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Conserved domains on  [gi|194380772|dbj|BAG58539|]
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unnamed protein product [Homo sapiens]

Protein Classification

CDC48 family AAA ATPase( domain architecture ID 13760303)

CDC48 family AAA ATPase is involved in the budding and transfer of membrane from the transitional endoplasmic reticulum to the Golgi apparatus; similar to yeast CDC48 (cell division control protein 48) and the human ortholog, transitional endoplasmic reticulum ATPase (valosin-containing protein)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CDC48 super family cl36852
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 273-743 3.18e-108

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.


The actual alignment was detected with superfamily member TIGR01243:

Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 351.90  E-value: 3.18e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  273 LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAglpavP 352
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEA----GAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIA-----P 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  353 EHEHSPDAVQSQRLAHALN--DMIKEfisMGSLVALIATSQSQqSLHPLLVSAQGvhiFQCVQHIQPPNQEQRCEILCNV 430
Cdd:TIGR01243 286 KREEVTGEVEKRVVAQLLTlmDGLKG---RGRVIVIGATNRPD-ALDPALRRPGR---FDREIVIRVPDKRARKEILKVH 358

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  431 IKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSR-----------QSI--STREKLVLTTLDFQKALR 497
Cdd:TIGR01243 359 TRNMPLAE-----DVDLDKLAEVTHGFVGADLAALAKEAAMAALRRfiregkinfeaEEIpaEVLKELKVTMKDFMEALK 433

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  498 GFLPASLRSVNLHKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSR 577
Cdd:TIGR01243 434 MVEPSAIREVLVEVP-NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG 512

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  578 MNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVY 656
Cdd:TIGR01243 513 ANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARfDTSVTDRIVNQLLTEMDGIQELSNVV 592

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  657 VLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEA 736
Cdd:TIGR01243 593 VIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAA 672


                  ....*..
gi 194380772  737 LHGMLLS 743
Cdd:TIGR01243 673 LRESIGS 679
PEX-2N pfam09263
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like ...
 17-91 3.82e-38

Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.


:

Pssm-ID: 462730  Cd Length: 83  Bit Score: 136.73  E-value: 3.82e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772   17 VTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVVWSH-QPAFLSWVEGRHFSDQGENVAEINRRVGQKLGLSNGGQ 91
Cdd:pfam09263   1 VTVVFNNAKNCFLHLPSKLVSQLSLQENQALELSWGHgQPVFLSWTEGRHSSDQDENVVELNRQLGEKLGLKDGEQ 76
 
Name Accession Description Interval E-value
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 273-743 3.18e-108

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: 351.90  E-value: 3.18e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  273 LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAglpavP 352
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEA----GAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIA-----P 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  353 EHEHSPDAVQSQRLAHALN--DMIKEfisMGSLVALIATSQSQqSLHPLLVSAQGvhiFQCVQHIQPPNQEQRCEILCNV 430
Cdd:TIGR01243 286 KREEVTGEVEKRVVAQLLTlmDGLKG---RGRVIVIGATNRPD-ALDPALRRPGR---FDREIVIRVPDKRARKEILKVH 358

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  431 IKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSR-----------QSI--STREKLVLTTLDFQKALR 497
Cdd:TIGR01243 359 TRNMPLAE-----DVDLDKLAEVTHGFVGADLAALAKEAAMAALRRfiregkinfeaEEIpaEVLKELKVTMKDFMEALK 433

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  498 GFLPASLRSVNLHKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSR 577
Cdd:TIGR01243 434 MVEPSAIREVLVEVP-NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG 512

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  578 MNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVY 656
Cdd:TIGR01243 513 ANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARfDTSVTDRIVNQLLTEMDGIQELSNVV 592

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  657 VLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEA 736
Cdd:TIGR01243 593 VIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAA 672


                  ....*..
gi 194380772  737 LHGMLLS 743
Cdd:TIGR01243 673 LRESIGS 679
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 526-683 1.20e-104

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: 322.07  E-value: 1.20e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19526    1 VKKALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 683
Cdd:cd19526   81 RAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 478-737 1.63e-92

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 296.53  E-value: 1.63e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 478 SISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILL 557
Cdd:COG1222   38 ALELLEEAPALLLNDANLTQKRLGTPRGTAVPAESPDVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLL 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 558 YGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNT-GVTD 636
Cdd:COG1222  118 YGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQ 197

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 637 RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASV 716
Cdd:COG1222  198 RTVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRDMPLADDVDLDKLAKL 277

                        250       260
                 ....*....|....*....|.
gi 194380772 717 TDSFTGADLKALLYNAQLEAL 737
Cdd:COG1222  278 TEGFSGADLKAIVTEAGMFAI 298
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 510-728 5.79e-66

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 226.64  E-value: 5.79e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 510 HKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELL 589
Cdd:PRK03992 124 ESP-NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV 202

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 590 SKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGvTDRVVN----QLLTQLDGVEGLQGVYVLAATSRPD 665
Cdd:PRK03992 203 QKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS-GDREVQrtlmQLLAEMDGFDPRGNVKIIAATNRID 281

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 194380772 666 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKAL 728
Cdd:PRK03992 282 ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAI 344
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 555-684 3.07e-47

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: 164.69  E-value: 3.07e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  555 ILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGV 634
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDSE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 194380772  635 TDRVVNQLLTQLDGVEGLQG-VYVLAATSRPDLIDPALLrpGRLDKCVYCP 684
Cdd:pfam00004  81 SRRVVNQLLTELDGFTSSNSkVIVIAATNRPDKLDPALL--GRFDRIIEFP 129
PEX-2N pfam09263
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like ...
 17-91 3.82e-38

Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.


