NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|544186102|ref|NP_001269606|]
View 

peroxisomal ATPase PEX1 isoform 2 [Homo sapiens]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 791-948 6.36e-105

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: 327.46  E-value: 6.36e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19526     1 VKKALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 948
Cdd:cd19526    81 RAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
CDC48 super family cl36852
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 595-1008 3.78e-99

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: 332.64  E-value: 3.78e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   595 LLLTGGKGSGKSTLAKAICKEA----------------------------------------FDKLDA----------HV 624
Cdd:TIGR01243  215 VLLYGPPGTGKTLLAKAVANEAgayfisingpeimskyygeseerlreifkeaeenapsiifIDEIDAiapkreevtgEV 294

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   625 ERVDCKALRALNDMIKEfisMGSLVALIATSQSQqSLHPLLVSAQGvhiFQCVQHIQPPNQEQRCEILCNVIKNKLDCDi 704
Cdd:TIGR01243  295 EKRVVAQLLTLMDGLKG---RGRVIVIGATNRPD-ALDPALRRPGR---FDREIVIRVPDKRARKEILKVHTRNMPLAE- 366

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   705 nkftDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSR-----------QSI--STREKLVLTTLDFQKALRGFLPASLRS 771
Cdd:TIGR01243  367 ----DVDLDKLAEVTHGFVGADLAALAKEAAMAALRRfiregkinfeaEEIpaEVLKELKVTMKDFMEALKMVEPSAIRE 442

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   772 VNLHKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGP 851
Cdd:TIGR01243  443 VLVEVP-NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGP 521

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   852 ELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPD 930
Cdd:TIGR01243  522 EILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARfDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPD 601

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102   931 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHGMLLS 1008
Cdd:TIGR01243  602 ILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGS 679
PEX-2N pfam09263
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like ...
 17-98 8.26e-45

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: 156.38  E-value: 8.26e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    17 VTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVVWSH-QPAFLSWVEGRHFSDQGENVAEINRQVGQKLGLSNGGQVFLK 95
Cdd:pfam09263    1 VTVVFNNAKNCFLHLPSKLVSQLSLQENQALELSWGHgQPVFLSWTEGRHSSDQDENVVELNRQLGEKLGLKDGEQVFLR 80


                   ...
gi 544186102    96 PCS 98
Cdd:pfam09263   81 PCS 83
PEX-1N pfam09262
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi ...
 104-179 8.52e-32

Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. 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: 462729  Cd Length: 77  Bit Score: 118.76  E-value: 8.52e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544186102   104 QQVEVEPLSADDWEILELHAVSLEQHLLDQIRIVFPKAIFPVWVDQQTYIFIQIVALIPAAS-YGRLETDTKLLIQP 179
Cdd:pfam09262    1 TTVEVEPLTSDDWEILELHAEFLEDNLLSQVRVVSPGQILPVWVSGTTVARFRVTSIEPANSpFARLSPDTEVIVAP 77
SpoVK super family cl33891
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 397-762 7.59e-10

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


The actual alignment was detected with superfamily member COG0464:

Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 62.62  E-value: 7.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  397 AIKYTKNVEVLHLGKVWIPDDLRKRLNIEMHAVVRITPVEVTPKIPRSLKLQPRENLPKDISEEDIKTVFYSWLQQSTTT 476
Cdd:COG0464     1 LAELLALAVALALALLLLDDAALRLLLLLLLALAAALLLLLLLLLLLLLALLLVELLLLLLSGALAALLLLALLLLALLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  477 MLPLVISEEEFIKLETKDGLKEFSLSIVHSWEKEKDKNIFLLSPNLLQKTTIQVLLDPMVKEENSEEIDFILPFLkLSSL 556
Cdd:COG0464    81 LLAALLSALELLLLGELLLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAI-LDDL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  557 GGVNSLgVSSLEHITHSLLGRPLSRQLMSLVAGLRngaLLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKAL---- 632
Cdd:COG0464   160 GGLEEV-KEELRELVALPLKRPELREEYGLPPPRG---LLLYGPPGTGKTLLARALAGE----LGLPLIEVDLSDLvsky 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  633 -----RALNDMIKE---------FI-----------SMGSLVALIATSQSQQSL----HPLLVSAQGVHI---------- 673
Cdd:COG0464   232 vgeteKNLREVFDKarglapcvlFIdeadalagkrgEVGDGVGRRVVNTLLTEMeelrSDVVVIAATNRPdlldpallrr 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  674 FQCVQHIQPPNQEQRCEILCNVIKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHS--RLSRQSISTReklv 751
Cdd:COG0464   312 FDEIIFFPLPDAEERLEIFRIHLRKRPLDE-----DVDLEELAEATEGLSGADIRNVVRRAALQalRLGREPVTTE---- 382

                         410
                  ....*....|.
gi 544186102  752 lttlDFQKALR 762
Cdd:COG0464   383 ----DLLEALE 389
 
Name Accession Description Interval E-value
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 791-948 6.36e-105

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: 327.46  E-value: 6.36e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19526     1 VKKALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 948
Cdd:cd19526    81 RAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 595-1008 3.78e-99

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: 332.64  E-value: 3.78e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   595 LLLTGGKGSGKSTLAKAICKEA----------------------------------------FDKLDA----------HV 624
Cdd:TIGR01243  215 VLLYGPPGTGKTLLAKAVANEAgayfisingpeimskyygeseerlreifkeaeenapsiifIDEIDAiapkreevtgEV 294

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   625 ERVDCKALRALNDMIKEfisMGSLVALIATSQSQqSLHPLLVSAQGvhiFQCVQHIQPPNQEQRCEILCNVIKNKLDCDi 704
Cdd:TIGR01243  295 EKRVVAQLLTLMDGLKG---RGRVIVIGATNRPD-ALDPALRRPGR---FDREIVIRVPDKRARKEILKVHTRNMPLAE- 366

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   705 nkftDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSR-----------QSI--STREKLVLTTLDFQKALRGFLPASLRS 771
Cdd:TIGR01243  367 ----DVDLDKLAEVTHGFVGADLAALAKEAAMAALRRfiregkinfeaEEIpaEVLKELKVTMKDFMEALKMVEPSAIRE 442

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   772 VNLHKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGP 851
Cdd:TIGR01243  443 VLVEVP-NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGP 521

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   852 ELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPD 930
Cdd:TIGR01243  522 EILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARfDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPD 601

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102   931 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHGMLLS 1008
Cdd:TIGR01243  602 ILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGS 679
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 743-1002 3.03e-93

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 302.31  E-value: 3.03e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  743 SISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILL 822
Cdd:COG1222    38 ALELLEEAPALLLNDANLTQKRLGTPRGTAVPAESPDVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLL 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  823 YGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNT-GVTD 901
Cdd:COG1222   118 YGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQ 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  902 RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASV 981
Cdd:COG1222   198 RTVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRDMPLADDVDLDKLAKL 277

                         250       260
                  ....*....|....*....|.
gi 544186102  982 TDSFTGADLKALLYNAQLEAL 1002
Cdd:COG1222   278 TEGFSGADLKAIVTEAGMFAI 298
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 765-1006 1.82e-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: 242.51  E-value: 1.82e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   765 LPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMN 844
Cdd:TIGR01243  160 REKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY 239

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   845 FISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLA 924
Cdd:TIGR01243  240 FISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIG 319

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   925 ATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHG 1004
Cdd:TIGR01243  320 ATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRR 399


                   ..
gi 544186102  1005 ML 1006
Cdd:TIGR01243  400 FI 401
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 775-993 4.57e-67

