcIVYIDEIDAVGKKRSTTMSGFSNteeeQTLNQLLVEMD 441
Cdd:TIGR03922 355 lIGqyiGESEAKTNEIIDSALGG---VLFLDEAYTLVETGYGQKDPFGL----EAIDTLLARME 411
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 343-378 3.32e-04

TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the pfam00004 domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities.TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases.


Pssm-ID: 399217 [Multi-domain]  Cd Length: 347  Bit Score: 42.68  E-value: 3.32e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 40806173   343 KGALLLGPPGCGKTLLAKAVATE--AQVPFLAMAGPEF 378
Cdd:pfam06068  51 RAVLIAGPPGTGKTALAIAISKElgEDTPFTSISGSEV 88
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
343-410 1.42e-03

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 40.15  E-value: 1.42e-03
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 40806173 343 KGALLLGPPGCGKTLLAKAVATEAqvpflAMAG--------PEFVEvigGLGAARV-RSLFKEAR--ARAPCIVyIDEI 410
Cdd:COG1484 100 ENLILLGPPGTGKTHLAIALGHEA-----CRAGyrvrfttaPDLVN---ELKEARAdGRLERLLKrlAKVDLLI-LDEL 169
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 346-376 2.26e-03

Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the RuvABC revolvasome which catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalyzed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.


Pssm-ID: 398900 [Multi-domain]  Cd Length: 159  Bit Score: 38.64  E-value: 2.26e-03
                          10        20        30
                  ....*....|....*....|....*....|.
gi 40806173   346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGP 376
Cdd:pfam05496  37 LLYGPPGLGKTTLANIIANEMGVNIRITSGP 67
YifB COG0606
Predicted Mg-chelatase, contains ChlI-like and ATPase domains, YifB family [Posttranslational ...
 308-364 2.74e-03

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


Pssm-ID: 440371 [Multi-domain]  Cd Length: 502  Bit Score: 40.02  E-value: 2.74e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173 308 FKDVAGMHEAK--LEVrefvdylksperflqlgakvpkgA-------LLLGPPGCGKTLLAKAVAT 364
Cdd:COG0606 191 LADVKGQEQAKraLEI-----------------------AaagghnlLMIGPPGSGKTMLARRLPG 233
IS21_help_AAA NF038214
IS21-like element helper ATPase IstB; This protein family model resembles PF01695, but was ...
 346-410 4.04e-03

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


Pssm-ID: 439516  Cd Length: 232  Bit Score: 38.99  E-value: 4.04e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 40806173  346 LLLGPPGCGKTLLAKAVATEAqvpflAMAG--------PEFVEViggLGAARV-RSLFKEAR--ARAPCIVyIDEI 410
Cdd:NF038214  94 LLLGPPGTGKTHLAIALGYAA-----CRQGyrvrfttaADLVEQ---LAQARAdGRLGRLLRrlARYDLLI-IDEL 160
RecA-like_superfamily cd01120
RecA-like_NTPases; RecA-like NTPases. This superfamily includes the NTP binding domain of F1 ...
 346-443 4.38e-03

RecA-like_NTPases; RecA-like NTPases. This superfamily 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: 410865 [Multi-domain]  Cd Length: 119  Bit Score: 37.10  E-value: 4.38e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173 346 LLLGPPGCGKTLLAKAVATEAqvpfLAMAGP----EFVEVIgglgAARVRSLFKEARaraPCIVYIDEIDAVgkkrsttM 421
Cdd:cd01120   2 LITGPPGSGKTTLLLQFAEQA----LLSDEPvifiSFLDTI----LEAIEDLIEEKK---LDIIIIDSLSSL-------A 63

                        90       100
                ....*....|....*....|..
gi 40806173 422 SGFSNTEEEQTLNQLLVEMDGA 443
Cdd:cd01120  64 RASQGDRSSELLEDLAKLLRAA 85
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 346-370 5.78e-03

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


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 38.61  E-value: 5.78e-03
                        10        20
                ....*....|....*....|....*
gi 40806173 346 LLLGPPGCGKTLLAKAVATEAQVPF 370
Cdd:COG0714  35 LLEGVPGVGKTTLAKALARALGLPF 59
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 346-415 9.38e-03

Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 38.05  E-value: 9.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 40806173   346 LLLGPPGCGKTLLAKAVATEAQVPFLAMAGPEFvEVIGGLGAArvRSLFKEARarapcIVYIDEIDAVGK 415
Cdd:TIGR00635  34 LLYGPPGLGKTTLAHIIANEMGVNLKITSGPAL-EKPGDLAAI--LTNLEEGD-----VLFIDEIHRLSP 95
 
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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