Pssm-ID: 462730  Cd Length: 83  Bit Score: 136.73  E-value: 3.82e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772   17 VTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVVWSH-QPAFLSWVEGRHFSDQGENVAEINRRVGQKLGLSNGGQ 91
Cdd:pfam09263   1 VTVVFNNAKNCFLHLPSKLVSQLSLQENQALELSWGHgQPVFLSWTEGRHSSDQDENVVELNRQLGEKLGLKDGEQ 76
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 555-687 1.02e-12

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: 66.63  E-value: 1.02e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772   555 ILLYGPPGTGKTLLAGVIAR---GSRMNFISVKGPELLS--------------KYIGASEQAVRDIFIRAQAAKPCILFF 617
Cdd:smart00382   5 ILIVGPPGSGKTTLARALARelgPPGGGVIYIDGEDILEevldqllliivggkKASGSGELRLRLALALARKLKPDVLIL 84

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772   618 DEFESIaprrgHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPgRLDKCVYCPPPD 687
Cdd:smart00382  85 DEITSL-----LDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
 
Name Accession Description Interval E-value
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 273-743 3.18e-108

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: 351.90  E-value: 3.18e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  273 LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAglpavP 352
Cdd:TIGR01243 215 VLLYGPPGTGKTLLAKAVANEA----GAYFISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIA-----P 285

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  353 EHEHSPDAVQSQRLAHALN--DMIKEfisMGSLVALIATSQSQqSLHPLLVSAQGvhiFQCVQHIQPPNQEQRCEILCNV 430
Cdd:TIGR01243 286 KREEVTGEVEKRVVAQLLTlmDGLKG---RGRVIVIGATNRPD-ALDPALRRPGR---FDREIVIRVPDKRARKEILKVH 358

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  431 IKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSR-----------QSI--STREKLVLTTLDFQKALR 497
Cdd:TIGR01243 359 TRNMPLAE-----DVDLDKLAEVTHGFVGADLAALAKEAAMAALRRfiregkinfeaEEIpaEVLKELKVTMKDFMEALK 433

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  498 GFLPASLRSVNLHKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSR 577
Cdd:TIGR01243 434 MVEPSAIREVLVEVP-NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESG 512

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  578 MNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVY 656
Cdd:TIGR01243 513 ANFIAVRGPEILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARfDTSVTDRIVNQLLTEMDGIQELSNVV 592

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  657 VLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEA 736
Cdd:TIGR01243 593 VIAATNRPDILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAA 672


                  ....*..
gi 194380772  737 LHGMLLS 743
Cdd:TIGR01243 673 LRESIGS 679
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 526-683 1.20e-104

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: 322.07  E-value: 1.20e-104
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19526    1 VKKALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFS 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 683
Cdd:cd19526   81 RAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 478-737 1.63e-92

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 296.53  E-value: 1.63e-92
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 478 SISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILL 557
Cdd:COG1222   38 ALELLEEAPALLLNDANLTQKRLGTPRGTAVPAESPDVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLL 117

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 558 YGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNT-GVTD 636
Cdd:COG1222  118 YGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQ 197

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 637 RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASV 716
Cdd:COG1222  198 RTVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRDMPLADDVDLDKLAKL 277

                        250       260
                 ....*....|....*....|.
gi 194380772 717 TDSFTGADLKALLYNAQLEAL 737
Cdd:COG1222  278 TEGFSGADLKAIVTEAGMFAI 298
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 526-683 2.50e-82

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: 262.60  E-value: 2.50e-82
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19511    1 VKRELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSKYVGESERAVREIFQ 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRGHDN-TGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 683
Cdd:cd19511   81 KARQAAPCIIFFDEIDSLAPRRGQSDsSGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDKLIYV 159
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 459-738 1.98e-78

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: 261.38  E-value: 1.98e-78
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 459 ARDFTVLVDRAIHSRLSRQSISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPA 538
Cdd:COG0464   98 LLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAILDDLGGLEEVKEELRELVALPL 177

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 539 KYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFD 618
Cdd:COG0464  178 KRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKYVGETEKNLREVFDKARGLAPCVLFID 257

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 619 EFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGlqGVYVLAATSRPDLIDPALLRpgRLDKCVYCPPPDQVSRLEILNVL 698
Cdd:COG0464  258 EADALAGKRGEVGDGVGRRVVNTLLTEMEELRS--DVVVIAATNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIH 333

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|
gi 194380772 699 SDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALH 738
Cdd:COG0464  334 LRKRPLDEDVDLEELAEATEGLSGADIRNVVRRAALQALR 373
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 526-682 4.36e-72

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: 235.08  E-value: 4.36e-72
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19529    1 VKQELKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATESNANFISVKGPELLSKWVGESEKAIREIFR 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 682
Cdd:cd19529   81 KARQVAPCVIFFDEIDSIAPRRGTTgDSGVTERVVNQLLTELDGLEEMNGVVVIAATNRPDIIDPALLRAGRFDRLIY 158
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 523-682 2.21e-69

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: 227.76  E-value: 2.21e-69
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 523 LHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRD 602
Cdd:cd19530    1 LDHVREELTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANESGANFISVKGPELLNKYVGESERAVRQ 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 603 IFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 682
Cdd:cd19530   81 VFQRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDKTLY 160
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 500-741 5.51e-67

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: 239.04  E-value: 5.51e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  500 LPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMN 579
Cdd:TIGR01243 160 REKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY 239

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  580 FISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLA 659
Cdd:TIGR01243 240 FISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIG 319

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  660 ATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHG 739
Cdd:TIGR01243 320 ATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRR 399


                  ..
gi 194380772  740 ML 741
Cdd:TIGR01243 400 FI 401
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 510-728 5.79e-66

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 226.64  E-value: 5.79e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 510 HKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELL 589
Cdd:PRK03992 124 ESP-NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV 202

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 590 SKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGvTDRVVN----QLLTQLDGVEGLQGVYVLAATSRPD 665
Cdd:PRK03992 203 QKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS-GDREVQrtlmQLLAEMDGFDPRGNVKIIAATNRID 281

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 194380772 666 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKAL 728
Cdd:PRK03992 282 ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAI 344
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 526-682 5.39e-65