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 231.64  E-value: 4.57e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  775 HKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELL 854
Cdd:PRK03992  124 ESP-NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  855 SKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGvTDRVVN----QLLTQLDGVEGLQGVYVLAATSRPD 930
Cdd:PRK03992  203 QKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS-GDREVQrtlmQLLAEMDGFDPRGNVKIIAATNRID 281

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544186102  931 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKAL 993
Cdd:PRK03992  282 ILDPAILRPGRFDRIIEVPLPDEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAI 344
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 820-949 3.76e-49

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: 170.47  E-value: 3.76e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGV 899
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDSE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 544186102   900 TDRVVNQLLTQLDGVEGLQG-VYVLAATSRPDLIDPALLrpGRLDKCVYCP 949
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 ...
 17-98 8.26e-45

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: 156.38  E-value: 8.26e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    17 VTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVVWSH-QPAFLSWVEGRHFSDQGENVAEINRQVGQKLGLSNGGQVFLK 95
Cdd:pfam09263    1 VTVVFNNAKNCFLHLPSKLVSQLSLQENQALELSWGHgQPVFLSWTEGRHSSDQDENVVELNRQLGEKLGLKDGEQVFLR 80


                   ...
gi 544186102    96 PCS 98
Cdd:pfam09263   81 PCS 83
PEX-1N pfam09262
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi ...
 104-179 8.52e-32

Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. 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: 462729  Cd Length: 77  Bit Score: 118.76  E-value: 8.52e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544186102   104 QQVEVEPLSADDWEILELHAVSLEQHLLDQIRIVFPKAIFPVWVDQQTYIFIQIVALIPAAS-YGRLETDTKLLIQP 179
Cdd:pfam09262    1 TTVEVEPLTSDDWEILELHAEFLEDNLLSQVRVVSPGQILPVWVSGTTVARFRVTSIEPANSpFARLSPDTEVIVAP 77
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 820-952 4.38e-14

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: 70.87  E-value: 4.38e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    820 ILLYGPPGTGKTLLAGVIARESRMNFISVK-----------------GPELLSKYIGASEQAVRDIFIRAQAAKPCILFF 882
Cdd:smart00382    5 ILIVGPPGSGKTTLARALARELGPPGGGVIyidgedileevldqlllIIVGGKKASGSGELRLRLALALARKLKPDVLIL 84

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    883 DEFESIaprrgHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPgRLDKCVYCPPPD 952
Cdd:smart00382   85 DEITSL-----LDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 397-762 7.59e-10

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 62.62  E-value: 7.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  397 AIKYTKNVEVLHLGKVWIPDDLRKRLNIEMHAVVRITPVEVTPKIPRSLKLQPRENLPKDISEEDIKTVFYSWLQQSTTT 476
Cdd:COG0464     1 LAELLALAVALALALLLLDDAALRLLLLLLLALAAALLLLLLLLLLLLLALLLVELLLLLLSGALAALLLLALLLLALLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  477 MLPLVISEEEFIKLETKDGLKEFSLSIVHSWEKEKDKNIFLLSPNLLQKTTIQVLLDPMVKEENSEEIDFILPFLkLSSL 556
Cdd:COG0464    81 LLAALLSALELLLLGELLLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAI-LDDL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  557 GGVNSLgVSSLEHITHSLLGRPLSRQLMSLVAGLRngaLLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKAL---- 632
Cdd:COG0464   160 GGLEEV-KEELRELVALPLKRPELREEYGLPPPRG---LLLYGPPGTGKTLLARALAGE----LGLPLIEVDLSDLvsky 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  633 -----RALNDMIKE---------FI-----------SMGSLVALIATSQSQQSL----HPLLVSAQGVHI---------- 673
Cdd:COG0464   232 vgeteKNLREVFDKarglapcvlFIdeadalagkrgEVGDGVGRRVVNTLLTEMeelrSDVVVIAATNRPdlldpallrr 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  674 FQCVQHIQPPNQEQRCEILCNVIKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHS--RLSRQSISTReklv 751
Cdd:COG0464   312 FDEIIFFPLPDAEERLEIFRIHLRKRPLDE-----DVDLEELAEATEGLSGADIRNVVRRAALQalRLGREPVTTE---- 382

                         410
                  ....*....|.
gi 544186102  752 lttlDFQKALR 762
Cdd:COG0464   383 ----DLLEALE 389
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 972-1003 3.75e-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: 3.75e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 544186102   972 DVDLQHVASVTDSFTGADLKALLYNAQLEALH 1003
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALR 32
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 581-642 1.79e-04

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: 43.29  E-value: 1.79e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 544186102  581 RQLMSLVAGLRNGALLLTGGKGSGKSTLAKAICKEAFDKlDAHVERVDCKALRALNDMIKEF 642
Cdd:cd00009     8 EALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP-GAPFLYLNASDLLEGLVVAELF 68
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 591-647 4.88e-03

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: 38.89  E-value: 4.88e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 544186102    591 RNGALLLTGGKGSGKSTLAKAICKEaFDKLDAHVERVDCKALRALNDMIKEFISMGS 647
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARE-LGPPGGGVIYIDGEDILEEVLDQLLLIIVGG 56
 
Name Accession Description Interval E-value
RecA-like_PEX1_r2 cd19526
second of two ATPase domains of Peroxisomal biogenesis factor 1 (PEX1); PEX1(also known as ...
 791-948 6.36e-105

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: 327.46  E-value: 6.36e-105
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19526     1 VKKALEETIEWPSKYPKIFASSPLRLRSGILLYGPPGCGKTLLASAIASECGLNFISVKGPELLNKYIGASEQNVRDLFS 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 948
Cdd:cd19526    81 RAQSAKPCILFFDEFDSIAPKRGHDSTGVTDRVVNQLLTQLDGVEGLDGVYVLAATSRPDLIDPALLRPGRLDKLVYC 158
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 595-1008 3.78e-99

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: 332.64  E-value: 3.78e-99
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   595 LLLTGGKGSGKSTLAKAICKEA----------------------------------------FDKLDA----------HV 624
Cdd:TIGR01243  215 VLLYGPPGTGKTLLAKAVANEAgayfisingpeimskyygeseerlreifkeaeenapsiifIDEIDAiapkreevtgEV 294

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   625 ERVDCKALRALNDMIKEfisMGSLVALIATSQSQqSLHPLLVSAQGvhiFQCVQHIQPPNQEQRCEILCNVIKNKLDCDi 704
Cdd:TIGR01243  295 EKRVVAQLLTLMDGLKG---RGRVIVIGATNRPD-ALDPALRRPGR---FDREIVIRVPDKRARKEILKVHTRNMPLAE- 366

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   705 nkftDLDLQHVAKETGGFVARDFTVLVDRAIHSRLSR-----------QSI--STREKLVLTTLDFQKALRGFLPASLRS 771
Cdd:TIGR01243  367 ----DVDLDKLAEVTHGFVGADLAALAKEAAMAALRRfiregkinfeaEEIpaEVLKELKVTMKDFMEALKMVEPSAIRE 442

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   772 VNLHKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGP 851
Cdd:TIGR01243  443 VLVEVP-NVRWSDIGGLEEVKQELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFIAVRGP 521

                          330       340       350       360       370       380       390       400
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   852 ELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPD 930
Cdd:TIGR01243  522 EILSKWVGESEKAIREIFRKARQAAPAIIFFDEIDAIAPARGARfDTSVTDRIVNQLLTEMDGIQELSNVVVIAATNRPD 601

                          410       420       430       440       450       460       470
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102   931 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHGMLLS 1008
Cdd:TIGR01243  602 ILDPALLRPGRFDRLILVPPPDEEARKEIFKIHTRSMPLAEDVDLEELAEMTEGYTGADIEAVCREAAMAALRESIGS 679
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 743-1002 3.03e-93

