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Conserved domains on  [gi|256580486|gb|ACU91621|]
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ATP-dependent protease La [Capnocytophaga ochracea DSM 7271]

Protein Classification

endopeptidase La( domain architecture ID 11422032)

endopeptidase La is an ATP-dependent serine protease that degrades polypeptides processively to yield small peptide fragments that are 5 to 10 amino acids long; it binds to DNA in a double-stranded, site-specific manner

CATH:  1.10.8.60
EC:  3.4.21.53
Gene Ontology:  GO:0005524|GO:0016887|GO:0004176|GO:0004252|GO:0043565
MEROPS:  S16
PubMed:  34563541|9115177

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 46-820 0e+00

ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones];


:

Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 1269.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  46 PHVLPILPLKNTVLFPGVVVPISAGRDASIHLINEAYATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPDGN 125
Cdd:COG0466   11 PETLPLLPLRDVVVFPGMVIPLFVGREKSIKALEEAMEGDKLIGLVAQKDAEVEDPGPDDLYEVGTVAKILQLLKLPDGT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 126 VTIIIQGKKRFEIESIVEEKPYIKAMIKEMPDVKPDanDKEFEATIEAVKDLSIKIVQENPNIPSEAAFAIRNIESTSFL 205
Cdd:COG0466   91 VKVLVEGLQRARIKEFVQEEPYLEAEVEPLEEEEED--DKELEALMRSLKEQFEEYVKLNPKIPPELLAALSNIEDPGRL 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 206 INFISSNMNATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELGGVS 285
Cdd:COG0466  169 ADFIASHLPLKIEEKQELLETLDVKERLEKLLELLEKEIEVLELEKKIRSRVKEQMEKSQREYYLREQLKAIQKELGEKD 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 286 -YEQEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDKEHY 364
Cdd:COG0466  249 dGEDEIEELREKIEKAKLPEEVKEKAEKELKKLERMPPMSAEATVIRNYLDWLLDLPWGKRTKDNLDLKKAEKILDEDHY 328

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 365 GLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAMPGR 444
Cdd:COG0466  329 GLEKVKERILEYLAVRKLKKKLKGPILCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGR 408

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 445 ILQQLKKAKTSNPVFVLDEIDKLGNnSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPALLD 524
Cdd:COG0466  409 IIQGLKKAGTKNPVFLLDEIDKMGS-DFRGDPASALLEVLDPEQNNTFSDHYLEVPFDLSKVMFIATANSLDTIPAPLLD 487

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 525 RMELINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLAMEE 604
Cdd:COG0466  488 RMEIIELSGYTEEEKLEIAKRYLIPKQLKEHGLKKEELKISDEALRKIIRGYTREAGVRNLEREIAKICRKVAKKIAEGK 567

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 605 AYDPKLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEY 684
Cdd:COG0466  568 KKKVTITPKNLEKYLGVPRFRYEKAEEEDQVGVVTGLAWTEVGGDILFIEATLMPGKGKLTLTGQLGDVMKESAQAALSY 647

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 685 LKANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKIL 764
Cdd:COG0466  648 VRSRAEELGIDPDFFEKYDIHIHVPEGATPKDGPSAGITMATALVSALTGRPVRSDVAMTGEITLRGRVLPIGGLKEKLL 727

                        730       740       750       760       770
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 256580486 765 AGKRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAITNQDVKHKK 820
Cdd:COG0466  728 AAHRAGIKTVILPKENEKDLEEIPEEVKKGLEFHPVEHIDEVLKIALEKEPEPLPK 783
 
Name Accession Description Interval E-value
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 46-820 0e+00

ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 1269.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  46 PHVLPILPLKNTVLFPGVVVPISAGRDASIHLINEAYATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPDGN 125
Cdd:COG0466   11 PETLPLLPLRDVVVFPGMVIPLFVGREKSIKALEEAMEGDKLIGLVAQKDAEVEDPGPDDLYEVGTVAKILQLLKLPDGT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 126 VTIIIQGKKRFEIESIVEEKPYIKAMIKEMPDVKPDanDKEFEATIEAVKDLSIKIVQENPNIPSEAAFAIRNIESTSFL 205
Cdd:COG0466   91 VKVLVEGLQRARIKEFVQEEPYLEAEVEPLEEEEED--DKELEALMRSLKEQFEEYVKLNPKIPPELLAALSNIEDPGRL 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 206 INFISSNMNATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELGGVS 285
Cdd:COG0466  169 ADFIASHLPLKIEEKQELLETLDVKERLEKLLELLEKEIEVLELEKKIRSRVKEQMEKSQREYYLREQLKAIQKELGEKD 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 286 -YEQEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDKEHY 364
Cdd:COG0466  249 dGEDEIEELREKIEKAKLPEEVKEKAEKELKKLERMPPMSAEATVIRNYLDWLLDLPWGKRTKDNLDLKKAEKILDEDHY 328

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 365 GLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAMPGR 444
Cdd:COG0466  329 GLEKVKERILEYLAVRKLKKKLKGPILCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGR 408

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 445 ILQQLKKAKTSNPVFVLDEIDKLGNnSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPALLD 524
Cdd:COG0466  409 IIQGLKKAGTKNPVFLLDEIDKMGS-DFRGDPASALLEVLDPEQNNTFSDHYLEVPFDLSKVMFIATANSLDTIPAPLLD 487

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 525 RMELINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLAMEE 604
Cdd:COG0466  488 RMEIIELSGYTEEEKLEIAKRYLIPKQLKEHGLKKEELKISDEALRKIIRGYTREAGVRNLEREIAKICRKVAKKIAEGK 567

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 605 AYDPKLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEY 684
Cdd:COG0466  568 KKKVTITPKNLEKYLGVPRFRYEKAEEEDQVGVVTGLAWTEVGGDILFIEATLMPGKGKLTLTGQLGDVMKESAQAALSY 647

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 685 LKANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKIL 764
Cdd:COG0466  648 VRSRAEELGIDPDFFEKYDIHIHVPEGATPKDGPSAGITMATALVSALTGRPVRSDVAMTGEITLRGRVLPIGGLKEKLL 727

                        730       740       750       760       770
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 256580486 765 AGKRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAITNQDVKHKK 820
Cdd:COG0466  728 AAHRAGIKTVILPKENEKDLEEIPEEVKKGLEFHPVEHIDEVLKIALEKEPEPLPK 783
lon TIGR00763
endopeptidase La; This protein, the ATP-dependent serine endopeptidase La, is induced by heat ...
 50-810 0e+00

endopeptidase La; This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273258 [Multi-domain]  Cd Length: 775  Bit Score: 889.34  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486   50 PILPLKNTVLFPGVVVPISAGRDASIHLINEA-YATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPD---GN 125
Cdd:TIGR00763   1 PLLPLRRRPLFPGMIKPIDVGREKSIKLIKEAlRLKQPYLGLFLQKDDDNEEPEEDDIYSVGVVAQILEMLPLPSsgtAT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  126 VTIIIQGKKRFEIESIVEEKPYIKAMIKEMPDVKPDANDKEFEATIEAVKDLSIKIVQENPN--IPSEAAFAIRNIESTS 203
Cdd:TIGR00763  81 YKVVVEGLRRIRIKELSDKGGYLVVRVDNLKEEPFDKDDEEIKALTREIKETFRELISLSKLfrEQPALLSALEDIDEPG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  204 FLINFISSNMN-ATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELG 282
Cdd:TIGR00763 161 RLADFVAASLQlKEKDELQEVLETVNIEKRLKKALELLKKELELLKLQNKITKKVEEKMEKTQREYYLREQLKAIKKELG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  283 -GVSYEQEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDK 361
Cdd:TIGR00763 241 iEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSSSEFTVTRNYLDWLTDLPWGKYSKENLDLKRAKEILDE 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  362 EHYGLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAM 441
Cdd:TIGR00763 321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAM 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  442 PGRILQQLKKAKTSNPVFVLDEIDKLGnNSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPA 521
Cdd:TIGR00763 401 PGRIIQGLKKAKTKNPLFLLDEIDKIG-SSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRP 479

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  522 LLDRMELINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLA 601
Cdd:TIGR00763 480 LLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGVRNLERQIEKICRKAAVKLV 559

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  602 ------MEEAYDPKLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMK 675
Cdd:TIGR00763 560 eqgekkKSEAESVVITPDNLKKYLGKPVFTYERAYEVTPPGVVMGLAWTPMGGDTLFIETTKVAGKGSLELTGQLGDVMK 639