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: 215.45  E-value: 5.39e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFAnLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19527    1 VKKEILDTIQLPLEHPELFS-SGLRKRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINMYIGESEANVREVFQ 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRGH--DNTGVTDRVVNQLLTQLDGVE-GLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 682
Cdd:cd19527   80 KARDAKPCVIFFDELDSLAPSRGNsgDSGGVMDRVVSQLLAELDGMSsSGQDVFVIGATNRPDLLDPALLRPGRFDKLLY 159
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 519-682 2.02e-64

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: 214.08  E-value: 2.02e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 519 KIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQ 598
Cdd:cd19503    1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSIVSKYLGESEK 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 599 AVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLD 678
Cdd:cd19503   81 NLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRRPGRFD 160


                 ....
gi 194380772 679 KCVY 682
Cdd:cd19503  161 REVE 164
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 526-682 2.10e-64

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: 213.91  E-value: 2.10e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19528    1 VKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFD 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRG---HDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 682
Cdd:cd19528   81 KARAAAPCVLFFDELDSIAKARGgniGDAGGAADRVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 160
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 517-679 2.65e-55

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: 189.09  E-value: 2.65e-55
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 517 WDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGAS 596
Cdd:cd19502    2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKYIGEG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 597 EQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGvTDRVVN----QLLTQLDGVEGLQGVYVLAATSRPDLIDPALL 672
Cdd:cd19502   82 ARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTG-GDREVQrtmlELLNQLDGFDPRGNIKVIMATNRPDILDPALL 160


                 ....*..
gi 194380772 673 RPGRLDK 679
Cdd:cd19502  161 RPGRFDR 167
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 520-679 1.51e-53

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: 183.79  E-value: 1.51e-53
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19519    2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESN 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDK 679
Cdd:cd19519   82 LRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDR 161
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 518-736 2.23e-52

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: 191.73  E-value: 2.23e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  518 DKIGGLHEVRQILMDTIQLpAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASE 597
Cdd:TIGR01241  55 KDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGA 133

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  598 QAVRDIFIRAQAAKPCILFFDEFESIAPRRG------HDntgVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPAL 671
Cdd:TIGR01241 134 SRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGaglgggND---EREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPAL 210

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194380772  672 LRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEA 736
Cdd:TIGR01241 211 LRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLA 275
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 514-707 4.85e-51

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: 187.99  E-value: 4.85e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  514 DLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIA----------RGSRMNFISV 583
Cdd:TIGR03689 178 DVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVAnslaarigaeGGGKSYFLNI 257

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  584 KGPELLSKYIGASEQAVRDIFIRAQAA----KPCILFFDEFESIAPRRGhdnTGVTD----RVVNQLLTQLDGVEGLQGV 655
Cdd:TIGR03689 258 KGPELLNKYVGETERQIRLIFQRAREKasegRPVIVFFDEMDSLFRTRG---SGVSSdvetTVVPQLLAEIDGVESLDNV 334

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 194380772  656 YVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEIL-NVLSDSLPLADD 707
Cdd:TIGR03689 335 IVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFaKYLTDDLPLPED 387
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 526-683 1.48e-50

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: 175.16  E-value: 1.48e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 526 VRQILMDTIQLPAKYPELFAnLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFI 605
Cdd:cd19481    1 LKASLREAVEAPRRGSRLRR-YGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVGESEKNLRKIFE 79

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194380772 606 RAQAAKPCILFFDEFESIAPRRG-HDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 683
Cdd:cd19481   80 RARRLAPCILFIDEIDAIGRKRDsSGESGELRRVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 502-737 1.12e-49

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 181.11  E-value: 1.12e-49
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 502 ASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFI 581
Cdd:PTZ00454 129 SSIQLLQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFI 208

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 582 SVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGV---TDRVVNQLLTQLDGVEGLQGVYVL 658
Cdd:PTZ00454 209 RVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGAdreVQRILLELLNQMDGFDQTTNVKVI 288

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194380772 659 AATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEAL 737
Cdd:PTZ00454 289 MATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAV 367
ftsH CHL00176
cell division protein; Validated
 518-734 2.41e-47

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 179.86  E-value: 2.41e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 518 DKIGGLHEVRQILMDTIQLpAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASE 597
Cdd:CHL00176 183 RDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGA 261

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 598 QAVRDIFIRAQAAKPCILFFDEFESIAPRRGhdnTGV------TDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPAL 671
Cdd:CHL00176 262 ARVRDLFKKAKENSPCIVFIDEIDAVGRQRG---AGIgggndeREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAAL 338

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 194380772 672 LRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQL 734
Cdd:CHL00176 339 LRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAI 401
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 555-684 3.07e-47

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: 164.69  E-value: 3.07e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  555 ILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGV 634
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDSE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 194380772  635 TDRVVNQLLTQLDGVEGLQG-VYVLAATSRPDLIDPALLrpGRLDKCVYCP 684
Cdd:pfam00004  81 SRRVVNQLLTELDGFTSSNSkVIVIAATNRPDKLDPALL--GRFDRIIEFP 129
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
530-739 6.64e-47

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 178.69  E-value: 6.64e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 530 LMDTIQLPAKYPELFANLPirqrTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQA 609
Cdd:PRK10733 167 LVEYLREPSRFQKLGGKIP----KGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKK 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 610 AKPCILFFDEFESIAPRRG------HDNTgvtDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 683
Cdd:PRK10733 243 AAPCIIFIDEIDAVGRQRGaglgggHDER---EQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 319

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772 684 PPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHG 739
Cdd:PRK10733 320 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARG 375
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
523-729 1.55e-46

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 176.38  E-value: 1.55e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 523 LHEVRQILMDtiqlPAKYPELFANLPirqrTGILLYGPPGTGKTLLA-------GViargsrmNFISVKGPELLSKY--I 593
Cdd:COG0465  154 LQEIVDFLKD----PEKFTRLGAKIP----KGVLLVGPPGTGKTLLAkavageaGV-------PFFSISGSDFVEMFvgV 218

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 594 GASEqaVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTD---RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPA 670
Cdd:COG0465  219 GASR--VRDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGHDereQTLNQLLVEMDGFEGNEGVIVIAATNRPDVLDPA 296