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 302.31  E-value: 3.03e-93
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  743 SISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILL 822
Cdd:COG1222    38 ALELLEEAPALLLNDANLTQKRLGTPRGTAVPAESPDVTFDDIGGLDEQIEEIREAVELPLKNPELFRKYGIEPPKGVLL 117

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  823 YGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNT-GVTD 901
Cdd:COG1222   118 YGPPGTGKTLLAKAVAGELGAPFIRVRGSELVSKYIGEGARNVREVFELAREKAPSIIFIDEIDAIAARRTDDGTsGEVQ 197

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  902 RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASV 981
Cdd:COG1222   198 RTVNQLLAELDGFESRGDVLIIAATNRPDLLDPALLRPGRFDRVIEVPLPDEEAREEILKIHLRDMPLADDVDLDKLAKL 277

                         250       260
                  ....*....|....*....|.
gi 544186102  982 TDSFTGADLKALLYNAQLEAL 1002
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 ...
 791-948 2.72e-83

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: 268.38  E-value: 2.72e-83
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19511     1 VKRELKEAVEWPLKHPDAFKRLGIRPPKGVLLYGPPGCGKTLLAKALASEAGLNFISVKGPELFSKYVGESERAVREIFQ 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRGHDN-TGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 948
Cdd:cd19511    81 KARQAAPCIIFFDEIDSLAPRRGQSDsSGVTDRVVSQLLTELDGIESLKGVVVIAATNRPDMIDPALLRPGRLDKLIYV 159
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 724-1003 2.07e-81

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: 272.55  E-value: 2.07e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  724 ARDFTVLVDRAIHSRLSRQSISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPA 803
Cdd:COG0464    98 LLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAILDDLGGLEEVKEELRELVALPL 177

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  804 KYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFD 883
Cdd:COG0464   178 KRPELREEYGLPPPRGLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKYVGETEKNLREVFDKARGLAPCVLFID 257

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  884 EFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGlqGVYVLAATSRPDLIDPALLRpgRLDKCVYCPPPDQVSRLEILNVL 963
Cdd:COG0464   258 EADALAGKRGEVGDGVGRRVVNTLLTEMEELRS--DVVVIAATNRPDLLDPALLR--RFDEIIFFPLPDAEERLEIFRIH 333

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|
gi 544186102  964 SDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALH 1003
Cdd:COG0464   334 LRKRPLDEDVDLEELAEATEGLSGADIRNVVRRAALQALR 373
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 791-947 2.87e-73

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: 240.48  E-value: 2.87e-73
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19529     1 VKQELKEAVEWPLLKPEVFKRLGIRPPKGILLYGPPGTGKTLLAKAVATESNANFISVKGPELLSKWVGESEKAIREIFR 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRGHD-NTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 947
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 ...
 788-947 5.48e-71

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: 233.92  E-value: 5.48e-71
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  788 LHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRD 867
Cdd:cd19530     1 LDHVREELTMSILRPIKRPDIYKALGIDLPTGVLLYGPPGCGKTLLAKAVANESGANFISVKGPELLNKYVGESERAVRQ 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  868 IFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 947
Cdd:cd19530    81 VFQRARASAPCVIFFDEVDALVPKRGDGGSWASERVVNQLLTEMDGLEERSNVFVIAATNRPDIIDPAMLRPGRLDKTLY 160
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 765-1006 1.82e-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: 242.51  E-value: 1.82e-67
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   765 LPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMN 844
Cdd:TIGR01243  160 REKPVREEIERKVPKVTYEDIGGLKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTLLAKAVANEAGAY 239

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   845 FISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLA 924
Cdd:TIGR01243  240 FISINGPEIMSKYYGESEERLREIFKEAEENAPSIIFIDEIDAIAPKREEVTGEVEKRVVAQLLTLMDGLKGRGRVIVIG 319

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   925 ATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHG 1004
Cdd:TIGR01243  320 ATNRPDALDPALRRPGRFDREIVIRVPDKRARKEILKVHTRNMPLAEDVDLDKLAEVTHGFVGADLAALAKEAAMAALRR 399


                   ..
gi 544186102  1005 ML 1006
Cdd:TIGR01243  400 FI 401
PRK03992 PRK03992
proteasome-activating nucleotidase; Provisional
 775-993 4.57e-67

proteasome-activating nucleotidase; Provisional


Pssm-ID: 179699 [Multi-domain]  Cd Length: 389  Bit Score: 231.64  E-value: 4.57e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  775 HKPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELL 854
Cdd:PRK03992  124 ESP-NVTYEDIGGLEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELV 202

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  855 SKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGvTDRVVN----QLLTQLDGVEGLQGVYVLAATSRPD 930
Cdd:PRK03992  203 QKFIGEGARLVRELFELAREKAPSIIFIDEIDAIAAKRTDSGTS-GDREVQrtlmQLLAEMDGFDPRGNVKIIAATNRID 281

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544186102  931 LIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKAL 993
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 ...
 791-947 1.11e-66

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: 221.62  E-value: 1.11e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFAnLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19527     1 VKKEILDTIQLPLEHPELFS-SGLRKRSGILLYGPPGTGKTLLAKAIATECSLNFLSVKGPELINMYIGESEANVREVFQ 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRGH--DNTGVTDRVVNQLLTQLDGVE-GLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 947
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 ...
 784-947 8.55e-66

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: 219.47  E-value: 8.55e-66
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  784 KIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQ 863
Cdd:cd19503     1 DIGGLDEQIASLKELIELPLKYPELFRALGLKPPRGVLLHGPPGTGKTLLARAVANEAGANFLSISGPSIVSKYLGESEK 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  864 AVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLD 943
Cdd:cd19503    81 NLREIFEEARSHAPSIIFIDEIDALAPKREEDQREVERRVVAQLLTLMDGMSSRGKVVVIAATNRPDAIDPALRRPGRFD 160


                  ....
gi 544186102  944 KCVY 947
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 ...
 791-947 3.34e-65

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: 217.76  E-value: 3.34e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19528     1 VKRELQELVQYPVEHPDKFLKFGMTPSKGVLFYGPPGCGKTLLAKAIANECQANFISVKGPELLTMWFGESEANVRDIFD 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRG---HDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVY 947
Cdd:cd19528    81 KARAAAPCVLFFDELDSIAKARGgniGDAGGAADRVINQILTEMDGMNTKKNVFIIGATNRPDIIDPAILRPGRLDQLIY 160
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 782-944 1.07e-56

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: 193.71  E-value: 1.07e-56
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  782 WDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGAS 861
Cdd:cd19502     2 YEDIGGLDEQIREIREVVELPLKHPELFEELGIEPPKGVLLYGPPGTGKTLLAKAVANHTDATFIRVVGSELVQKYIGEG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  862 EQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGvTDRVVN----QLLTQLDGVEGLQGVYVLAATSRPDLIDPALL 937
Cdd:cd19502    82 ARLVRELFEMAREKAPSIIFIDEIDAIGAKRFDSGTG-GDREVQrtmlELLNQLDGFDPRGNIKVIMATNRPDILDPALL 160


                  ....*..
gi 544186102  938 RPGRLDK 944
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 ...
 785-944 4.01e-55

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: 189.18  E-value: 4.01e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19519     2 IGGCRKQLAQIREMVELPLRHPELFKAIGIKPPRGILLYGPPGTGKTLIARAVANETGAFFFLINGPEIMSKLAGESESN 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDK 944
Cdd:cd19519    82 LRKAFEEAEKNAPAIIFIDEIDAIAPKREKTHGEVERRIVSQLLTLMDGLKQRAHVIVMAATNRPNSIDPALRRFGRFDR 161
FtsH_fam TIGR01241
ATP-dependent metalloprotease FtsH; HflB(FtsH) is a pleiotropic protein required for correct ...
 783-1001 1.54e-53