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  676 ESATIALEYLKANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLP 755
Cdd:TIGR00763 640 ESAQIALTYVRSIAADLGISPNFFEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLP 719

                         730       740       750       760       770
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 256580486  756 VGGLKEKILAGKRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLA 810
Cdd:TIGR00763 720 IGGLKEKTIAAKRAGIKTIILPEKNRRDLEELPENVKEGLEIHFVKHYDEVLKKA 774
PRK10787 PRK10787
DNA-binding ATP-dependent protease La; Provisional
 49-813 0e+00

DNA-binding ATP-dependent protease La; Provisional


Pssm-ID: 182730 [Multi-domain]  Cd Length: 784  Bit Score: 680.12  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  49 LPILPLKNTVLFPGVVVPISAGRDASIHLINEAYATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPDGNVTI 128
Cdd:PRK10787  11 IPVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHDKKIMLVAQKEASTDEPGVNDLFTVGTVASILQMLKLPDGTVKV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 129 IIQGKKRFEIESIVEEKPYIKAMIKEMPdvKPDANDKEFEATIEAVKDLSIKIVQENPNIPSEAAFAIRNIESTSFLINF 208
Cdd:PRK10787  91 LVEGLQRARISALSDNGEHFSAKAEYLE--SPTIDEREQEVLVRTAISQFEGYIKLNKKIPPEVLTSLNSIDDPARLADT 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 209 ISSNMNATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELGGVS-YE 287
Cdd:PRK10787 169 IAAHMPLKLADKQSVLEMSDVNERLEYLMAMMESEIDLLQVEKRIRNRVKKQMEKSQREYYLNEQMKAIQKELGEMDdAP 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 288 QEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDKEHYGLE 367
Cdd:PRK10787 249 DENEALKRKIDAAKMPKEAKEKAEAELQKLKMMSPMSAEATVVRGYIDWMVQVPWNARSKVKKDLRQAQEILDTDHYGLE 328

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 368 EVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAMPGRILQ 447
Cdd:PRK10787 329 RVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQ 408

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 448 QLKKAKTSNPVFVLDEIDKLGNNsYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPaLLDRME 527
Cdd:PRK10787 409 KMAKVGVKNPLFLLDEIDKMSSD-MRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAP-LLDRME 486

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 528 LINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLAMEEAYD 607
Cdd:PRK10787 487 VIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKAVKQLLLDKSLK 566

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 608 P-KLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEYLK 686
Cdd:PRK10787 567 HiEINGDNLHDYLGVQRFDYGRADNENRVGQVTGLAWTEVGGDLLTIETACVPGKGKLTYTGSLGEVMQESIQAALTVVR 646

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 687 ANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKILAG 766
Cdd:PRK10787 647 ARAEKLGINPDFYEKRDIHVHVPEGATPKDGPSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLAA 726

                        730       740       750       760
                 ....*....|....*....|....*....|....*....|....*..
gi 256580486 767 KRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAITN 813
Cdd:PRK10787 727 HRGGIKTVLIPFENKRDLEEIPDNVIADLDIHPVKRIEEVLTLALQN 773
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 352-534 2.10e-119

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


Pssm-ID: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 358.02  E-value: 2.10e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 352 LKRAQKILDKEHYGLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIR 431
Cdd:cd19500    1 IKKARKVLDADHYGLEDVKERILEYLAVRKLKGSMKGPILCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 432 GHRKTYIGAMPGRILQQLKKAKTSNPVFVLDEIDKLGnNSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIAT 511
Cdd:cd19500   81 GHRRTYVGAMPGRIIQALKKAGTNNPVFLLDEIDKIG-SSFRGDPASALLEVLDPEQNSTFSDHYLDVPFDLSKVLFIAT 159

                        170       180
                 ....*....|....*....|...
gi 256580486 512 ANDLSTIQPALLDRMELINVTGY 534
Cdd:cd19500  160 ANSLDTIPGPLLDRMEIIELSGY 182
Lon_C pfam05362
Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP ...
 609-812 1.10e-92

Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.


Pssm-ID: 428442 [Multi-domain]  Cd Length: 205  Bit Score: 289.52  E-value: 1.10e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  609 KLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEYLKAN 688
Cdd:pfam05362   1 KVTAKNLEKYLGVPRFRYGEAEKEDQVGVVTGLAWTEVGGDLLTIEAVIMPGKGKLTLTGQLGDVMKESAQAALSYVRSR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  689 AERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKILAGKR 768
Cdd:pfam05362  81 AEELGIDPDFFEKKDIHIHVPEGATPKDGPSAGVTMATALVSALTGIPVRKDVAMTGEITLRGRVLPIGGLKEKLLAAHR 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 256580486  769 AGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAIT 812
Cdd:pfam05362 161 AGIKTVIIPKENEKDLEDIPENVREGLEIIPVEHVDEVLKHALV 204
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 387-526 7.20e-07

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 49.68  E-value: 7.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486   387 KSPILCFYGPPGVGKTSLGRSIAKALSRE-----YVRMSLGGLHDEAEIRGHRKTYIGAMPGRILQQ---LKKAKTSNP- 457
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPgggviYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLrlaLALARKLKPd 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 256580486   458 VFVLDEIDKLgnnsyqGDPSSAMLEVLDPEqnkefyDNFLEMGYDLSKVMFIATANDLSTIQPALLDRM 526
Cdd:smart00382  81 VLILDEITSL------LDAEQEALLLLLEE------LRLLLLLKSEKNLTVILTTNDEKDLGPALLRRR 137
 
Name Accession Description Interval E-value
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 46-820 0e+00

ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 1269.56  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  46 PHVLPILPLKNTVLFPGVVVPISAGRDASIHLINEAYATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPDGN 125
Cdd:COG0466   11 PETLPLLPLRDVVVFPGMVIPLFVGREKSIKALEEAMEGDKLIGLVAQKDAEVEDPGPDDLYEVGTVAKILQLLKLPDGT 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 126 VTIIIQGKKRFEIESIVEEKPYIKAMIKEMPDVKPDanDKEFEATIEAVKDLSIKIVQENPNIPSEAAFAIRNIESTSFL 205
Cdd:COG0466   91 VKVLVEGLQRARIKEFVQEEPYLEAEVEPLEEEEED--DKELEALMRSLKEQFEEYVKLNPKIPPELLAALSNIEDPGRL 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 206 INFISSNMNATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELGGVS 285
Cdd:COG0466  169 ADFIASHLPLKIEEKQELLETLDVKERLEKLLELLEKEIEVLELEKKIRSRVKEQMEKSQREYYLREQLKAIQKELGEKD 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 286 -YEQEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDKEHY 364
Cdd:COG0466  249 dGEDEIEELREKIEKAKLPEEVKEKAEKELKKLERMPPMSAEATVIRNYLDWLLDLPWGKRTKDNLDLKKAEKILDEDHY 328

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 365 GLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAMPGR 444
Cdd:COG0466  329 GLEKVKERILEYLAVRKLKKKLKGPILCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRGHRRTYIGAMPGR 408

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 445 ILQQLKKAKTSNPVFVLDEIDKLGNnSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPALLD 524
Cdd:COG0466  409 IIQGLKKAGTKNPVFLLDEIDKMGS-DFRGDPASALLEVLDPEQNNTFSDHYLEVPFDLSKVMFIATANSLDTIPAPLLD 487

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 525 RMELINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLAMEE 604
Cdd:COG0466  488 RMEIIELSGYTEEEKLEIAKRYLIPKQLKEHGLKKEELKISDEALRKIIRGYTREAGVRNLEREIAKICRKVAKKIAEGK 567

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 605 AYDPKLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEY 684
Cdd:COG0466  568 KKKVTITPKNLEKYLGVPRFRYEKAEEEDQVGVVTGLAWTEVGGDILFIEATLMPGKGKLTLTGQLGDVMKESAQAALSY 647

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 685 LKANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKIL 764
Cdd:COG0466  648 VRSRAEELGIDPDFFEKYDIHIHVPEGATPKDGPSAGITMATALVSALTGRPVRSDVAMTGEITLRGRVLPIGGLKEKLL 727

                        730       740       750       760       770
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 256580486 765 AGKRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAITNQDVKHKK 820
Cdd:COG0466  728 AAHRAGIKTVILPKENEKDLEEIPEEVKKGLEFHPVEHIDEVLKIALEKEPEPLPK 783
lon TIGR00763
endopeptidase La; This protein, the ATP-dependent serine endopeptidase La, is induced by heat ...
 50-810 0e+00

endopeptidase La; This protein, the ATP-dependent serine endopeptidase La, is induced by heat shock and other stresses in E. coli, B. subtilis, and other species. The yeast member, designated PIM1, is located in the mitochondrial matrix, required for mitochondrial function, and also induced by heat shock. [Protein fate, Degradation of proteins, peptides, and glycopeptides]