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 194380772 671 LLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALL 729
Cdd:COG0465  297 LLRPGRFDRQVVVDLPDVKGREAILKVHARKKPLAPDVDLEVIARRTPGFSGADLANLV 355
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 517-737 5.92e-46

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 171.49  E-value: 5.92e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 517 WDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGAS 596
Cdd:PTZ00361 182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDG 261

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 597 EQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVT---DRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLR 673
Cdd:PTZ00361 262 PKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEkeiQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIR 341

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 194380772 674 PGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEAL 737
Cdd:PTZ00361 342 PGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLAL 405
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 520-682 1.62e-45

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: 161.25  E-value: 1.62e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLpAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19501    6 VAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASR 84

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTD---RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGR 676
Cdd:cd19501   85 VRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDereQTLNQLLVEMDGFESNTGVIVIAATNRPDVLDPALLRPGR 164


                 ....*.
gi 194380772 677 LDKCVY 682
Cdd:cd19501  165 FDRQVY 170
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
552-737 1.14e-43

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 158.89  E-value: 1.14e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 552 RTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAqAAKPCILFFDEFESIAPRRGHDN 631
Cdd:COG1223   35 PRKILFYGPPGTGKTMLAEALAGELKLPLLTVRLDSLIGSYLGETARNLRKLFDFA-RRAPCVIFFDEFDAIAKDRGDQN 113

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 632 -TGVTDRVVNQLLTQLDGVEGlqGVYVLAATSRPDLIDPALLRpgRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDL 710
Cdd:COG1223  114 dVGEVKRVVNALLQELDGLPS--GSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEILELNLKKFPLPFELDL 189

                        170       180
                 ....*....|....*....|....*..
gi 194380772 711 QHVASVTDSFTGADLKALLYNAQLEAL 737
Cdd:COG1223  190 KKLAKKLEGLSGADIEKVLKTALKKAI 216
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 520-682 1.36e-42

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: 152.51  E-value: 1.36e-42
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19509    1 IAGLDDAKEALKEAVILPSLRPDLFPGLRGPPR-GILLYGPPGTGKTLLARAVASESGSTFFSISASSLVSKWVGESEKI 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEG--LQGVYVLAATSRPDLIDPALLRpgRL 677
Cdd:cd19509   80 VRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVLNkpEDRVLVLGATNRPWELDEAFLR--RF 157


                 ....*
gi 194380772 678 DKCVY 682
Cdd:cd19509  158 EKRIY 162
RecA-like_NSF-SEC18_r1-like cd19504
first of two ATPase domains of NSF and SEC18, and similar ATPase domains; ...
 541-678 7.73e-40

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: 145.33  E-value: 7.73e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 541 PELFANLPIRQRTGILLYGPPGTGKTLLAGVIarGSRMNFIS---VKGPELLSKYIGASEQAVRDIFIRAQAAKPC---- 613
Cdd:cd19504   24 PEIVEQLGCKHVKGILLYGPPGTGKTLMARQI--GKMLNAREpkiVNGPEILNKYVGESEANIRKLFADAEEEQRRlgan 101

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194380772 614 ----ILFFDEFESIAPRRGH--DNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLD 678
Cdd:cd19504  102 sglhIIIFDEIDAICKQRGSmaGSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 520-679 1.98e-39

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: 143.70  E-value: 1.98e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19518    2 IGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGELKVPFLKISATEIVSGVSGESEEK 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGL----QGVYVLAATSRPDLIDPALLRPG 675
Cdd:cd19518   82 IRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELNNEktagGPVLVIGATNRPDSLDPALRRAG 161


                 ....
gi 194380772 676 RLDK 679
Cdd:cd19518  162 RFDR 165
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 520-679 3.42e-39

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: 143.03  E-value: 3.42e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIA-----RGSRMNFISVKGPELLSKYIG 594
Cdd:cd19517    2 IGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAaecskGGQKVSFFMRKGADCLSKWVG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 595 ASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRP 674
Cdd:cd19517   82 EAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRRP 161


                 ....*
gi 194380772 675 GRLDK 679
Cdd:cd19517  162 GRFDR 166
PEX-2N pfam09263
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like ...
 17-91 3.82e-38

Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like fold, with a beta-alpha-beta(3) arrangement. It has been suggested that this domain may be involved in interactions with ubiquitin, ubiquitin-like protein modifiers, or ubiquitin-like domains, such as Ubx. Furthermore, the domain may possess a putative adaptor or substrate binding site, allowing for peroxisomal biogenesis, membrane fusion and protein translocation.


Pssm-ID: 462730  Cd Length: 83  Bit Score: 136.73  E-value: 3.82e-38
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772   17 VTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVVWSH-QPAFLSWVEGRHFSDQGENVAEINRRVGQKLGLSNGGQ 91
Cdd:pfam09263   1 VTVVFNNAKNCFLHLPSKLVSQLSLQENQALELSWGHgQPVFLSWTEGRHSSDQDENVVELNRQLGEKLGLKDGEQ 76
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 511-682 5.76e-34

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: 128.44  E-value: 5.76e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 511 KPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLS 590
Cdd:cd19521    1 KP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLFTGNRKPWS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 591 KYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGV-EGLQGVYVLAATSRPDLIDP 669
Cdd:cd19521   79 KWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVgNDSQGVLVLGATNIPWQLDS 158

                        170
                 ....*....|...
gi 194380772 670 ALLRpgRLDKCVY 682
Cdd:cd19521  159 AIRR--RFEKRIY 169
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 520-673 6.66e-34

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: 127.93  E-value: 6.66e-34
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRT-GILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQ 598
Cdd:cd19520    2 IGGLDEVITELKELVILPLQRPELFDNSRLLQPPkGVLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWYGESQK 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 194380772 599 AVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGV--EGLQGVYVLAATSRPDLIDPALLR 673
Cdd:cd19520   82 LVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLstDGNCRVIVMGATNRPQDLDEAILR 158
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 520-682 7.62e-32