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: 195.97  E-value: 1.54e-53
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   783 DKIGGLHEVRQILMDTIQLpAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASE 862
Cdd:TIGR01241   55 KDVAGIDEAKEELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGA 133

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   863 QAVRDIFIRAQAAKPCILFFDEFESIAPRRG------HDntgVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPAL 936
Cdd:TIGR01241  134 SRVRDLFEQAKKNAPCIIFIDEIDAVGRQRGaglgggND---EREQTLNQLLVEMDGFGTNTGVIVIAATNRPDVLDPAL 210

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544186102   937 LRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEA 1001
Cdd:TIGR01241  211 LRPGRFDRQVVVDLPDIKGREEILKVHAKNKKLAPDVDLKAVARRTPGFSGADLANLLNEAALLA 275
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 791-948 5.52e-53

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: 182.48  E-value: 5.52e-53
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  791 VRQILMDTIQLPAKYPELFAnLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFI 870
Cdd:cd19481     1 LKASLREAVEAPRRGSRLRR-YGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVGESEKNLRKIFE 79

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544186102  871 RAQAAKPCILFFDEFESIAPRRG-HDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 948
Cdd:cd19481    80 RARRLAPCILFIDEIDAIGRKRDsSGESGELRRVLNQLLTELDGVNSRSKVLVIAATNRPDLLDPALLRPGRFDEVIEF 158
pup_AAA TIGR03689
proteasome ATPase; In the Actinobacteria, as shown for Mycobacterium tuberculosis, some ...
 779-972 9.23e-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: 9.23e-51
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   779 DLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIA----------RESRMNFISV 848
Cdd:TIGR03689  178 DVTYADIGGLGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTLIAKAVAnslaarigaeGGGKSYFLNI 257

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   849 KGPELLSKYIGASEQAVRDIFIRAQAA----KPCILFFDEFESIAPRRGhdnTGVTD----RVVNQLLTQLDGVEGLQGV 920
Cdd:TIGR03689  258 KGPELLNKYVGETERQIRLIFQRAREKasegRPVIVFFDEMDSLFRTRG---SGVSSdvetTVVPQLLAEIDGVESLDNV 334

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|...
gi 544186102   921 YVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEIL-NVLSDSLPLADD 972
Cdd:TIGR03689  335 IVIGASNREDMIDPAILRPGRLDVKIRIERPDAEAAADIFaKYLTDDLPLPED 387
PTZ00454 PTZ00454
26S protease regulatory subunit 6B-like protein; Provisional
 767-1002 5.24e-50

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


Pssm-ID: 240423 [Multi-domain]  Cd Length: 398  Bit Score: 182.66  E-value: 5.24e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  767 ASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFI 846
Cdd:PTZ00454  129 SSIQLLQMSEKPDVTYSDIGGLDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTMLAKAVAHHTTATFI 208

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  847 SVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGV---TDRVVNQLLTQLDGVEGLQGVYVL 923
Cdd:PTZ00454  209 RVVGSEFVQKYLGEGPRMVRDVFRLARENAPSIIFIDEVDSIATKRFDAQTGAdreVQRILLELLNQMDGFDQTTNVKVI 288

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544186102  924 AATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEAL 1002
Cdd:PTZ00454  289 MATNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAV 367
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 820-949 3.76e-49

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: 170.47  E-value: 3.76e-49
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGV 899
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAGSRGSGGDSE 80

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|.
gi 544186102   900 TDRVVNQLLTQLDGVEGLQG-VYVLAATSRPDLIDPALLrpGRLDKCVYCP 949
Cdd:pfam00004   81 SRRVVNQLLTELDGFTSSNSkVIVIAATNRPDKLDPALL--GRFDRIIEFP 129
HflB COG0465
ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones];
788-994 1.33e-48

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


Pssm-ID: 440233 [Multi-domain]  Cd Length: 583  Bit Score: 183.31  E-value: 1.33e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  788 LHEVRQILMDtiqlPAKYPELFANLPirqrTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKY--IGASEqaV 865
Cdd:COG0465   154 LQEIVDFLKD----PEKFTRLGAKIP----KGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFvgVGASR--V 223

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  866 RDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTD---RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRL 942
Cdd:COG0465   224 RDLFEQAKKNAPCIIFIDEIDAVGRQRGAGLGGGHDereQTLNQLLVEMDGFEGNEGVIVIAATNRPDVLDPALLRPGRF 303

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|..
gi 544186102  943 DKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALL 994
Cdd:COG0465   304 DRQVVVDLPDVKGREAILKVHARKKPLAPDVDLEVIARRTPGFSGADLANLV 355
ftsH CHL00176
cell division protein; Validated
 783-999 1.61e-48

cell division protein; Validated


Pssm-ID: 214386 [Multi-domain]  Cd Length: 638  Bit Score: 184.10  E-value: 1.61e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  783 DKIGGLHEVRQILMDTIQLpAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASE 862
Cdd:CHL00176  183 RDIAGIEEAKEEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSISGSEFVEMFVGVGA 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  863 QAVRDIFIRAQAAKPCILFFDEFESIAPRRGhdnTGV------TDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPAL 936
Cdd:CHL00176  262 ARVRDLFKKAKENSPCIVFIDEIDAVGRQRG---AGIgggndeREQTLNQLLTEMDGFKGNKGVIVIAATNRVDILDAAL 338

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544186102  937 LRPGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQL 999
Cdd:CHL00176  339 LRPGRFDRQITVSLPDREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAI 401
hflB PRK10733
ATP-dependent zinc metalloprotease FtsH;
795-1004 1.07e-47

ATP-dependent zinc metalloprotease FtsH;


Pssm-ID: 182683 [Multi-domain]  Cd Length: 644  Bit Score: 181.77  E-value: 1.07e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  795 LMDTIQLPAKYPELFANLPirqrTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQA 874
Cdd:PRK10733  167 LVEYLREPSRFQKLGGKIP----KGVLMVGPPGTGKTLLAKAIAGEAKVPFFTISGSDFVEMFVGVGASRVRDMFEQAKK 242

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  875 AKPCILFFDEFESIAPRRG------HDNTgvtDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYC 948
Cdd:PRK10733  243 AAPCIIFIDEIDAVGRQRGaglgggHDER---EQTLNQMLVEMDGFEGNEGIIVIAATNRPDVLDPALLRPGRFDRQVVV 319

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 544186102  949 PPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEALHG 1004
Cdd:PRK10733  320 GLPDVRGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARG 375
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 785-947 4.76e-47

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: 166.25  E-value: 4.76e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLpAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19501     6 VAGCEEAKEELKEVVEF-LKNPEKFTKLGAKIPKGVLLVGPPGTGKTLLAKAVAGEAGVPFFSISGSDFVEMFVGVGASR 84

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTD---RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGR 941
Cdd:cd19501    85 VRDLFEQAKKNAPCIVFIDEIDAVGRKRGAGLGGGHDereQTLNQLLVEMDGFESNTGVIVIAATNRPDVLDPALLRPGR 164


                  ....*.
gi 544186102  942 LDKCVY 947
Cdd:cd19501   165 FDRQVY 170
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 782-1002 8.54e-47

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 174.57  E-value: 8.54e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  782 WDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGAS 861
Cdd:PTZ00361  182 YADIGGLEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTLLAKAVANETSATFLRVVGSELIQKYLGDG 261

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  862 EQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVT---DRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLR 938
Cdd:PTZ00361  262 PKLVRELFRVAEENAPSIVFIDEIDAIGTKRYDATSGGEkeiQRTMLELLNQLDGFDSRGDVKVIMATNRIESLDPALIR 341