Pssm-ID: 273258 [Multi-domain]  Cd Length: 775  Bit Score: 889.34  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486   50 PILPLKNTVLFPGVVVPISAGRDASIHLINEA-YATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPD---GN 125
Cdd:TIGR00763   1 PLLPLRRRPLFPGMIKPIDVGREKSIKLIKEAlRLKQPYLGLFLQKDDDNEEPEEDDIYSVGVVAQILEMLPLPSsgtAT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  126 VTIIIQGKKRFEIESIVEEKPYIKAMIKEMPDVKPDANDKEFEATIEAVKDLSIKIVQENPN--IPSEAAFAIRNIESTS 203
Cdd:TIGR00763  81 YKVVVEGLRRIRIKELSDKGGYLVVRVDNLKEEPFDKDDEEIKALTREIKETFRELISLSKLfrEQPALLSALEDIDEPG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  204 FLINFISSNMN-ATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELG 282
Cdd:TIGR00763 161 RLADFVAASLQlKEKDELQEVLETVNIEKRLKKALELLKKELELLKLQNKITKKVEEKMEKTQREYYLREQLKAIKKELG 240

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  283 -GVSYEQEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDK 361
Cdd:TIGR00763 241 iEKDDKDELEKLKEKLEELKLPEEVKKVIEKELTKLSLLEPSSSEFTVTRNYLDWLTDLPWGKYSKENLDLKRAKEILDE 320

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  362 EHYGLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAM 441
Cdd:TIGR00763 321 DHYGLKKVKERILEYLAVQKLRGKMKGPILCLVGPPGVGKTSLGKSIAKALNRKFVRFSLGGVRDEAEIRGHRRTYVGAM 400

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  442 PGRILQQLKKAKTSNPVFVLDEIDKLGnNSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPA 521
Cdd:TIGR00763 401 PGRIIQGLKKAKTKNPLFLLDEIDKIG-SSFRGDPASALLEVLDPEQNNAFSDHYLDVPFDLSKVIFIATANSIDTIPRP 479

                         490       500       510       520       530       540       550       560
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  522 LLDRMELINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLA 601
Cdd:TIGR00763 480 LLDRMEVIELSGYTEEEKLEIAKKYLIPKALEDHGLKPDELKITDEALLLLIKYYTREAGVRNLERQIEKICRKAAVKLV 559

                         570       580       590       600       610       620       630       640
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  602 ------MEEAYDPKLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMK 675
Cdd:TIGR00763 560 eqgekkKSEAESVVITPDNLKKYLGKPVFTYERAYEVTPPGVVMGLAWTPMGGDTLFIETTKVAGKGSLELTGQLGDVMK 639

                         650       660       670       680       690       700       710       720
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  676 ESATIALEYLKANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLP 755
Cdd:TIGR00763 640 ESAQIALTYVRSIAADLGISPNFFEKADIHLHVPEGATPKDGPSAGITMATALLSLATGKPVRPDVAMTGEITLRGKVLP 719

                         730       740       750       760       770
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 256580486  756 VGGLKEKILAGKRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLA 810
Cdd:TIGR00763 720 IGGLKEKTIAAKRAGIKTIILPEKNRRDLEELPENVKEGLEIHFVKHYDEVLKKA 774
PRK10787 PRK10787
DNA-binding ATP-dependent protease La; Provisional
 49-813 0e+00

DNA-binding ATP-dependent protease La; Provisional


Pssm-ID: 182730 [Multi-domain]  Cd Length: 784  Bit Score: 680.12  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  49 LPILPLKNTVLFPGVVVPISAGRDASIHLINEAYATTKTIGVVAQLDEKTEIPEGKDLFRFGTVARILRVLKMPDGNVTI 128
Cdd:PRK10787  11 IPVLPLRDVVVYPHMVIPLFVGREKSIRCLEAAMDHDKKIMLVAQKEASTDEPGVNDLFTVGTVASILQMLKLPDGTVKV 90

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 129 IIQGKKRFEIESIVEEKPYIKAMIKEMPdvKPDANDKEFEATIEAVKDLSIKIVQENPNIPSEAAFAIRNIESTSFLINF 208
Cdd:PRK10787  91 LVEGLQRARISALSDNGEHFSAKAEYLE--SPTIDEREQEVLVRTAISQFEGYIKLNKKIPPEVLTSLNSIDDPARLADT 168

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 209 ISSNMNATVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELGGVS-YE 287
Cdd:PRK10787 169 IAAHMPLKLADKQSVLEMSDVNERLEYLMAMMESEIDLLQVEKRIRNRVKKQMEKSQREYYLNEQMKAIQKELGEMDdAP 248

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 288 QEMEELKKKAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDKEHYGLE 367
Cdd:PRK10787 249 DENEALKRKIDAAKMPKEAKEKAEAELQKLKMMSPMSAEATVVRGYIDWMVQVPWNARSKVKKDLRQAQEILDTDHYGLE 328

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 368 EVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIRGHRKTYIGAMPGRILQ 447
Cdd:PRK10787 329 RVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRTYIGSMPGKLIQ 408

                        410       420       430       440       450       460       470       480
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 448 QLKKAKTSNPVFVLDEIDKLGNNsYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIATANDLSTIQPaLLDRME 527
Cdd:PRK10787 409 KMAKVGVKNPLFLLDEIDKMSSD-MRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMNIPAP-LLDRME 486

                        490       500       510       520       530       540       550       560
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 528 LINVTGYTIEEKTEIAKRHLLPKQLKEHGMKTTDLQLGKKEIERIVEGYTRESGVRALEKEIAKVVRYGAKNLAMEEAYD 607
Cdd:PRK10787 487 VIRLSGYTEDEKLNIAKRHLLPKQIERNALKKGELTVDDSAIIGIIRYYTREAGVRSLEREISKLCRKAVKQLLLDKSLK 566

                        570       580       590       600       610       620       630       640
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 608 P-KLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEYLK 686
Cdd:PRK10787 567 HiEINGDNLHDYLGVQRFDYGRADNENRVGQVTGLAWTEVGGDLLTIETACVPGKGKLTYTGSLGEVMQESIQAALTVVR 646

                        650       660       670       680       690       700       710       720
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 687 ANAERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKILAG 766
Cdd:PRK10787 647 ARAEKLGINPDFYEKRDIHVHVPEGATPKDGPSAGIAMCTALVSCLTGNPVRADVAMTGEITLRGQVLPIGGLKEKLLAA 726

                        730       740       750       760
                 ....*....|....*....|....*....|....*....|....*..
gi 256580486 767 KRAGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAITN 813
Cdd:PRK10787 727 HRGGIKTVLIPFENKRDLEEIPDNVIADLDIHPVKRIEEVLTLALQN 773
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 352-534 2.10e-119

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


Pssm-ID: 410908 [Multi-domain]  Cd Length: 182  Bit Score: 358.02  E-value: 2.10e-119
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 352 LKRAQKILDKEHYGLEEVKRRIIEYLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAEIR 431
Cdd:cd19500    1 IKKARKVLDADHYGLEDVKERILEYLAVRKLKGSMKGPILCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 432 GHRKTYIGAMPGRILQQLKKAKTSNPVFVLDEIDKLGnNSYQGDPSSAMLEVLDPEQNKEFYDNFLEMGYDLSKVMFIAT 511
Cdd:cd19500   81 GHRRTYVGAMPGRIIQALKKAGTNNPVFLLDEIDKIG-SSFRGDPASALLEVLDPEQNSTFSDHYLDVPFDLSKVLFIAT 159

                        170       180
                 ....*....|....*....|...
gi 256580486 512 ANDLSTIQPALLDRMELINVTGY 534
Cdd:cd19500  160 ANSLDTIPGPLLDRMEIIELSGY 182
Lon_C pfam05362
Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP ...
 609-812 1.10e-92

Lon protease (S16) C-terminal proteolytic domain; The Lon serine proteases must hydrolyse ATP to degrade protein substrates. In Escherichia coli, these proteases are involved in turnover of intracellular proteins, including abnormal proteins following heat-shock. The active site for protease activity resides in a C-terminal domain. The Lon proteases are classified as family S16 in Merops.