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: 122.02  E-value: 7.62e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPiRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19522    2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKYRGESEKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRG-HDNTGVTDRVVNQLLTQLDGVEGLQG-------VYVLAATSRPDLIDPAL 671
Cdd:cd19522   81 VRLLFEMARFYAPTTIFIDEIDSICSRRGtSEEHEASRRVKSELLVQMDGVGGASEnddpskmVMVLAATNFPWDIDEAL 160

                        170
                 ....*....|.
gi 194380772 672 LRpgRLDKCVY 682
Cdd:cd19522  161 RR--RLEKRIY 169
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 520-682 2.42e-30

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: 117.64  E-value: 2.42e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19524    2 IAGQDLAKQALQEMVILPSLRPELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQG--VYVLAATSRPDLIDPALLRpgRL 677
Cdd:cd19524   81 VRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAVLR--RF 158


                 ....*
gi 194380772 678 DKCVY 682
Cdd:cd19524  159 TKRVY 163
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 514-682 1.21e-29

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: 116.63  E-value: 1.21e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 514 DLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYI 593
Cdd:cd19525   18 PINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWV 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 594 GASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGL--QGVYVLAATSRPDLIDPAL 671
Cdd:cd19525   97 GEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSseDRILVVGATNRPQEIDEAA 176

                        170
                 ....*....|.
gi 194380772 672 LRpgRLDKCVY 682
Cdd:cd19525  177 RR--RLVKRLY 185
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 547-685 1.83e-23

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: 97.60  E-value: 1.83e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 547 LPIRQRTGILLYGPPGTGKTLLAGVIAR---GSRMNFISVKGPELLSKYIGASEQ---AVRDIFIRAQAAKPCILFFDEF 620
Cdd:cd00009   14 LELPPPKNLLLYGPPGTGKTTLARAIANelfRPGAPFLYLNASDLLEGLVVAELFghfLVRLLFELAEKAKPGVLFIDEI 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 194380772 621 ESIAPRrghdntgVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 685
Cdd:cd00009   94 DSLSRG-------AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 520-673 2.38e-19

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: 86.09  E-value: 2.38e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTgILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQA 599
Cdd:cd19523    2 IAGLGALKAAIKEEVLWPLLRPDAFSGLLRLPRS-ILLFGPRGTGKTLLGRCLASQLGATFLRLRGSTLVAKWAGEGEKI 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772 600 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTdRVVNQLLTQLDGV--EGLQGVYVLAATSRPDLIDPALLR 673
Cdd:cd19523   81 LQASFLAARCRQPSVLFISDLDALLSSQDDEASPVG-RLQVELLAQLDGVlgSGEDGVLVVCTTSKPEEIDESLRR 155
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 273-409 1.70e-17

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: 79.56  E-value: 1.70e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  273 LLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAGlpavp 352
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKE----LGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAG----- 71

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 194380772  353 eHEHSPDAVQSQRLAHALNDMIKEFISMGSLVALIATSQSQQSLHPLLVSAQGVHIF 409
Cdd:pfam00004  72 -SRGSGGDSESRRVVNQLLTELDGFTSSNSKVIVIAATNRPDKLDPALLGRFDRIIE 127
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 520-678 1.76e-16

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: 77.79  E-value: 1.76e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 520 IGGLHEVRQILMdtIQLPAKYPELFA-NLPIRQrtGILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQ 598
Cdd:cd19507    2 VGGLDNLKDWLK--KRKAAFSKQASAyGLPTPK--GLLLVGIQGTGKSLTAKAIAGVWQLPLLRLDMGRLFGGLVGESES 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 599 AVRDIFIRAQAAKPCILFFDEFES-IAPRRGHDNTGVTDRVVNQLLTQLDgvEGLQGVYVLAATSRPDLIDPALLRPGRL 677
Cdd:cd19507   78 RLRQMIQTAEAIAPCVLWIDEIEKgFSNADSKGDSGTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRF 155


                 .
gi 194380772 678 D 678
Cdd:cd19507  156 D 156
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 91-497 2.84e-14

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: 75.72  E-value: 2.84e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  91 QIPDDLRKRLNIEMHAVVRITPVEVTPKIPRSLKLQPRENLPKDISEEDIKTVFYSWLQQSTTTMLPLVISEEEFIKLET 170
Cdd:COG0464   17 LLDDAALRLLLLLLLALAAALLLLLLLLLLLLLALLLVELLLLLLSGALAALLLLALLLLALLALLAALLSALELLLLGE 96

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 171 KDGLKEFSLSIVHSWEKEKDKNIFLLSPNLLQKTTIQVLLDPMVKEENSEEIDFILPFLkLSSLGGVNSLgVSSLEHITH 250
Cdd:COG0464   97 LLLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAI-LDDLGGLEEV-KEELRELVA 174

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 251 SLLGRPLSRQLMSLVAGLRngaLLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKALRGKRLENIQKTLEVAFSEAV 330
Cdd:COG0464  175 LPLKRPELREEYGLPPPRG---LLLYGPPGTGKTLLARALAGE----LGLPLIEVDLSDLVSKYVGETEKNLREVFDKAR 247

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 331 WMQPSVVLLDDLDLIAGlpavpehehSPDAVQSQRLAHALNDMIKEfisMGSL---VALIATSQSQQSLHPLLVSAqgvh 407
Cdd:COG0464  248 GLAPCVLFIDEADALAG---------KRGEVGDGVGRRVVNTLLTE---MEELrsdVVVIAATNRPDLLDPALLRR---- 311

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 408 iFQCVQHIQPPNQEQRCEILCNVIKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHS--RLSRQSISTRekl 485
Cdd:COG0464  312 -FDEIIFFPLPDAEERLEIFRIHLRKRPLDE-----DVDLEELAEATEGLSGADIRNVVRRAALQalRLGREPVTTE--- 382

                        410
                 ....*....|..
gi 194380772 486 vlttlDFQKALR 497
Cdd:COG0464  383 -----DLLEALE 389
ycf46 CHL00195
Ycf46; Provisional
 554-738 1.18e-13