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 544186102  939 PGRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDLQHVASVTDSFTGADLKALLYNAQLEAL 1002
Cdd:PTZ00361  342 PGRIDRKIEFPNPDEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLAL 405
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
817-1002 1.71e-45

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 164.29  E-value: 1.71e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  817 RTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAqAAKPCILFFDEFESIAPRRGHDN 896
Cdd:COG1223    35 PRKILFYGPPGTGKTMLAEALAGELKLPLLTVRLDSLIGSYLGETARNLRKLFDFA-RRAPCVIFFDEFDAIAKDRGDQN 113

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  897 -TGVTDRVVNQLLTQLDGVEGlqGVYVLAATSRPDLIDPALLRpgRLDKCVYCPPPDQVSRLEILNVLSDSLPLADDVDL 975
Cdd:COG1223   114 dVGEVKRVVNALLQELDGLPS--GSVVIAATNHPELLDSALWR--RFDEVIEFPLPDKEERKEILELNLKKFPLPFELDL 189

                         170       180
                  ....*....|....*....|....*..
gi 544186102  976 QHVASVTDSFTGADLKALLYNAQLEAL 1002
Cdd:COG1223   190 KKLAKKLEGLSGADIEKVLKTALKKAI 216
PEX-2N pfam09263
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a Cdc48 domain 2-like ...
 17-98 8.26e-45

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: 156.38  E-value: 8.26e-45
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    17 VTVAFTNARDCFLHLPRRLVAQLHLLQNQAIEVVWSH-QPAFLSWVEGRHFSDQGENVAEINRQVGQKLGLSNGGQVFLK 95
Cdd:pfam09263    1 VTVVFNNAKNCFLHLPSKLVSQLSLQENQALELSWGHgQPVFLSWTEGRHSSDQDENVVELNRQLGEKLGLKDGEQVFLR 80


                   ...
gi 544186102    96 PCS 98
Cdd:pfam09263   81 PCS 83
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 785-947 5.02e-44

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: 157.13  E-value: 5.02e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19509     1 IAGLDDAKEALKEAVILPSLRPDLFPGLRGPPR-GILLYGPPGTGKTLLARAVASESGSTFFSISASSLVSKWVGESEKI 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEG--LQGVYVLAATSRPDLIDPALLRpgRL 942
Cdd:cd19509    80 VRALFALARELQPSIIFIDEIDSLLSERGSGEHEASRRVKTEFLVQMDGVLNkpEDRVLVLGATNRPWELDEAFLR--RF 157


                  ....*
gi 544186102  943 DKCVY 947
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; ...
 806-943 2.19e-41

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: 149.95  E-value: 2.19e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  806 PELFANLPIRQRTGILLYGPPGTGKTLLAGVI-----ARESRMnfisVKGPELLSKYIGASEQAVRDIFIRAQAA-KPC- 878
Cdd:cd19504    24 PEIVEQLGCKHVKGILLYGPPGTGKTLMARQIgkmlnAREPKI----VNGPEILNKYVGESEANIRKLFADAEEEqRRLg 99

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 544186102  879 ------ILFFDEFESIAPRRGH--DNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLD 943
Cdd:cd19504   100 ansglhIIIFDEIDAICKQRGSmaGSTGVHDTVVNQLLSKIDGVEQLNNILVIGMTNRKDLIDEALLRPGRLE 172
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 785-944 3.18e-41

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: 149.48  E-value: 3.18e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19518     2 IGGMDSTLKELCELLIHPILPPEYFQHLGVEPPRGVLLHGPPGCGKTMLANAIAGELKVPFLKISATEIVSGVSGESEEK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGL----QGVYVLAATSRPDLIDPALLRPG 940
Cdd:cd19518    82 IRELFDQAISNAPCIVFIDEIDAITPKRESAQREMERRIVSQLLTCMDELNNEktagGPVLVIGATNRPDSLDPALRRAG 161


                  ....
gi 544186102  941 RLDK 944
Cdd:cd19518   162 RFDR 165
RecA-like_Yta7-like cd19517
ATPase domain of Saccharomyces cerevisiae Yta7 and similar ATPase domains; Saccharomyces ...
 785-944 9.02e-40

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: 145.34  E-value: 9.02e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESR-----MNFISVKGPELLSKYIG 859
Cdd:cd19517     2 IGGLSHYINQLKEMVFFPLLYPEVFAKFKITPPRGVLFHGPPGTGKTLMARALAAECSkggqkVSFFMRKGADCLSKWVG 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  860 ASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRP 939
Cdd:cd19517    82 EAERQLRLLFEEAYRMQPSIIFFDEIDGLAPVRSSKQEQIHASIVSTLLALMDGLDNRGQVVVIGATNRPDALDPALRRP 161


                  ....*
gi 544186102  940 GRLDK 944
Cdd:cd19517   162 GRFDR 166
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 785-942 3.51e-35

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: 131.78  E-value: 3.51e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRT-GILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQ 863
Cdd:cd19520     2 IGGLDEVITELKELVILPLQRPELFDNSRLLQPPkGVLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWYGESQK 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  864 AVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGV--EGLQGVYVLAATSRPDLIDPALLR--P 939
Cdd:cd19520    82 LVAAVFSLASKLQPSIIFIDEIDSFLRQRSSTDHEATAMMKAEFMSLWDGLstDGNCRVIVMGATNRPQDLDEAILRrmP 161


                  ...
gi 544186102  940 GRL 942
Cdd:cd19520   162 KRF 164
RecA-like_VPS4 cd19521
ATPase domain of vacuolar protein sorting-associated protein 4; Vacuolar protein ...
 776-947 7.19e-35

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: 131.14  E-value: 7.19e-35
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  776 KPrDLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLS 855
Cdd:cd19521     1 KP-NVKWEDVAGLEGAKEALKEAVILPVKFPHLFTGNRKPWS-GILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVS 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  856 KYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGV-EGLQGVYVLAATSRPDLIDP 934
Cdd:cd19521    79 KWMGESEKLVKQLFAMARENKPSIIFIDEVDSLCGTRGEGESEASRRIKTELLVQMNGVgNDSQGVLVLGATNIPWQLDS 158

                         170
                  ....*....|...
gi 544186102  935 ALLRpgRLDKCVY 947
Cdd:cd19521   159 AIRR--RFEKRIY 169
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 785-947 6.79e-33

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: 125.48  E-value: 6.79e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPiRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19522     2 IADLEEAKKLLEEAVVLPMWMPEFFKGIR-RPWKGVLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLTSKYRGESEKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRG-HDNTGVTDRVVNQLLTQLDGVEGLQG-------VYVLAATSRPDLIDPAL 936
Cdd:cd19522    81 VRLLFEMARFYAPTTIFIDEIDSICSRRGtSEEHEASRRVKSELLVQMDGVGGASEnddpskmVMVLAATNFPWDIDEAL 160

                         170
                  ....*....|.
gi 544186102  937 LRpgRLDKCVY 947
Cdd:cd19522   161 RR--RLEKRIY 169
RecA-like_spastin cd19524
ATPase domain of spastin; Spastin is an ATP-dependent microtubule-severing protein involved in ...
 785-947 7.57e-32

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: 122.27  E-value: 7.57e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19524     2 IAGQDLAKQALQEMVILPSLRPELFTGLRAPAR-GLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQG--VYVLAATSRPDLIDPALLRpgRL 942
Cdd:cd19524    81 VRALFAVARELQPSIIFIDEVDSLLSERSEGEHEASRRLKTEFLIEFDGVQSNGDdrVLVMGATNRPQELDDAVLR--RF 158


                  ....*
gi 544186102  943 DKCVY 947
Cdd:cd19524   159 TKRVY 163
PEX-1N pfam09262
Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi ...
 104-179 8.52e-32