Pssm-ID: 428442 [Multi-domain]  Cd Length: 205  Bit Score: 289.52  E-value: 1.10e-92
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  609 KLTIETIEKILGPARLERDKYEDNEVAGVVTGLAWTSVGGDILFIESALSKGKGVLNITGNLGQVMKESATIALEYLKAN 688
Cdd:pfam05362   1 KVTAKNLEKYLGVPRFRYGEAEKEDQVGVVTGLAWTEVGGDLLTIEAVIMPGKGKLTLTGQLGDVMKESAQAALSYVRSR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  689 AERYNLNVKLFDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKILAGKR 768
Cdd:pfam05362  81 AEELGIDPDFFEKKDIHIHVPEGATPKDGPSAGVTMATALVSALTGIPVRKDVAMTGEITLRGRVLPIGGLKEKLLAAHR 160

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 256580486  769 AGIKEYILCKDNEKDILEIKQEYLKGLTFHYVTDMEEVIRLAIT 812
Cdd:pfam05362 161 AGIKTVIIPKENEKDLEDIPENVREGLEIIPVEHVDEVLKHALV 204
LON_substr_bdg pfam02190
ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be ...
 48-241 5.33e-44

ATP-dependent protease La (LON) substrate-binding domain; This domain has been shown to be part of the PUA superfamily. This domain represents a general protein and polypeptide interaction domain for the ATP-dependent serine peptidase, LON, Peptidase_S16, pfam05362. ATP-dependent Lon proteases are conserved in all living organizms and catalyze rapid turnover of short-lived regulatory proteins and many damaged or denatured proteins.


Pssm-ID: 426647 [Multi-domain]  Cd Length: 195  Bit Score: 157.50  E-value: 5.33e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486   48 VLPILPLKNTVLFPGVVVPISAGRDASIHLINEAYATTKTIGV--VAQLDEKTEIPEGKDLFRFGTVARILRVLKMPDGN 125
Cdd:pfam02190   1 ELPLLPLRNTVLFPGMVLPLFVGRPRSIAAIEAALNKDKLYGVllVSQKDAEDEEPTPDDLYEVGTVAKIVQILKLPDGT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  126 VTIIIQGKKRFEIESIVE-EKPYIKAMIkempDVKPDANDKEFEATIEAVKDLSIKIVQENPNI-PSEAAFAIRNIESTS 203
Cdd:pfam02190  81 YKVLVEGLERVRIVELVKkEEPYLRAEV----EDLPEDSDELSEALKALVKELIEKLRRLLKLLlPLELLLKIKDIENPG 156

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 256580486  204 FLINFISSNMNATVLEKQGVLEIDELKERATAILKYLN 241
Cdd:pfam02190 157 RLADLVAAILPLSPEEKQELLETLDVKERLEKVLELLN 194
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 391-529 1.18e-29

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: 114.23  E-value: 1.18e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  391 LCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDeaeirghrkTYIGAMPGRILQQLKKAKTSNP-VFVLDEIDKLGN 469
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVS---------KYVGESEKRLRELFEAAKKLAPcVIFIDEIDALAG 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 256580486  470 NSYQG------DPSSAMLEVLDPEQNKEfydnflemgydlSKVMFIATANDLSTIQPALLDRMELI 529
Cdd:pfam00004  72 SRGSGgdsesrRVVNQLLTELDGFTSSN------------SKVIVIAATNRPDKLDPALLGRFDRI 125
LON/PUA COG2802
Uncharacterized conserved protein, LON_N-like domain, ASCH/PUA-like superfamily [Function ...
 46-242 5.91e-25

Uncharacterized conserved protein, LON_N-like domain, ASCH/PUA-like superfamily [Function unknown];


Pssm-ID: 442054 [Multi-domain]  Cd Length: 194  Bit Score: 103.03  E-value: 5.91e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  46 PHVLPILPLkNTVLFPGVVVPIsagrdasiH--------LINEAYATTKTIGVVaQLDEKTEIPEGKDLFRFGTVARILR 117
Cdd:COG2802    4 PMELPLFPL-GAVLFPGGRLPL--------HifepryldMVRDCLAGDRPFGVV-LIREGREVGGPPPLYDVGTLARITD 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 118 VLKMPDGNVTIIIQGKKRFEIESIV-EEKPYIKAMIKEMPDVKPDANDKEFEATIEAVKDLsikiVQENPNIPSEAafAI 196
Cdd:COG2802   74 FEELEDGRLDITLRGVQRFRILEELqEDDPYRVAEVEWLPDEPDLPVPEELEALRERLLRL----LRRYPELAGLE--AD 147

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*.
gi 256580486 197 RNIESTSFLINFISSNMNATVLEKQGVLEIDELKERATAILKYLNI 242
Cdd:COG2802  148 PDLDDPEWLSNRLAELLPLDPEEKQALLEAPDLLERLELLLALLER 193
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 365-619 3.74e-20

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: 93.44  E-value: 3.74e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 365 GLEEVKRRIIEYLAVL----KLRNDMKSPI---LCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEaeirghrktY 437
Cdd:COG0464  161 GLEEVKEELRELVALPlkrpELREEYGLPPprgLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSK---------Y 231

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 438 IGAMPGRILQQLKKAKTSNPVFVL-DEIDKLGNNSYQGDPSSAMLEVldpeqnkefyDNFL-EMGYDLSKVMFIATANDL 515
Cdd:COG0464  232 VGETEKNLREVFDKARGLAPCVLFiDEADALAGKRGEVGDGVGRRVV----------NTLLtEMEELRSDVVVIAATNRP 301

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 516 STIQPALLDRM-ELINVTGYTIEEKTEIAKRHLLPKQLKEhgmkttDLQLgkKEIERIVEGYT-ResgvralekEIAKVV 593
Cdd:COG0464  302 DLLDPALLRRFdEIIFFPLPDAEERLEIFRIHLRKRPLDE------DVDL--EELAEATEGLSgA---------DIRNVV 364

                        250       260
                 ....*....|....*....|....*.
gi 256580486 594 RYgAKNLAMEEAyDPKLTIETIEKIL 619
Cdd:COG0464  365 RR-AALQALRLG-REPVTTEDLLEAL 388
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 366-531 1.08e-18

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: 83.87  E-value: 1.08e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 366 LEEVKRRIIEYLAVLKLR--NDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEAeirghrKTYIGAMPG 443
Cdd:cd19481    2 KASLREAVEAPRRGSRLRryGLGLPKGILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKY------VGESEKNLR 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 444 RILQQLKkaKTSNPVFVLDEIDKLG-------NNSYQGDPSSAMLEVLDPEQNkefydnflemgydLSKVMFIATANDLS 516
Cdd:cd19481   76 KIFERAR--RLAPCILFIDEIDAIGrkrdssgESGELRRVLNQLLTELDGVNS-------------RSKVLVIAATNRPD 140

                        170
                 ....*....|....*...
gi 256580486 517 TIQPALLDR---MELINV 531
Cdd:cd19481  141 LLDPALLRPgrfDEVIEF 158
COG1750 COG1750
Predicted archaeal serine protease, S18 family [General function prediction only];
699-810 1.26e-15

Predicted archaeal serine protease, S18 family [General function prediction only];


Pssm-ID: 441356 [Multi-domain]  Cd Length: 213  Bit Score: 76.56  E-value: 1.26e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 699 FDSYDVHIHVPEGATPKDGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKILAGKRAGIKEYILCK 778
Cdd:COG1750   91 LSSYDVYISIESDSPIVGGPSAGGAMTVATYAALLGLPLNKSVTMTGMINPDGSIGPVGGVYEKLEAAASAGAKYFLIPK 170

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 256580486 779 DNEKDILEIKQEYLK----------GLTFHYVTDMEEVIRLA 810
Cdd:COG1750  171 GQAILTGYNTQVGETvdlveygkelGVKVIEVSTIADALQYF 212
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 364-529 1.91e-14

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


Pssm-ID: 99707 [Multi-domain]  Cd Length: 151  Bit Score: 71.41  E-value: 1.91e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 364 YGLEEVKRRIIEYLAVLKLRNdmkspiLCFYGPPGVGKTSLGRSIAKALSR---EYVRMSLGGLHDEAEIRGHRKTYIga 440
Cdd:cd00009    1 VGQEEAIEALREALELPPPKN------LLLYGPPGTGKTTLARAIANELFRpgaPFLYLNASDLLEGLVVAELFGHFL-- 72

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 441 mpgRILQQLKKAKTSNPVFVLDEIDKLGNNSyqgdpSSAMLEVLdpeqnkefyDNFLEMGYDLSKVMFIATAND--LSTI 518
Cdd:cd00009   73 ---VRLLFELAEKAKPGVLFIDEIDSLSRGA-----QNALLRVL---------ETLNDLRIDRENVRVIGATNRplLGDL 135