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 74.67  E-value: 1.18e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 554 GILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFE-SIAPRRGHDNT 632
Cdd:CHL00195 261 GLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDkAFSNSESKGDS 340

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 633 GVTDRVVNQLLTQLDgvEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNV-LSDSLPLA-DDVDL 710
Cdd:CHL00195 341 GTTNRVLATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIhLQKFRPKSwKKYDI 418

                        170       180
                 ....*....|....*....|....*...
gi 194380772 711 QHVASVTDSFTGADlkalLYNAQLEALH 738
Cdd:CHL00195 419 KKLSKLSNKFSGAE----IEQSIIEAMY 442
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 555-687 1.02e-12

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: 66.63  E-value: 1.02e-12
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772   555 ILLYGPPGTGKTLLAGVIAR---GSRMNFISVKGPELLS--------------KYIGASEQAVRDIFIRAQAAKPCILFF 617
Cdd:smart00382   5 ILIVGPPGSGKTTLARALARelgPPGGGVIYIDGEDILEevldqllliivggkKASGSGELRLRLALALARKLKPDVLIL 84

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772   618 DEFESIaprrgHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPgRLDKCVYCPPPD 687
Cdd:smart00382  85 DEITSL-----LDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 555-671 9.21e-11

ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as Thyroid hormone receptor interactor 13 (TRIP13) and 16E1BP) is a key regulator of specific chromosomal events, like the control of G2/prophase processes such as DNA break formation and recombination, checkpoint signaling, and chromosome synapsis. 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: 410916 [Multi-domain]  Cd Length: 199  Bit Score: 62.08  E-value: 9.21e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 555 ILLYGPPGTGKTLLAGVIAR--GSRMNF-------ISVKGPELLSKYIGASEQAVRDIF--IRAQAAKPCILFF---DEF 620
Cdd:cd19508   55 VLLHGPPGTGKTSLCKALAQklSIRLSSryrygqlIEINSHSLFSKWFSESGKLVTKMFqkIQELIDDKDALVFvliDEV 134

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 194380772 621 ESIAPRRGHDNTGV--TD--RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPAL 671
Cdd:cd19508  135 ESLAAARSASSSGTepSDaiRVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 530-682 9.65e-10

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: 58.13  E-value: 9.65e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 530 LMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARGSRMNFI------SVKGPELLSKYIGASEQA---- 599
Cdd:cd19510    1 IIDDLKDFIKNEDWYNDRGIPYRRGYLLYGPPGTGKSSFIAALAGELDYDICdlnlseVVLTDDRLNHLLNTAPKQsiil 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 600 VRDIfiraqaakPCILFFDEFESIAPRRGHDNTGVTdrvVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDK 679
Cdd:cd19510   81 LEDI--------DAAFESREHNKKNPSAYGGLSRVT---FSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149


                 ...
gi 194380772 680 CVY 682
Cdd:cd19510  150 KIY 152
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 252-347 1.05e-08

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: 55.37  E-value: 1.05e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 252 LLGRPLSRQLMSLVAGLrngalLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKALRGKRLENIQKTLEVAFSEAVW 331
Cdd:cd19481   13 RRGSRLRRYGLGLPKGI-----LLYGPPGTGKTLLAKALAGE----LGLPLIVVKLSSLLSKYVGESEKNLRKIFERARR 83

                         90
                 ....*....|....*.
gi 194380772 332 MQPSVVLLDDLDLIAG 347
Cdd:cd19481   84 LAPCILFIDEIDAIGR 99
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 273-390 3.78e-08

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


Pssm-ID: 410911 [Multi-domain]  Cd Length: 165  Bit Score: 53.83  E-value: 3.78e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 273 LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAglpavP 352
Cdd:cd19503   37 VLLHGPPGTGKTLLARAVANEA----GANFLSISGPSIVSKYLGESEKNLREIFEEARSHAPSIIFIDEIDALA-----P 107

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 194380772 353 EHEHSPDAVQSQRLAHALNDMiKEFISMGSLVALIATS 390
Cdd:cd19503  108 KREEDQREVERRVVAQLLTLM-DGMSSRGKVVVIAATN 144
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 259-346 1.46e-07

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: 51.76  E-value: 1.46e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 259 RQLMSLVAGLRNGALLLTGGKGSGKSTLAKAICKEAFDKlDAHVERVDCKALRGK---RLENIQKTLEVAFSEAVWMQPS 335
Cdd:cd00009    8 EALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP-GAPFLYLNASDLLEGlvvAELFGHFLVRLLFELAEKAKPG 86

                         90
                 ....*....|.
gi 194380772 336 VVLLDDLDLIA 346
Cdd:cd00009   87 VLFIDEIDSLS 97
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 707-738 3.91e-07

AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the C-terminus of AAA domains.


Pssm-ID: 465537 [Multi-domain]  Cd Length: 45  Bit Score: 47.53  E-value: 3.91e-07
                          10        20        30
                  ....*....|....*....|....*....|..
gi 194380772  707 DVDLQHVASVTDSFTGADLKALLYNAQLEALH 738
Cdd:pfam17862   1 DVDLEELAERTEGFSGADLEALCREAALAALR 32
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 555-619 4.00e-07

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 53.52  E-value: 4.00e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772 555 ILLYGPPGTGKTLLAGVIARGSRMNFISvkgpelLSkyigaseqAV-------RDIFIRAQAA----KPCILFFDE 619
Cdd:COG2256   52 MILWGPPGTGKTTLARLIANATDAEFVA------LS--------AVtsgvkdiREVIEEARERraygRRTILFVDE 113
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 269-419 4.84e-07

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 50.06  E-value: 4.84e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772   269 RNGALLLTGGKGSGKSTLAKAICKEaFDKLDAHVERVDCKALRGKRLENIQ--------------KTLEVAFSEAVWMQP 334
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARE-LGPPGGGVIYIDGEDILEEVLDQLLliivggkkasgsgeLRLRLALALARKLKP 79