Peroxisome biogenesis factor 1, N-terminal; Members of this family adopt a double psi beta-barrel fold, similar in structure to the Cdc48 N-terminal domain. 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: 462729  Cd Length: 77  Bit Score: 118.76  E-value: 8.52e-32
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 544186102   104 QQVEVEPLSADDWEILELHAVSLEQHLLDQIRIVFPKAIFPVWVDQQTYIFIQIVALIPAAS-YGRLETDTKLLIQP 179
Cdd:pfam09262    1 TTVEVEPLTSDDWEILELHAEFLEDNLLSQVRVVSPGQILPVWVSGTTVARFRVTSIEPANSpFARLSPDTEVIVAP 77
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 779-947 4.64e-30

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: 118.17  E-value: 4.64e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  779 DLGWDKIGGLHEVRQILMDTIQLPAKYPELFANLPIRQRtGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYI 858
Cdd:cd19525    18 PINWADIAGLEFAKKTIKEIVVWPMLRPDIFTGLRGPPK-GILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWV 96

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  859 GASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGL--QGVYVLAATSRPDLIDPAL 936
Cdd:cd19525    97 GEGEKMVRALFSVARCKQPAVIFIDEIDSLLSQRGEGEHESSRRIKTEFLVQLDGATTSseDRILVVGATNRPQEIDEAA 176

                         170
                  ....*....|.
gi 544186102  937 LRpgRLDKCVY 947
Cdd:cd19525   177 RR--RLVKRLY 185
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 812-950 6.34e-25

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: 101.84  E-value: 6.34e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  812 LPIRQRTGILLYGPPGTGKTLLAGVIARESRM---NFISVKGPELLSKYIGASEQ---AVRDIFIRAQAAKPCILFFDEF 885
Cdd:cd00009    14 LELPPPKNLLLYGPPGTGKTTLARAIANELFRpgaPFLYLNASDLLEGLVVAELFghfLVRLLFELAEKAKPGVLFIDEI 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 544186102  886 ESIAPRrghdntgVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPP 950
Cdd:cd00009    94 DSLSRG-------AQNALLRVLETLNDLRIDRENVRVIGATNRPLLGDLDRALYDRLDIRIVIPL 151
RecA-like_fidgetin cd19523
ATPase domain of fidgetin; Fidgetin (FIGN) is a ATP-dependent microtubule severing protein. ...
 785-938 1.64e-20

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: 89.94  E-value: 1.64e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMDTIQLPAKYPELFANLPIRQRTgILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQA 864
Cdd:cd19523     2 IAGLGALKAAIKEEVLWPLLRPDAFSGLLRLPRS-ILLFGPRGTGKTLLGRCLASQLGATFLRLRGSTLVAKWAGEGEKI 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544186102  865 VRDIFIRAQAAKPCILFFDEFESIAPRRGHDNTGVTdRVVNQLLTQLDGV--EGLQGVYVLAATSRPDLIDPALLR 938
Cdd:cd19523    81 LQASFLAARCRQPSVLFISDLDALLSSQDDEASPVG-RLQVELLAQLDGVlgSGEDGVLVVCTTSKPEEIDESLRR 155
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 785-943 4.05e-17

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: 80.11  E-value: 4.05e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  785 IGGLHEVRQILMdtIQLPAKYPELFA-NLPIRQrtGILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQ 863
Cdd:cd19507     2 VGGLDNLKDWLK--KRKAAFSKQASAyGLPTPK--GLLLVGIQGTGKSLTAKAIAGVWQLPLLRLDMGRLFGGLVGESES 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  864 AVRDIFIRAQAAKPCILFFDEFES-IAPRRGHDNTGVTDRVVNQLLTQLDgvEGLQGVYVLAATSRPDLIDPALLRPGRL 942
Cdd:cd19507    78 RLRQMIQTAEAIAPCVLWIDEIEKgFSNADSKGDSGTSSRVLGTFLTWLQ--EKKKPVFVVATANNVQSLPPELLRKGRF 155


                  .
gi 544186102  943 D 943
Cdd:cd19507   156 D 156
ycf46 CHL00195
Ycf46; Provisional
 819-1003 2.68e-14

Ycf46; Provisional


Pssm-ID: 177094 [Multi-domain]  Cd Length: 489  Bit Score: 76.98  E-value: 2.68e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  819 GILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFE-SIAPRRGHDNT 897
Cdd:CHL00195  261 GLLLVGIQGTGKSLTAKAIANDWQLPLLRLDVGKLFGGIVGESESRMRQMIRIAEALSPCILWIDEIDkAFSNSESKGDS 340

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  898 GVTDRVVNQLLTQLDgvEGLQGVYVLAATSRPDLIDPALLRPGRLDKCVYCPPPDQVSRLEILNV-LSDSLPLA-DDVDL 975
Cdd:CHL00195  341 GTTNRVLATFITWLS--EKKSPVFVVATANNIDLLPLEILRKGRFDEIFFLDLPSLEEREKIFKIhLQKFRPKSwKKYDI 418

                         170       180
                  ....*....|....*....|....*...
gi 544186102  976 QHVASVTDSFTGADlkalLYNAQLEALH 1003
Cdd:CHL00195  419 KKLSKLSNKFSGAE----IEQSIIEAMY 442
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 820-952 4.38e-14

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: 70.87  E-value: 4.38e-14
                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    820 ILLYGPPGTGKTLLAGVIARESRMNFISVK-----------------GPELLSKYIGASEQAVRDIFIRAQAAKPCILFF 882
Cdd:smart00382    5 ILIVGPPGSGKTTLARALARELGPPGGGVIyidgedileevldqlllIIVGGKKASGSGELRLRLALALARKLKPDVLIL 84

                            90       100       110       120       130       140       150
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102    883 DEFESIaprrgHDNTGVTDRVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPgRLDKCVYCPPPD 952
Cdd:smart00382   85 DEITSL-----LDAEQEALLLLLEELRLLLLLKSEKNLTVILTTNDEKDLGPALLRR-RFDRRIVLLLIL 148
RecA-like_BCS1 cd19510
Mitochondrial chaperone BCS1; Mitochondrial chaperone BCS1 is necessary for the assembly of ...
 795-947 4.79e-11

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: 62.37  E-value: 4.79e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  795 LMDTIQLPAKYPELFANLPIRQRTGILLYGPPGTGKTLLAGVIARESRMNFI------SVKGPELLSKYIGASEQA---- 864
Cdd:cd19510     1 IIDDLKDFIKNEDWYNDRGIPYRRGYLLYGPPGTGKSSFIAALAGELDYDICdlnlseVVLTDDRLNHLLNTAPKQsiil 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  865 VRDIfiraqaakPCILFFDEFESIAPRRGHDNTGVTdrvVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPALLRPGRLDK 944
Cdd:cd19510    81 LEDI--------DAAFESREHNKKNPSAYGGLSRVT---FSGLLNALDGVASSEERIVFMTTNHIERLDPALIRPGRVDM 149


                  ...
gi 544186102  945 CVY 947
Cdd:cd19510   150 KIY 152
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 820-936 1.00e-10

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: 62.46  E-value: 1.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  820 ILLYGPPGTGKTLLAGVIARE--SRMNF-------ISVKGPELLSKYIGASEQAVRDIF--IRAQAAKPCILFF---DEF 885
Cdd:cd19508    55 VLLHGPPGTGKTSLCKALAQKlsIRLSSryrygqlIEINSHSLFSKWFSESGKLVTKMFqkIQELIDDKDALVFvliDEV 134