                        170
                 ....*....|.
gi 256580486 519 QPALLDRMELI 529
Cdd:cd00009  136 DRALYDRLDIR 146
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
364-628 1.98e-12

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 67.99  E-value: 1.98e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 364 YGLEEVK---RRIIEYLAVLKLRNDMKSP----ILcFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEaeirghrkt 436
Cdd:COG1223    5 VGQEEAKkklKLIIKELRRRENLRKFGLWpprkIL-FYGPPGTGKTMLAEALAGELKLPLLTVRLDSLIGS--------- 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 437 YIGAMPGRILQQLKKAKTSNPVFVLDEIDKLGNnsyQGDPSSAMLEVldpeqnKEFYDNFL-EMGYDLSKVMFIATANDL 515
Cdd:COG1223   75 YLGETARNLRKLFDFARRAPCVIFFDEFDAIAK---DRGDQNDVGEV------KRVVNALLqELDGLPSGSVVIAATNHP 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 516 STIQPALLDRMEL-INVTGYTIEEKTEIAKRHLlpkqlkehgmKTTDLQLgKKEIERIVEGYTRESGvraleKEIAKVVR 594
Cdd:COG1223  146 ELLDSALWRRFDEvIEFPLPDKEERKEILELNL----------KKFPLPF-ELDLKKLAKKLEGLSG-----ADIEKVLK 209

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 256580486 595 YGAKN--LAMEEAYDPKLTIETIEKILGPARLERDK 628
Cdd:COG1223  210 TALKKaiLEDREKVTKEDLEEALKQRKERKKEPKKE 245
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 391-526 1.60e-10

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


Pssm-ID: 400191 [Multi-domain]  Cd Length: 135  Bit Score: 59.61  E-value: 1.60e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  391 LCFYGPPGVGKTSLGRSIAKALS-REYVRMSLGGLHDEAEIRGHRKtYIGAMPGRILQQLKKAKTSNPVFVLDEIDKlGN 469
Cdd:pfam07728   2 VLLVGPPGTGKTELAERLAAALSnRPVFYVQLTRDTTEEDLFGRRN-IDPGGASWVDGPLVRAAREGEIAVLDEINR-AN 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 256580486  470 NSYQGdpssAMLEVLDpeqNKEFY--DNFLEMGYDLSKVMFIATANDL----STIQPALLDRM 526
Cdd:pfam07728  80 PDVLN----SLLSLLD---ERRLLlpDGGELVKAAPDGFRLIATMNPLdrglNELSPALRSRF 135
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 365-592 1.18e-08

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 57.71  E-value: 1.18e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 365 GLEEVKRRIIEYLaVLKLRN-------DMKSP--ILcFYGPPGVGKTSLGRSIAKALSREYVRMSLgglhdeAEIRghRK 435
Cdd:COG1222   82 GLDEQIEEIREAV-ELPLKNpelfrkyGIEPPkgVL-LYGPPGTGKTLLAKAVAGELGAPFIRVRG------SELV--SK 151

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 436 tYIGAmPGRILQQL-KKAKTSNPVFV-LDEIDKLGnnSYQGDPSS---------AMLEVLDpeqnkefydnflemGYD-L 503
Cdd:COG1222  152 -YIGE-GARNVREVfELAREKAPSIIfIDEIDAIA--ARRTDDGTsgevqrtvnQLLAELD--------------GFEsR 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 504 SKVMFIATANDLSTIQPALL-----DRmeLINVTGYTIEEKTEIAKRHLLPKQLKEhgmkttDLQLgkKEIERIVEGYT- 577
Cdd:COG1222  214 GDVLIIAATNRPDLLDPALLrpgrfDR--VIEVPLPDEEAREEILKIHLRDMPLAD------DVDL--DKLAKLTEGFSg 283

                        250       260
                 ....*....|....*....|..
gi 256580486 578 -------RESGVRALEKEIAKV 592
Cdd:COG1222  284 adlkaivTEAGMFAIREGRDTV 305
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 351-529 1.68e-07

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


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 51.79  E-value: 1.68e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 351 DLKRAQKILDKEHYGLEEVKRRIIEylAVLKLRNDMKSP-----ILCFYGPPGVGKTSLGRSIAKALS---REYVRMSLG 422
Cdd:cd19499    1 KLLNLEERLHERVVGQDEAVKAVSD--AIRRARAGLSDPnrpigSFLFLGPTGVGKTELAKALAELLFgdeDNLIRIDMS 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 423 GLHDEAEIrghrKTYIGAMPGRI----LQQLKKAKTSNP--VFVLDEIDKlgnnsyqGDPS--SAMLEVLDpeqnkefyD 494
Cdd:cd19499   79 EYMEKHSV----SRLIGAPPGYVgyteGGQLTEAVRRKPysVVLLDEIEK-------AHPDvqNLLLQVLD--------D 139

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 256580486 495 NFLEMGY----DLSKVMFIATANDLStiqPALLDRMELI 529
Cdd:cd19499  140 GRLTDSHgrtvDFKNTIIIMTSNHFR---PEFLNRIDEI 175
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 387-526 7.20e-07

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 49.68  E-value: 7.20e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486   387 KSPILCFYGPPGVGKTSLGRSIAKALSRE-----YVRMSLGGLHDEAEIRGHRKTYIGAMPGRILQQ---LKKAKTSNP- 457
Cdd:smart00382   1 PGEVILIVGPPGSGKTTLARALARELGPPgggviYIDGEDILEEVLDQLLLIIVGGKKASGSGELRLrlaLALARKLKPd 80

                           90       100       110       120       130       140
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 256580486   458 VFVLDEIDKLgnnsyqGDPSSAMLEVLDPEqnkefyDNFLEMGYDLSKVMFIATANDLSTIQPALLDRM 526
Cdd:smart00382  81 VLILDEITSL------LDAEQEALLLLLEE------LRLLLLLKSEKNLTVILTTNDEKDLGPALLRRR 137
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 371-464 1.73e-06

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 51.24  E-value: 1.73e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 371 RRIIEylavlklrNDMKSPILcFYGPPGVGKTSLGRSIAKALSREYVRMS--LGGLhdeAEIRghrktyigampgRILQQ 448
Cdd:PRK13342  28 RRMIE--------AGRLSSMI-LWGPPGTGKTTLARIIAGATDAPFEALSavTSGV---KDLR------------EVIEE 83

                         90
                 ....*....|....*...
gi 256580486 449 LKKAKTS--NPVFVLDEI 464
Cdd:PRK13342  84 ARQRRSAgrRTILFIDEI 101
rfc PRK00440
replication factor C small subunit; Reviewed
 339-419 7.12e-06

replication factor C small subunit; Reviewed


Pssm-ID: 234763 [Multi-domain]  Cd Length: 319  Bit Score: 48.72  E-value: 7.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 339 ELPWNE-YSKDNFDlkraqkildkEHYGLEEVKRRIIEYLAvlklRNDMksPILCFYGPPGVGKTSLGRSIAKALSREYV 417
Cdd:PRK00440   4 EEIWVEkYRPRTLD----------EIVGQEEIVERLKSYVK----EKNM--PHLLFAGPPGTGKTTAALALARELYGEDW 67


                 ..
gi 256580486 418 RM 419
Cdd:PRK00440  68 RE 69
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 395-523 7.54e-06

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: 46.98  E-value: 7.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 395 GPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEaeirghrktYIGAMPGRILQQLKKAKTSNP-VFVLDEIDK-LGNNSY 472
Cdd:cd19507   38 GIQGTGKSLTAKAIAGVWQLPLLRLDMGRLFGG---------LVGESESRLRQMIQTAEAIAPcVLWIDEIEKgFSNADS 108

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 256580486 473 QGDPSSAmlevldpeqnKEFYDNFLE-MGYDLSKVMFIATANDLSTIQPALL 523
Cdd:cd19507  109 KGDSGTS----------SRVLGTFLTwLQEKKKPVFVVATANNVQSLPPELL 150
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 371-420 7.67e-06

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 49.28  E-value: 7.67e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 256580486 371 RRIIEylavlklrNDMKSPILcFYGPPGVGKTSLGRSIAKALSREYVRMS 420
Cdd:COG2256   41 RRAIE--------AGRLSSMI-LWGPPGTGKTTLARLIANATDAEFVALS 81
SdrC COG3480
Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];
675-772 1.45e-05

Predicted secreted protein YlbL, contains PDZ domain [Signal transduction mechanisms];