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772   335 SVVLLDDLDLIAglpavpehehspDAVQSQRLAHALNDMIKEFISMGSLVALIATSQSQQSLHPLLVsaqgVHIFQCVQH 414
Cdd:smart00382  80 DVLILDEITSLL------------DAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALL----RRRFDRRIV 143


                   ....*
gi 194380772   415 IQPPN 419
Cdd:smart00382 144 LLLIL 148
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 555-619 1.33e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 52.01  E-value: 1.33e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194380772 555 ILLYGPPGTGKTLLAGVIARGSRMNFISVKGPEllskyigASEQAVRDIFIRAQAA----KPCILFFDE 619
Cdd:PRK13342  39 MILWGPPGTGKTTLARIIAGATDAPFEALSAVT-------SGVKDLREVIEEARQRrsagRRTILFIDE 100
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 547-647 4.07e-06

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: 50.61  E-value: 4.07e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  547 LPIRQRTG-ILLYGPPGTGKTLLAGVIAR---G----SRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAkpcILFFD 618
Cdd:TIGR03922 306 LPVAQTSNhMLFAGPPGTGKTTIARVVAKiycGlgvlRKPLVREVSRADLIGQYIGESEAKTNEIIDSALGG---VLFLD 382

                          90       100
                  ....*....|....*....|....*....
gi 194380772  619 EFESIAPRRGHDNTGVTDRVVNQLLTQLD 647
Cdd:TIGR03922 383 EAYTLVETGYGQKDPFGLEAIDTLLARME 411
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 272-357 9.26e-06

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


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 46.96  E-value: 9.26e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 272 ALLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAGLPAV 351
Cdd:cd19509   34 GILLYGPPGTGKTLLARAVASE----SGSTFFSISASSLVSKWVGESEKIVRALFALARELQPSIIFIDEIDSLLSERGS 109


                 ....*.
gi 194380772 352 PEHEHS 357
Cdd:cd19509  110 GEHEAS 115
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
554-601 1.33e-05

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 48.81  E-value: 1.33e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 194380772 554 GILLYGPPGTGKTLLAGVIAR--GSRMNFISVKGPELLSKYIGASE---QAVR 601
Cdd:COG1224   66 GILIVGPPGTGKTALAVAIARelGEDTPFVAISGSEIYSAELKKTEflmQALR 118
RecA-like_ATAD3-like cd19512
ATPase domains of ATPase AAA-domain protein 3A (ATAD3A), -3B, and -3C, and similar ATPase ...
 555-681 3.37e-05

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: 44.82  E-value: 3.37e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 555 ILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSkyIGASE-QAVRDIFIRAQAA-KPCILFFDEFESIAPRRGHDNT 632
Cdd:cd19512   25 ILFYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAP--MGREGvTAIHKVFDWANTSrRGLLLFVDEADAFLRKRSTEKI 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|
gi 194380772 633 GVTDR-VVNQLLTQLdGVEGLQGVYVLaATSRPDLIDPALlrPGRLDKCV 681
Cdd:cd19512  103 SEDLRaALNAFLYRT-GEQSNKFMLVL-ASNQPEQFDWAI--NDRIDEMV 148
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 264-357 3.45e-05

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: 45.23  E-value: 3.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 264 LVAGLRNGA--LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDD 341
Cdd:cd19524   25 LFTGLRAPArgLLLFGPPGNGKTMLAKAVAAES----NATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDE 100

                         90
                 ....*....|....*.
gi 194380772 342 LDLIAGLPAVPEHEHS 357
Cdd:cd19524  101 VDSLLSERSEGEHEAS 116
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 554-681 9.90e-05

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: 43.90  E-value: 9.90e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 554 GILLYGPPGTGKTLLAGVIARGSRMNFISVKGPELLSK-----------YIGASEQAVRDI---FIRAQAAKPCILFF-D 618
Cdd:cd19505   14 GILLIGSIETGRSYLIKSLAANSYVPLIRISLNKLLYNkpdfgnddwidGMLILKESLHRLnlqFELAKAMSPCIIWIpN 93

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772 619 EFESIAPRRGHDNTGVTDRVVNQLLTQL-DGVEG--LQGVYVLAATSRPDLIDPALLRPGRLDKCV 681
Cdd:cd19505   94 IHELNVNRSTQNLEEDPKLLLGLLLNYLsRDFEKssTRNILVIASTHIPQKVDPALIAPNRLDTCI 159
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 554-601 1.04e-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: 45.76  E-value: 1.04e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 194380772  554 GILLYGPPGTGKTLLAGVIAR--GSRMNFISVKGPELLSKYIGASE---QAVR 601
Cdd:pfam06068  52 AVLIAGPPGTGKTALAIAISKelGEDTPFTSISGSEVYSLEMKKTEaltQAFR 104
PRK13341 PRK13341
AAA family ATPase;
556-619 1.48e-04

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 45.82  E-value: 1.48e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 194380772 556 LLYGPPGTGKTLLAGVIARGSRMNFIS-------VKgpELLSKYIGASEQavrdifiRAQAAKPCILFFDE 619
Cdd:PRK13341  56 ILYGPPGVGKTTLARIIANHTRAHFSSlnavlagVK--DLRAEVDRAKER-------LERHGKRTILFIDE 117
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
555-588 2.01e-04

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 44.74  E-value: 2.01e-04
                         10        20        30
                 ....*....|....*....|....*....|....
gi 194380772 555 ILLYGPPGTGKTLLAGVIARGSRMNFISVKGPEL 588
Cdd:PRK00080  54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 555-588 2.43e-04

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: 42.49  E-value: 2.43e-04
                          10        20        30
                  ....*....|....*....|....*....|....
gi 194380772  555 ILLYGPPGTGKTLLAGVIARGSRMNFISVKGPEL 588
Cdd:pfam05496  36 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAI 69
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 273-355 3.49e-04

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


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 42.41  E-value: 3.49e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 273 LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAGLPAVP 352
Cdd:cd19520   38 VLLYGPPGCGKTMLAKATAKEA----GARFINLQVSSLTDKWYGESQKLVAAVFSLASKLQPSIIFIDEIDSFLRQRSST 113