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 544186102  886 ESIAPRRGHDNTGV--TD--RVVNQLLTQLDGVEGLQGVYVLAATSRPDLIDPAL 936
Cdd:cd19508   135 ESLAAARSASSSGTepSDaiRVVNAVLTQIDRIKRYHNNVILLTSNLLEKIDVAF 189
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 397-762 7.59e-10

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


Pssm-ID: 440232 [Multi-domain]  Cd Length: 397  Bit Score: 62.62  E-value: 7.59e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  397 AIKYTKNVEVLHLGKVWIPDDLRKRLNIEMHAVVRITPVEVTPKIPRSLKLQPRENLPKDISEEDIKTVFYSWLQQSTTT 476
Cdd:COG0464     1 LAELLALAVALALALLLLDDAALRLLLLLLLALAAALLLLLLLLLLLLLALLLVELLLLLLSGALAALLLLALLLLALLA 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  477 MLPLVISEEEFIKLETKDGLKEFSLSIVHSWEKEKDKNIFLLSPNLLQKTTIQVLLDPMVKEENSEEIDFILPFLkLSSL 556
Cdd:COG0464    81 LLAALLSALELLLLGELLLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAI-LDDL 159

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  557 GGVNSLgVSSLEHITHSLLGRPLSRQLMSLVAGLRngaLLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKAL---- 632
Cdd:COG0464   160 GGLEEV-KEELRELVALPLKRPELREEYGLPPPRG---LLLYGPPGTGKTLLARALAGE----LGLPLIEVDLSDLvsky 231

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  633 -----RALNDMIKE---------FI-----------SMGSLVALIATSQSQQSL----HPLLVSAQGVHI---------- 673
Cdd:COG0464   232 vgeteKNLREVFDKarglapcvlFIdeadalagkrgEVGDGVGRRVVNTLLTEMeelrSDVVVIAATNRPdlldpallrr 311

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  674 FQCVQHIQPPNQEQRCEILCNVIKNKLDCDinkftDLDLQHVAKETGGFVARDFTVLVDRAIHS--RLSRQSISTReklv 751
Cdd:COG0464   312 FDEIIFFPLPDAEERLEIFRIHLRKRPLDE-----DVDLEELAEATEGLSGADIRNVVRRAALQalRLGREPVTTE---- 382

                         410
                  ....*....|.
gi 544186102  752 lttlDFQKALR 762
Cdd:COG0464   383 ----DLLEALE 389
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 820-884 1.21e-07

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 55.83  E-value: 1.21e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544186102  820 ILLYGPPGTGKTLLAGVIARESRMNFISvkgpelLSkyigaseqAV-------RDIFIRAQAA----KPCILFFDE 884
Cdd:COG2256    52 MILWGPPGTGKTTLARLIANATDAEFVA------LS--------AVtsgvkdiREVIEEARERraygRRTILFVDE 113
AAA_lid_3 pfam17862
AAA+ lid domain; This entry represents the alpha helical AAA+ lid domain that is found to the ...
 972-1003 3.75e-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: 3.75e-07
                           10        20        30
                   ....*....|....*....|....*....|..
gi 544186102   972 DVDLQHVASVTDSFTGADLKALLYNAQLEALH 1003
Cdd:pfam17862    1 DVDLEELAERTEGFSGADLEALCREAALAALR 32
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 820-884 5.96e-07

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 53.16  E-value: 5.96e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 544186102  820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPEllskyigASEQAVRDIFIRAQAA----KPCILFFDE 884
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 ...
 812-912 2.69e-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: 51.77  E-value: 2.69e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   812 LPIRQRTG-ILLYGPPGTGKTLLA----------GVIAREsrmNFISVKGPELLSKYIGASEQAVRDIFIRAQAAkpcIL 880
Cdd:TIGR03922  306 LPVAQTSNhMLFAGPPGTGKTTIArvvakiycglGVLRKP---LVREVSRADLIGQYIGESEAKTNEIIDSALGG---VL 379

                           90       100       110
                   ....*....|....*....|....*....|..
gi 544186102   881 FFDEFESIAPRRGHDNTGVTDRVVNQLLTQLD 912
Cdd:TIGR03922  380 FLDEAYTLVETGYGQKDPFGLEAIDTLLARME 411
ruvB PRK00080
Holliday junction branch migration DNA helicase RuvB;
820-853 4.54e-06

Holliday junction branch migration DNA helicase RuvB;


Pssm-ID: 234619 [Multi-domain]  Cd Length: 328  Bit Score: 50.13  E-value: 4.54e-06
                          10        20        30
                  ....*....|....*....|....*....|....
gi 544186102  820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPEL 853
Cdd:PRK00080   54 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAL 87
RuvB_N pfam05496
Holliday junction DNA helicase RuvB P-loop domain; The RuvB protein makes up part of the ...
 820-853 5.13e-06

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: 47.88  E-value: 5.13e-06
                           10        20        30
                   ....*....|....*....|....*....|....
gi 544186102   820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPEL 853
Cdd:pfam05496   36 VLLYGPPGLGKTTLANIIANEMGVNIRITSGPAI 69
TIP49 COG1224
DNA helicase TIP49, TBP-interacting protein [Transcription];
819-866 1.54e-05

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


Pssm-ID: 440837 [Multi-domain]  Cd Length: 452  Bit Score: 48.81  E-value: 1.54e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 544186102  819 GILLYGPPGTGKTLLAGVIARE--SRMNFISVKGPELLSKYIGASE---QAVR 866
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 ...
 820-946 2.23e-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: 45.60  E-value: 2.23e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSkyIGASE-QAVRDIFIRAQAA-KPCILFFDEFESIAPRRGHDNT 897
Cdd:cd19512    25 ILFYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAP--MGREGvTAIHKVFDWANTSrRGLLLFVDEADAFLRKRSTEKI 102

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 544186102  898 GVTDR-VVNQLLTQLdGVEGLQGVYVLaATSRPDLIDPALlrPGRLDKCV 946
Cdd:cd19512   103 SEDLRaALNAFLYRT-GEQSNKFMLVL-ASNQPEQFDWAI--NDRIDEMV 148
RuvB COG2255
Holliday junction resolvasome RuvABC, ATP-dependent DNA helicase subunit RuvB [Replication, ...
 820-851 3.30e-05

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


Pssm-ID: 441856 [Multi-domain]  Cd Length: 337  Bit Score: 47.38  E-value: 3.30e-05
                          10        20        30
                  ....*....|....*....|....*....|..
gi 544186102  820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGP 851
Cdd:COG2255    57 VLLYGPPGLGKTTLAHIIANEMGVNIRITSGP 88
RecA-like_Ycf2 cd19505
ATPase domain of plant YCF2; Ycf2 is a chloroplast ATPase which has an essential function; ...
 819-946 4.18e-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: 45.06  E-value: 4.18e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  819 GILLYGPPGTGKTLLAGVIARESRMNFISVKGPELLSK-----------YIGASEQAVRDI---FIRAQAAKPCILFF-D 883
Cdd:cd19505    14 GILLIGSIETGRSYLIKSLAANSYVPLIRISLNKLLYNkpdfgnddwidGMLILKESLHRLnlqFELAKAMSPCIIWIpN 93

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 544186102  884 EFESIAPRRGHDNTGVTDRVVNQLLTQL-DGVEG--LQGVYVLAATSRPDLIDPALLRPGRLDKCV 946
Cdd:cd19505    94 IHELNVNRSTQNLEEDPKLLLGLLLNYLsRDFEKssTRNILVIASTHIPQKVDPALIAPNRLDTCI 159
DnaC COG1484
DNA replication protein DnaC [Replication, recombination and repair];
814-849 6.60e-05