Pssm-ID: 442703 [Multi-domain]  Cd Length: 344  Bit Score: 47.88  E-value: 1.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 675 KESATIALEYLKANAERYNLNVKLFDSY----DVHIHVPE-GatpkdGPSAGiamltsLMslFT----QKRVK------K 739
Cdd:COG3480  198 EKTVTVTLVKLPDDDGRAGIGISLVTKVdfpfDVDIDLGDiG-----GPSAG------LM--FAlgiyDQLTPgdltggK 264

                         90       100       110
                 ....*....|....*....|....*....|...
gi 256580486 740 HLAMTGEITLRGKVLPVGGLKEKILAGKRAGIK 772
Cdd:COG3480  265 KIAGTGTIDADGTVGPIGGIDQKVVAARRAGAT 297
T7SS_EccA TIGR03922
type VII secretion AAA-ATPase EccA; This model represents the AAA family ATPase, EccA, of the ...
 341-545 3.00e-05

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: 47.53  E-value: 3.00e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  341 PWN---EYSKDNFD-----------LKRAQKILDkEHYGLEEVKRRIIEY---LAVLKLRNDMKSPI------LCFYGPP 397
Cdd:TIGR03922 243 PWDpssAPSRAEFVdpaaaerkaklLAEAEAELA-EQIGLERVKRQVAALkssTAMALARAERGLPVaqtsnhMLFAGPP 321

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  398 GVGKTSLGRSIAKALSreyvrmSLGGLHDEAEIRGHRKTYIGAMPGRilqqlKKAKTS-------NPVFVLDEIDKLGNN 470
Cdd:TIGR03922 322 GTGKTTIARVVAKIYC------GLGVLRKPLVREVSRADLIGQYIGE-----SEAKTNeiidsalGGVLFLDEAYTLVET 390

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  471 SY-QGDP--SSAMLEVLDPEQNKEFYDNFLEMGY--DLSKVMfiatandlsTIQPALLDRM-ELINVTGYTIEEKTEIAK 544
Cdd:TIGR03922 391 GYgQKDPfgLEAIDTLLARMENDRDRLVVIGAGYrkDLDKFL---------EVNEGLRSRFtRVIEFPSYSPDELVEIAR 461


                  .
gi 256580486  545 R 545
Cdd:TIGR03922 462 R 462
RecA-like_VCP_r2 cd19529
second of two ATPase domains of Valosin-containing protein-like ATPase (VAT) and similar ...
 394-523 5.15e-05

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: 44.41  E-value: 5.15e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 394 YGPPGVGKTSLGRSIAKALSREYVrmslgglhdeaEIRGHR--KTYIGAMPGRILQQLKKAKTSNP-VFVLDEIDKLGNN 470
Cdd:cd19529   33 YGPPGTGKTLLAKAVATESNANFI-----------SVKGPEllSKWVGESEKAIREIFRKARQVAPcVIFFDEIDSIAPR 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 256580486 471 SYQGDPSSAMLEVLDpeQNKEFYDNFLEMGydlsKVMFIATANDLSTIQPALL 523
Cdd:cd19529  102 RGTTGDSGVTERVVN--QLLTELDGLEEMN----GVVVIAATNRPDIIDPALL 148
RecA-like_CDC48_r2-like cd19511
second of two ATPase domains of CDC48/p97, PEX1 and -6, VAT and NVL, and similar ATPase ...
 393-523 5.52e-05

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


Pssm-ID: 410919 [Multi-domain]  Cd Length: 159  Bit Score: 44.20  E-value: 5.52e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 393 FYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEaeirghrktYIGAMPGRILQQLKKAKTSNP-VFVLDEIDKLGNNS 471
Cdd:cd19511   32 LYGPPGCGKTLLAKALASEAGLNFISVKGPELFSK---------YVGESERAVREIFQKARQAAPcIIFFDEIDSLAPRR 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 256580486 472 YQGDPSSAMLEVLDPEQNkefydnflEM-GYDLSK-VMFIATANDLSTIQPALL 523
Cdd:cd19511  103 GQSDSSGVTDRVVSQLLT--------ELdGIESLKgVVVIAATNRPDMIDPALL 148
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 216-472 5.55e-05

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


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 46.69  E-value: 5.55e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 216 TVLEKQGVLEIDELKERATAILKYLNIDLQRLTLRNEVQSKTRIDIDQQQREYFLHQQMRTIQEELGGVSYEQEMEELKK 295
Cdd:COG1401   59 RAARATELVEELSAALEVVVLLLDLEKVELNEKLALSEAAVAIEELYELEADSEIEAVGLLLELAERSDALEALERARLL 138

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 296 KAKTKKWDDKIKELFEKELSKLQRTNPNSPDYGIQRNYLEVLLELPWNEYSKDNFDLKRAQKILDKEHYgleevKRRIIE 375
Cdd:COG1401  139 LELADLEERAALETEVLEALEAELEELLAAPEDLSADALAAELSAAEELYSEDLESEDDYLKDLLREKF-----EETLEA 213

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 376 YLAVLKlrndmKSPILCFYGPPGVGKTSLGRSIAKALS---REYVRM-----SlggLHDEAEIRGHR-----KTYIgAMP 442
Cdd:COG1401  214 FLAALK-----TKKNVILAGPPGTGKTYLARRLAEALGgedNGRIEFvqfhpS---WSYEDFLLGYRpsldeGKYE-PTP 284

                        250       260       270
                 ....*....|....*....|....*....|....
gi 256580486 443 GRILQQLKKAKtSNP----VFVLDEIDkLGNNSY 472
Cdd:COG1401  285 GIFLRFCLKAE-KNPdkpyVLIIDEIN-RANVEK 316
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 365-523 1.00e-04

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: 43.76  E-value: 1.00e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 365 GLEEVKRRIIEYLAVLK-----LRNDMKSP--ILcFYGPPGVGKTSLGRSIAK-------ALS-REYVRMslgglhdeae 429
Cdd:cd19501    8 GCEEAKEELKEVVEFLKnpekfTKLGAKIPkgVL-LVGPPGTGKTLLAKAVAGeagvpffSISgSDFVEM---------- 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 430 irghrktYIGAMPGRILQQLKKAKTSNP--VFVlDEIDKLGNNSYQGDPSSAmlevldPEQNKEFYDNFLEM-GYDLSK- 505
Cdd:cd19501   77 -------FVGVGASRVRDLFEQAKKNAPciVFI-DEIDAVGRKRGAGLGGGH------DEREQTLNQLLVEMdGFESNTg 142

                        170
                 ....*....|....*...
gi 256580486 506 VMFIATANDLSTIQPALL 523
Cdd:cd19501  143 VIVIAATNRPDVLDPALL 160
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 365-619 1.18e-04

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


Pssm-ID: 273521 [Multi-domain]  Cd Length: 733  Bit Score: 45.67  E-value: 1.18e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  365 GLEEVKRRIIE-------YLAVLKLRNDMKSPILCFYGPPGVGKTSLGRSIAKALSREYVrmslgglhdeaEIRGHR--K 435
Cdd:TIGR01243 457 GLEEVKQELREavewplkHPEIFEKMGIRPPKGVLLFGPPGTGKTLLAKAVATESGANFI-----------AVRGPEilS 525

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  436 TYIGAMPGRILQQLKKAKTSNPVFV-LDEIDKLGNNSYQGDPSSAMLEVLDpeQNKEFYDNFLEmgydLSKVMFIATAND 514
Cdd:TIGR01243 526 KWVGESEKAIREIFRKARQAAPAIIfFDEIDAIAPARGARFDTSVTDRIVN--QLLTEMDGIQE----LSNVVVIAATNR 599

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  515 LSTIQPALL-----DRmeLINVTGYTIEEKTEIAKRHLLPKQLKEhgmkttDLQLgkKEIERIVEGYT--------RESG 581
Cdd:TIGR01243 600 PDILDPALLrpgrfDR--LILVPPPDEEARKEIFKIHTRSMPLAE------DVDL--EELAEMTEGYTgadieavcREAA 669

                         250       260       270
                  ....*....|....*....|....*....|....*...
gi 256580486  582 VRALEKEIAKVVRYGAKNLAMEEAYDPKLTIETIEKIL 619
Cdd:TIGR01243 670 MAALRESIGSPAKEKLEVGEEEFLKDLKVEMRHFLEAL 707
LON smart00464
Found in ATP-dependent protease La (LON); N-terminal domain of the ATP-dependent protease La ...
 48-102 2.43e-04

Found in ATP-dependent protease La (LON); N-terminal domain of the ATP-dependent protease La (LON), present also in other bacterial ORFs.


Pssm-ID: 197740 [Multi-domain]  Cd Length: 92  Bit Score: 40.88  E-value: 2.43e-04
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 256580486    48 VLPILPLKNTVLFPGVVVPISAGRDASIHLINEAYA-TTKTIGVVAQLDEKTEIPE 102
Cdd:smart00464   1 TLPLLPIRRRPLFPGFVLPIPVKRPKSVAAIKEALRrSQPYVIVFLLQDDPTETPE 56
RecA-like_PAN_like cd19502
proteasome activating nucleotidase PAN and related proteasome subunits; This subfamily ...
 394-523 2.78e-04

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


Pssm-ID: 410910 [Multi-domain]  Cd Length: 171  Bit Score: 42.32  E-value: 2.78e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 394 YGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDEaeirghrktYIGAMPGRILQQLKKAKTSNPVFV-LDEIDKLGNNSY 472
Cdd:cd19502   43 YGPPGTGKTLLAKAVANHTDATFIRVVGSELVQK---------YIGEGARLVRELFEMAREKAPSIIfIDEIDAIGAKRF 113

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 256580486 473 QGDPSS------AMLEVLDpeqnkefydnflEM-GYD-LSKVMFIATANDLSTIQPALL 523
Cdd:cd19502  114 DSGTGGdrevqrTMLELLN------------QLdGFDpRGNIKVIMATNRPDILDPALL 160
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 395-546 2.87e-04

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


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 43.62  E-value: 2.87e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 395 GPPGVGKTSLGRSIAKALSREYVRM----SLgglhDEAEIRGH-------RKTYIgaMPGRILQQlkkaktsnpVFVLDE 463
Cdd:COG0714   38 GVPGVGKTTLAKALARALGLPFIRIqftpDL----LPSDILGTyiydqqtGEFEF--RPGPLFAN---------VLLADE 102

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 464 IDKlgnnsyqGDP--SSAMLEVLdpeQNKEFYdnfLEMG-YDLSKVMF-IATAN--------DLStiqPALLDRMEL-IN 530
Cdd:COG0714  103 INR-------APPktQSALLEAM---EERQVT---IPGGtYKLPEPFLvIATQNpieqegtyPLP---EAQLDRFLLkLY 166

                        170
                 ....*....|....*..
gi 256580486 531 VtGY-TIEEKTEIAKRH 546
Cdd:COG0714  167 I-GYpDAEEEREILRRH 182
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 361-412 6.60e-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: 42.67  E-value: 6.60e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 256580486  361 KEHYGLEEVKRRIIEYLAVLKLRNDMKSPILcFYGPPGVGKTSLGRSIAKAL 412
Cdd:TIGR00635   4 AEFIGQEKVKEQLQLFIEAAKMRQEALDHLL-LYGPPGLGKTTLAHIIANEM 54
RecA-like_CDC48_r2-like cd19528
second of two ATPase domains of CDC48 and similar ATPase domains; CDC48 in yeast and p97 or ...
 393-523 9.41e-04

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: 40.57  E-value: 9.41e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 393 FYGPPGVGKTSLGRSIAKALSREYVrmslgglhdeaEIRGHR--KTYIGAMPGRILQQLKKAKTSNP-VFVLDEIDKLGN 469
Cdd:cd19528   32 FYGPPGCGKTLLAKAIANECQANFI-----------SVKGPEllTMWFGESEANVRDIFDKARAAAPcVLFFDELDSIAK 100

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 256580486 470 --NSYQGDPSSAMLEVLDpeqnkefyDNFLEM-GYDLSKVMF-IATANDLSTIQPALL 523
Cdd:cd19528  101 arGGNIGDAGGAADRVIN--------QILTEMdGMNTKKNVFiIGATNRPDIIDPAIL 150
44 PHA02544
clamp loader, small subunit; Provisional
 389-544 1.26e-03

clamp loader, small subunit; Provisional


Pssm-ID: 222866 [Multi-domain]  Cd Length: 316  Bit Score: 41.90  E-value: 1.26e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 389 PILCFYGP-PGVGKTslgrSIAKALSRE------YVRMSLGGLHDeaeIRGHRKTYIGAMpgrilQQLKKAKtsnpVFVL 461
Cdd:PHA02544  43 PNMLLHSPsPGTGKT----TVAKALCNEvgaevlFVNGSDCRIDF---VRNRLTRFASTV-----SLTGGGK----VIII 106

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 462 DEIDKLGNNSYQGDPSSAMlevldpeqnKEFYDNflemgydlskVMFIATANDLSTIQPALLDRMELINVTGYTIEEKTE 541
Cdd:PHA02544 107 DEFDRLGLADAQRHLRSFM---------EAYSKN----------CSFIITANNKNGIIEPLRSRCRVIDFGVPTKEEQIE 167


                 ...
gi 256580486 542 IAK 544
Cdd:PHA02544 168 MMK 170
FlhF COG1419
Flagellar biosynthesis GTPase FlhF [Cell motility];
306-467 1.47e-03

Flagellar biosynthesis GTPase FlhF [Cell motility];


Pssm-ID: 441029 [Multi-domain]  Cd Length: 361  Bit Score: 41.77  E-value: 1.47e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 306 IKELFEKELSKLQRTNPNSPDygIQRNYLEVLLELpwneyskdNFDLKRAQKILDK--EHYGLEEVKRRIIEYLA--VLK 381
Cdd:COG1419   86 LKELLEEQLSGLAGESARLPP--ELAELLERLLEA--------GVSPELARELLEKlpEDLSAEEAWRALLEALArrLPV 155

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 382 LRNDMKSP--ILCFYGPPGVGKTSlgrSIAKaLSREYVrmslgglhdeaeIRGHRK-------TY-IGAmpgriLQQLKK 451
Cdd:COG1419  156 AEDPLLDEggVIALVGPTGVGKTT---TIAK-LAARFV------------LRGKKKvalittdTYrIGA-----VEQLKT 214

                        170
                 ....*....|....*...
gi 256580486 452 -AKTSN-PVFVLDEIDKL 467
Cdd:COG1419  215 yARILGvPVEVAYDPEEL 232
LonB COG1067
Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones] ...
 716-763 1.55e-03

Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 440686 [Multi-domain]  Cd Length: 742  Bit Score: 42.24  E-value: 1.55e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 256580486 716 DGPSAGIAMLTSLMSLFTQKRVKKHLAMTGEITLRGKVLPVGGLKEKI 763
Cdd:COG1067  592 DGDSASSAELYALLSALSGVPIRQDIAVTGSVNQHGEVQPIGGVNEKI 639
RecA-like_Pch2-like cd19508
ATPase domain of Pachytene checkpoint 2 (Pch2) and similar ATPase domains; Pch2 (known as ...
 367-525 1.98e-03

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: 40.12  E-value: 1.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 367 EEVKRRIIEYLAVLKL---RNDMKSPILC-----FYGPPGVGKTSLGRSIAKALSreyVRMSLGGLHDE-AEIRGHR--- 434
Cdd:cd19508   23 SNLKSRLLDYVTTTLLfsdKNVNTNLITWnrlvlLHGPPGTGKTSLCKALAQKLS---IRLSSRYRYGQlIEINSHSlfs 99

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 435 ------KTYIGAMPGRIlQQLKKAKtSNPVFVL-DEIDKLG----NNSYQGDPSSAMLEVldpeqnkefydNFLEMGYDL 503
Cdd:cd19508  100 kwfsesGKLVTKMFQKI-QELIDDK-DALVFVLiDEVESLAaarsASSSGTEPSDAIRVV-----------NAVLTQIDR 166

                        170       180
                 ....*....|....*....|....*.
gi 256580486 504 SK----VMFIATANDLSTIQPALLDR 525
Cdd:cd19508  167 IKryhnNVILLTSNLLEKIDVAFVDR 192
COG1373 COG1373
Predicted ATPase, AAA+ superfamily [General function prediction only];
366-464 2.63e-03

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


Pssm-ID: 440984 [Multi-domain]  Cd Length: 405  Bit Score: 41.08  E-value: 2.63e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 366 LEEVKRRIIEYLavlkLRNDMKSPILCFYGPPGVGKTSLGRSIAKALsREYVRMSLgglhDEAEIRGhrktYIGAMPGRI 445
Cdd:COG1373    2 MIMIKRKILDKL----LKLLDNRKAVVITGPRQVGKTTLLKQLAKEL-ENILYINL----DDPRLRA----LAEEDPDDL 68

                         90
                 ....*....|....*....
gi 256580486 446 LQQLKKAKTSNPVFVLDEI 464
Cdd:COG1373   69 LEALKELYPGKTYLFLDEI 87
PTZ00361 PTZ00361
26 proteosome regulatory subunit 4-like protein; Provisional
 394-523 3.32e-03

26 proteosome regulatory subunit 4-like protein; Provisional


Pssm-ID: 185575 [Multi-domain]  Cd Length: 438  Bit Score: 40.91  E-value: 3.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 394 YGPPGVGKTSLGRSIAKALSREYVRMSLGGLhdeaeirghRKTYIGAMPGRILQQLKKAKTSNPVFV-LDEIDKLGNNSY 472
Cdd:PTZ00361 223 YGPPGTGKTLLAKAVANETSATFLRVVGSEL---------IQKYLGDGPKLVRELFRVAEENAPSIVfIDEIDAIGTKRY 293

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 256580486 473 QGDPSSA------MLEVLdpeqnkefydNFLEmGYD-LSKVMFIATANDLSTIQPALL 523
Cdd:PTZ00361 294 DATSGGEkeiqrtMLELL----------NQLD-GFDsRGDVKVIMATNRIESLDPALI 340
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 393-522 3.51e-03

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: 39.20  E-value: 3.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 393 FYGPPGVGKTSLGRSIAKALSREYVRMSlgglhdeaeirGHrkTYIGAMPGRILQQLK----KAKTSNP-VFVLDEIDKL 467
Cdd:cd19503   39 LHGPPGTGKTLLARAVANEAGANFLSIS-----------GP--SIVSKYLGESEKNLReifeEARSHAPsIIFIDEIDAL 105

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 256580486 468 GNN--SYQGDPSSAM----LEVLDPEQNKefydnflemgydlSKVMFIATANDLSTIQPAL 522
Cdd:cd19503  106 APKreEDQREVERRVvaqlLTLMDGMSSR-------------GKVVVIAATNRPDAIDPAL 153
HolB COG0470
DNA polymerase III, delta prime subunit [Replication, recombination and repair];
366-412 3.69e-03

DNA polymerase III, delta prime subunit [Replication, recombination and repair];


Pssm-ID: 440238 [Multi-domain]  Cd Length: 289  Bit Score: 40.34  E-value: 3.69e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 256580486 366 LEEVKRRIIEYLAvlklRNDMKSPILcFYGPPGVGKTSLGRSIAKAL 412
Cdd:COG0470    1 QEEAWEQLLAAAE----SGRLPHALL-LHGPPGIGKTTLALALARDL 42
cbbX CHL00181
CbbX; Provisional
 344-452 3.93e-03

CbbX; Provisional


Pssm-ID: 177083 [Multi-domain]  Cd Length: 287  Bit Score: 40.09  E-value: 3.93e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 344 EYSKDnfDLKRAQKILDKEHYGLEEVKRRIIEYLAVL---KLRNDM----KSPIL--CFYGPPGVGKTSLGRSIAKALSR 414
Cdd:CHL00181   8 EYEKT--QIQEVLDILDEELVGLAPVKTRIREIAALLlidRLRKNLgltsSNPGLhmSFTGSPGTGKTTVALKMADILYK 85

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 256580486 415 -EYVRmslgglhdeaeiRGHRKT---------YIGAMPGRILQQLKKA 452
Cdd:CHL00181  86 lGYIK------------KGHLLTvtrddlvgqYIGHTAPKTKEVLKKA 121
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 391-416 4.69e-03

RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.


Pssm-ID: 459992  Cd Length: 102  Bit Score: 37.20  E-value: 4.69e-03
                          10        20
                  ....*....|....*....|....*.
gi 256580486  391 LCFYGPPGVGKTSLGRSIAKALSREY 416
Cdd:pfam00910   1 IWLYGPPGCGKSTLAKYLARALLKKL 26
AAA_22 pfam13401
AAA domain;
390-467 4.75e-03

AAA domain;


Pssm-ID: 379165 [Multi-domain]  Cd Length: 129  Bit Score: 38.09  E-value: 4.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486  390 ILCFYGPPGVGKTSLGRSIAKAL---SREYVRMSLGGLHDEAEIR-------GHRKTYIG---AMPGRILQQLKKAKTSn 456
Cdd:pfam13401   7 ILVLTGESGTGKTTLLRRLLEQLpevRDSVVFVDLPSGTSPKDLLrallralGLPLSGRLskeELLAALQQLLLALAVA- 85

                          90
                  ....*....|.
gi 256580486  457 PVFVLDEIDKL 467
Cdd:pfam13401  86 VVLIIDEAQHL 96
RecA-like_PEX6_r2 cd19527
second of two ATPase domains of Peroxisomal biogenesis factor 6 (PEX6); PEX6(also known as ...
 387-480 4.91e-03

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


Pssm-ID: 410935 [Multi-domain]  Cd Length: 160  Bit Score: 38.65  E-value: 4.91e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 387 KSPILcFYGPPGVGKTSLGRSIAKALSREYVRMSLGGLHDeaeirghrkTYIGAMPGRILQQLKKAKTSNP-VFVLDEID 465
Cdd:cd19527   26 RSGIL-LYGPPGTGKTLLAKAIATECSLNFLSVKGPELIN---------MYIGESEANVREVFQKARDAKPcVIFFDELD 95

                         90
                 ....*....|....*.
gi 256580486 466 KLG-NNSYQGDPSSAM 480
Cdd:cd19527   96 SLApSRGNSGDSGGVM 111
SK cd00464
Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic ...
 395-417 5.27e-03

Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.


Pssm-ID: 238260 [Multi-domain]  Cd Length: 154  Bit Score: 38.31  E-value: 5.27e-03
                         10        20
                 ....*....|....*....|...
gi 256580486 395 GPPGVGKTSLGRSIAKALSREYV 417
Cdd:cd00464    6 GMMGAGKTTVGRLLAKALGLPFV 28
RecA-like_NVL_r2-like cd19530
second of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 394-523 5.51e-03

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: 38.62  E-value: 5.51e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 394 YGPPGVGKTSLGRSIAKALSREYvrMSLGGlhdeAEIrghRKTYIGAMPGRILQQLKKAKTSNP-VFVLDEIDKLGNNSY 472
Cdd:cd19530   36 YGPPGCGKTLLAKAVANESGANF--ISVKG----PEL---LNKYVGESERAVRQVFQRARASAPcVIFFDEVDALVPKRG 106

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 256580486 473 QGDpSSAMLEVLdpeqnkefyDNFL-EM--GYDLSKVMFIATANDLSTIQPALL 523
Cdd:cd19530  107 DGG-SWASERVV---------NQLLtEMdgLEERSNVFVIAATNRPDIIDPAML 150
COG2842 COG2842
Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons]; ...
 390-467 5.75e-03

Bacteriophage DNA transposition protein, AAA+ family ATPase [Mobilome: prophages, transposons];


Pssm-ID: 442090 [Multi-domain]  Cd Length: 254  Bit Score: 39.55  E-value: 5.75e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 390 ILCFYGPPGVGKTslgrSIAKALSRE-----YVRMS--------LGGLHDEAEIRGHRKTyIGAMPGRILQQLKKaktSN 456
Cdd:COG2842   52 IGVVYGESGVGKT----TAAREYANRnpnviYVTASpswtskelLEELAEELGIPAPPGT-IADLRDRILERLAG---TG 123

                         90
                 ....*....|.
gi 256580486 457 PVFVLDEIDKL 467
Cdd:COG2842  124 RLLIIDEADHL 134
PRK13341 PRK13341
AAA family ATPase;
391-475 7.23e-03

AAA family ATPase;


Pssm-ID: 237354 [Multi-domain]  Cd Length: 725  Bit Score: 40.04  E-value: 7.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 256580486 391 LCFYGPPGVGKTSLGRSIAKALSREYVRMSlGGLHDEAEIRGHRKTYIgampgrilQQLKKAKTSNPVFVlDEIDKLgnN 470
Cdd:PRK13341  55 LILYGPPGVGKTTLARIIANHTRAHFSSLN-AVLAGVKDLRAEVDRAK--------ERLERHGKRTILFI-DEVHRF--N 122


                 ....*
gi 256580486 471 SYQGD 475
Cdd:PRK13341 123 KAQQD 127
PRK04195 PRK04195
replication factor C large subunit; Provisional
 367-416 9.19e-03

replication factor C large subunit; Provisional


Pssm-ID: 235250 [Multi-domain]  Cd Length: 482  Bit Score: 39.52  E-value: 9.19e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 256580486 367 EEVKRRIIEYLAVLKLRNDMKSPILcfYGPPGVGKTSLgrsiAKALSREY 416
Cdd:PRK04195  20 EKAKEQLREWIESWLKGKPKKALLL--YGPPGVGKTSL----AHALANDY 63
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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