                 ...
gi 194380772 353 EHE 355
Cdd:cd19520  114 DHE 116
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 272-367 5.10e-04

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: 41.79  E-value: 5.10e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 272 ALLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIagLPAV 351
Cdd:cd19523   35 SILLFGPRGTGKTLLGRCLASQ----LGATFLRLRGSTLVAKWAGEGEKILQASFLAARCRQPSVLFISDLDAL--LSSQ 108

                         90
                 ....*....|....*..
gi 194380772 352 PEhEHSP-DAVQSQRLA 367
Cdd:cd19523  109 DD-EASPvGRLQVELLA 124
PRK08116 PRK08116
hypothetical protein; Validated
 550-607 7.03e-04

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 42.70  E-value: 7.03e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 194380772 550 RQRTGILLYGPPGTGKTLLAGVIA-----RGSRMNFISVkgPELLSK---YIGASEQAVRDIFIRA 607
Cdd:PRK08116 112 KENVGLLLWGSVGTGKTYLAACIAnelieKGVPVIFVNF--PQLLNRiksTYKSSGKEDENEIIRS 175
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
549-584 7.85e-04

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 42.08  E-value: 7.85e-04
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 194380772 549 IRQRTGILLYGPPGTGKTLLAGVIARGSRMNFISVK 584
Cdd:COG1484   96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVR 131
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 555-574 8.78e-04

Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, recombination and repair];


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 42.76  E-value: 8.78e-04
                         10        20
                 ....*....|....*....|
gi 194380772 555 ILLYGPPGTGKTLLAGVIAR 574
Cdd:COG2255   57 VLLYGPPGLGKTTLAHIIAN 76
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 444-620 1.49e-03

5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB [Defense mechanisms];


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 42.06  E-value: 1.49e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 444 DLDLQHVAKETGGFVARDFTVLVDRAIHSRLSRQSISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWD---KI 520
Cdd:COG1401  110 DSEIEAVGLLLELAERSDALEALERARLLLELADLEERAALETEVLEALEAELEELLAAPEDLSADALAAELSAAeelYS 189

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 521 GGLHEVRQILMDTIQlpAKYPELFANLPIRQRTG--ILLYGPPGTGKTLLAGVIARG------SRMNFISV----KGPEL 588
Cdd:COG1401  190 EDLESEDDYLKDLLR--EKFEETLEAFLAALKTKknVILAGPPGTGKTYLARRLAEAlggednGRIEFVQFhpswSYEDF 267

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|..
gi 194380772 589 LSKY---IGASEQAVRD-IFIRA--QAA----KPCILFFDEF 620
Cdd:COG1401  268 LLGYrpsLDEGKYEPTPgIFLRFclKAEknpdKPYVLIIDEI 309
COG0645 COG0645
Predicted kinase, contains AAA domain [General function prediction only];
273-324 1.53e-03

Predicted kinase, contains AAA domain [General function prediction only];


Pssm-ID: 440410 [Multi-domain]  Cd Length: 164  Bit Score: 40.28  E-value: 1.53e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 194380772 273 LLLTGGK-GSGKSTLAKAICKEafdkLDAHVERVD--CKALRGKRLENIQKTLEV 324
Cdd:COG0645    1 LILVCGLpGSGKSTLARALAER----LGAVRLRSDvvRKRLFGAGLAPLERSPEA 51
APS_kinase pfam01583
Adenylylsulphate kinase; Enzyme that catalyzes the phosphorylation of adenylylsulphate to 3 ...
 273-329 1.62e-03

Adenylylsulphate kinase; Enzyme that catalyzes the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.


Pssm-ID: 396247 [Multi-domain]  Cd Length: 154  Bit Score: 39.99  E-value: 1.62e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 194380772  273 LLLTGGKGSGKSTLAKAICKEAFDK------LDAHVERVD-CKAL---RGKRLENIQKTLEVA--FSEA 329
Cdd:pfam01583   5 IWLTGLSGAGKSTIANALERKLFEQgrsvyvLDGDNVRHGlNKDLgfsEEDRTENIRRIGEVAklFADA 73
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 555-625 1.86e-03

AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 40.26  E-value: 1.86e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772  555 ILLYGPPGTGKTLLAGVIAR---GSRMNFISVKGPELL-----SKYIGASEQAVRD----IFIRAQAAKP-CILFFDEFE 621
Cdd:pfam07724   6 FLFLGPTGVGKTELAKALAEllfGDERALIRIDMSEYMeehsvSRLIGAPPGYVGYeeggQLTEAVRRKPySIVLIDEIE 85


                  ....
gi 194380772  622 SIAP 625
Cdd:pfam07724  86 KAHP 89
RecA-like_CDC48_r1-like cd19519
first of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or VCP ...
 273-400 6.68e-03

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


Pssm-ID: 410927 [Multi-domain]  Cd Length: 166  Bit Score: 38.57  E-value: 6.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 194380772 273 LLLTGGKGSGKSTLAKAICKEAfdklDAHVERVDCKALRGKRLENIQKTLEVAFSEAVWMQPSVVLLDDLDLIAglpavP 352
Cdd:cd19519   37 ILLYGPPGTGKTLIARAVANET----GAFFFLINGPEIMSKLAGESESNLRKAFEEAEKNAPAIIFIDEIDAIA-----P 107

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 194380772 353 EHEHSPDAVQSQRLAHALNDMikEFISMGSLVALIATSQSQQSLHPLL 400
Cdd:cd19519  108 KREKTHGEVERRIVSQLLTLM--DGLKQRAHVIVMAATNRPNSIDPAL 153
PRK04195 PRK04195
replication factor C large subunit; Provisional
 555-574 9.36e-03

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 39.52  E-value: 9.36e-03
                         10        20
                 ....*....|....*....|
gi 194380772 555 ILLYGPPGTGKTLLAGVIAR 574
Cdd:PRK04195  42 LLLYGPPGVGKTSLAHALAN 61
 
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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