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


Pssm-ID: 441093 [Multi-domain]  Cd Length: 242  Bit Score: 45.93  E-value: 6.60e-05
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 544186102  814 IRQRTGILLYGPPGTGKTLLAGVIARESRMNFISVK 849
Cdd:COG1484    96 IERGENLILLGPPGTGKTHLAIALGHEACRAGYRVR 131
PRK13341 PRK13341
AAA family ATPase;
821-884 9.27e-05

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 46.59  E-value: 9.27e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 544186102  821 LLYGPPGTGKTLLAGVIARESRMNFIS-------VKgpELLSKYIGASEQavrdifiRAQAAKPCILFFDE 884
Cdd:PRK13341   56 ILYGPPGVGKTTLARIIANHTRAHFSSlnavlagVK--DLRAEVDRAKER-------LERHGKRTILFIDE 117
TIP49 pfam06068
TIP49 P-loop domain; This family consists of the C-terminal region of several eukaryotic and ...
 819-866 1.66e-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: 45.38  E-value: 1.66e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|...
gi 544186102   819 GILLYGPPGTGKTLLAGVIARE--SRMNFISVKGPELLSKYIGASE---QAVR 866
Cdd:pfam06068   52 AVLIAGPPGTGKTALAIAISKElgEDTPFTSISGSEVYSLEMKKTEaltQAFR 104
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 581-642 1.79e-04

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: 43.29  E-value: 1.79e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 544186102  581 RQLMSLVAGLRNGALLLTGGKGSGKSTLAKAICKEAFDKlDAHVERVDCKALRALNDMIKEF 642
Cdd:cd00009     8 EALREALELPPPKNLLLYGPPGTGKTTLARAIANELFRP-GAPFLYLNASDLLEGLVVAELF 68
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 595-633 2.68e-04

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: 42.20  E-value: 2.68e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 544186102   595 LLLTGGKGSGKSTLAKAICKEafdkLDAHVERVDCKALR 633
Cdd:pfam00004    1 LLLYGPPGTGKTTLAKAVAKE----LGAPFIEISGSELV 35
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 709-885 5.81e-04

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


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 43.99  E-value: 5.81e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  709 DLDLQHVAKETGGFVARDFTVLVDRAIHSRLSRQSISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWD---KI 785
Cdd:COG1401   110 DSEIEAVGLLLELAERSDALEALERARLLLELADLEERAALETEVLEALEAELEELLAAPEDLSADALAAELSAAeelYS 189

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  786 GGLHEVRQILMDTIQlpAKYPELFANLPIRQRTG--ILLYGPPGTGKTLLAGVIAR------ESRMNFISV----KGPEL 853
Cdd:COG1401   190 EDLESEDDYLKDLLR--EKFEETLEAFLAALKTKknVILAGPPGTGKTYLARRLAEalggedNGRIEFVQFhpswSYEDF 267

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|..
gi 544186102  854 LSKY---IGASEQAVRD-IFIRA--QAA----KPCILFFDEF 885
Cdd:COG1401   268 LLGYrpsLDEGKYEPTPgIFLRFclKAEknpdKPYVLIIDEI 309
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 820-890 5.85e-04

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


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 43.44  E-value: 5.85e-04
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 544186102   820 ILLYGPPGTGKTLLAGVIARESRMNFISVKGPELlskyigaseQAVRDIF-IRAQAAKPCILFFDEFESIAP 890
Cdd:TIGR00635   33 LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPAL---------EKPGDLAaILTNLEEGDVLFIDEIHRLSP 95
PRK08116 PRK08116
hypothetical protein; Validated
 815-872 6.44e-04

hypothetical protein; Validated


Pssm-ID: 236153 [Multi-domain]  Cd Length: 268  Bit Score: 43.09  E-value: 6.44e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 544186102  815 RQRTGILLYGPPGTGKTLLAGVIARESRMNFISVKG---PELLSK---YIGASEQAVRDIFIRA 872
Cdd:PRK08116  112 KENVGLLLWGSVGTGKTYLAACIANELIEKGVPVIFvnfPQLLNRiksTYKSSGKEDENEIIRS 175
PRK04195 PRK04195
replication factor C large subunit; Provisional
 820-845 1.88e-03

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 42.22  E-value: 1.88e-03
                          10        20
                  ....*....|....*....|....*.
gi 544186102  820 ILLYGPPGTGKTLLAGVIAREsrMNF 845
Cdd:PRK04195   42 LLLYGPPGVGKTSLAHALAND--YGW 65
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 820-890 3.15e-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: 39.87  E-value: 3.15e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   820 ILLYGPPGTGKTLLAGVIARESRM---NFISVKGPELL-----SKYIGASEQAVRD----IFIRAQAAKP-CILFFDEFE 886
Cdd:pfam07724    6 FLFLGPTGVGKTELAKALAELLFGderALIRIDMSEYMeehsvSRLIGAPPGYVGYeeggQLTEAVRRKPySIVLIDEIE 85


                   ....
gi 544186102   887 SIAP 890
Cdd:pfam07724   86 KAHP 89
NACHT COG5635
Predicted NTPase, NACHT family domain [Signal transduction mechanisms];
724-938 3.56e-03

Predicted NTPase, NACHT family domain [Signal transduction mechanisms];


Pssm-ID: 444362 [Multi-domain]  Cd Length: 935  Bit Score: 41.71  E-value: 3.56e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  724 ARDFTVLVDRAIHSRLSRQSISTREKLVLTTLDFQKALRGFLPASLRSVNLHKPRDLGWDKIGGLHEVRQILMDTIQLPA 803
Cdd:COG5635    73 LARALSALLLVLLLLESLLLLLLLLLLLAEALLALLELAALLKAVLLSLSGGSDLVLLLSESDLLLALLILLLDADGLLV 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  804 KYPELFANLPIRQRTG--------------ILLYGPPGTGKTLLAGVIARESRMNFISVKGP-----------------E 852
Cdd:COG5635   153 SLDDLYVPLNLLERIEslkrlelleakkkrLLILGEPGSGKTTLLRYLALELAERYLDAEDPipilielrdlaeeasleD 232

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102  853 LLSKYIGASEQAVRDIFIRAQAAKPCILFFDEFESIAPRRGHdntgvtDRVVNQLLTQLDGVEGLQGVyvlaATSRPDLI 932
Cdd:COG5635   233 LLAEALEKRGGEPEDALERLLRNGRLLLLLDGLDEVPDEADR------DEVLNQLRRFLERYPKARVI----ITSRPEGY 302


                  ....*.
gi 544186102  933 DPALLR 938
Cdd:COG5635   303 DSSELE 308
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 591-647 4.88e-03

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: 38.89  E-value: 4.88e-03
                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*..
gi 544186102    591 RNGALLLTGGKGSGKSTLAKAICKEaFDKLDAHVERVDCKALRALNDMIKEFISMGS 647
Cdd:smart00382    1 PGEVILIVGPPGSGKTTLARALARE-LGPPGGGVIYIDGEDILEEVLDQLLLIIVGG 56
AAA_16 pfam13191
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 807-923 8.65e-03

AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily.


Pssm-ID: 433025 [Multi-domain]  Cd Length: 167  Bit Score: 38.64  E-value: 8.65e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 544186102   807 ELFANLPIRQRTGILLYGPPGTGKTLLAGVIAR---ESRMNFISVKGPELLSkYIGASEQAVRDIFIRA----QAAKPCI 879
Cdd:pfam13191   14 DALDRVRSGRPPSVLLTGEAGTGKTTLLRELLRaleRDGGYFLRGKCDENLP-YSPLLEALTREGLLRQlldeLESSLLE 92

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....
gi 544186102   880 LFFDEFESIAPRRGHDNTGVTDRVVNQLLTQLDGVEGLQGVYVL 923
Cdd:pfam13191   93 AWRAALLEALAPVPELPGDLAERLLDLLLRLLDLLARGERPLVL 136
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH