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Conserved domains on  [gi|124261099|gb|ABM96093|]
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putative ATPase [Methylibium petroleiphilum PM1]

Protein Classification

P-loop NTPase family protein( domain architecture ID 1562424)

P-loop NTPase (nucleoside triphosphate hydrolase) family protein contains two conserved sequence signatures, the Walker A motif (the P-loop proper) and Walker B motif which bind, respectively, the beta and gamma phosphate moieties of the bound nucleotide (typically ATP or GTP), and a Mg(2+) cation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
P-loop_NTPase super family cl38936
P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain ...
 79-249 1.30e-28

P-loop containing Nucleoside Triphosphate Hydrolases; Members of the P-loop NTPase domain superfamily are characterized by a conserved nucleotide phosphate-binding motif, also referred to as the Walker A motif (GxxxxGK[S/T], where x is any residue), and the Walker B motif (hhhh[D/E], where h is a hydrophobic residue). The Walker A and B motifs bind the beta-gamma phosphate moiety of the bound nucleotide (typically ATP or GTP) and the Mg2+ cation, respectively. The P-loop NTPases are involved in diverse cellular functions, and they can be divided into two major structural classes: the KG (kinase-GTPase) class which includes Ras-like GTPases and its circularly permutated YlqF-like; and the ASCE (additional strand catalytic E) class which includes ATPase Binding Cassette (ABC), DExD/H-like helicases, 4Fe-4S iron sulfur cluster binding proteins of NifH family, RecA-like F1-ATPases, and ATPases Associated with a wide variety of Activities (AAA). Also included are a diverse set of nucleotide/nucleoside kinase families.


The actual alignment was detected with superfamily member cd19500:

Pssm-ID: 476819 [Multi-domain]  Cd Length: 182  Bit Score: 109.19  E-value: 1.30e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  79 EQLPNFHDVLDDVKRQ-------LALCHDSRDALeitpMLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSG 151
Cdd:cd19500    6 KVLDADHYGLEDVKERileylavRKLKGSMKGPI----LCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 152 ASSQWKGARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALYGLLEHDTAGSFTDEFAEVAIDASQVIWVATAN 231
Cdd:cd19500   82 HRRTYVGAMPGRIIQALKKAGTNNPVFLLDEIDKIGSSFRGDPASALLEVLDPEQNSTFSDHYLDVPFDLSKVLFIATAN 161

                        170
                 ....*....|....*...
gi 124261099 232 DARAIPEPILNRMNVFEV 249
Cdd:cd19500  162 SLDTIPGPLLDRMEIIEL 179
 
Name Accession Description Interval E-value
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 79-249 1.30e-28

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: 109.19  E-value: 1.30e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  79 EQLPNFHDVLDDVKRQ-------LALCHDSRDALeitpMLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSG 151
Cdd:cd19500    6 KVLDADHYGLEDVKERileylavRKLKGSMKGPI----LCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 152 ASSQWKGARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALYGLLEHDTAGSFTDEFAEVAIDASQVIWVATAN 231
Cdd:cd19500   82 HRRTYVGAMPGRIIQALKKAGTNNPVFLLDEIDKIGSSFRGDPASALLEVLDPEQNSTFSDHYLDVPFDLSKVLFIATAN 161

                        170
                 ....*....|....*...
gi 124261099 232 DARAIPEPILNRMNVFEV 249
Cdd:cd19500  162 SLDTIPGPLLDRMEIIEL 179
PRK10787 PRK10787
DNA-binding ATP-dependent protease La; Provisional
 79-246 4.18e-18

DNA-binding ATP-dependent protease La; Provisional


Pssm-ID: 182730 [Multi-domain]  Cd Length: 784  Bit Score: 85.38  E-value: 4.18e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  79 EQLPNFHDVLDDVKRQLA--LCHDSRDALEITPML-LLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSGASSQ 155
Cdd:PRK10787 318 EILDTDHYGLERVKDRILeyLAVQSRVNKIKGPILcLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRT 397

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 156 WKGARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALYGLLEHDTAGSFTDEFAEVAIDASQVIWVATANDARa 235
Cdd:PRK10787 398 YIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMN- 476

                        170
                 ....*....|.
gi 124261099 236 IPEPILNRMNV 246
Cdd:PRK10787 477 IPAPLLDRMEV 487
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 85-249 3.60e-16

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


Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 79.29  E-value: 3.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  85 HDVLDDVK---------RQLA-------LChdsrdaleitpmlLLGPPGVGKTHFAREMAQLLGTGlgFLSMSsltagwv 148
Cdd:COG0466  327 HYGLEKVKerileylavRKLKkklkgpiLC-------------LVGPPGVGKTSLGKSIARALGRK--FVRIS------- 384

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 149 LSGAssqwK-------------GARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALyglLE-------Hdtag 208
Cdd:COG0466  385 LGGV----RdeaeirghrrtyiGAMPGRIIQGLKKAGTKNPVFLLDEIDKMGSDFRGDPASAL---LEvldpeqnN---- 453

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 124261099 209 SFTDEFAEVAIDASQVIWVATANDARAIPEPILNRMNVFEV 249
Cdd:COG0466  454 TFSDHYLEVPFDLSKVMFIATANSLDTIPAPLLDRMEIIEL 494
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 110-247 1.23e-15

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: 72.24  E-value: 1.23e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVlsgassqwkGARPGKVFETLVDGQYANP-VMVVDEIDK--- 185
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYV---------GESEKRLRELFEAAKKLAPcVIFIDEIDAlag 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124261099  186 ----TGGEHAYDPLGALYGLLEhdtagsftdefaEVAIDASQVIWVATANDARAIPEPILNRMNVF 247
Cdd:pfam00004  72 srgsGGDSESRRVVNQLLTELD------------GFTSSNSKVIVIAATNRPDKLDPALLGRFDRI 125
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 109-185 2.18e-04

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: 40.82  E-value: 2.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   109 PMLLLGPPGVGKTHFAREMAQLLG-TGLGFLsmsSLTAGWVLSGASSQWKGARPGKVFETLVDGQYA-----------NP 176
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGpPGGGVI---YIDGEDILEEVLDQLLLIIVGGKKASGSGELRLrlalalarklkPD 80


                   ....*....
gi 124261099   177 VMVVDEIDK 185
Cdd:smart00382  81 VLILDEITS 89
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 22-184 3.82e-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: 42.20  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   22 IAHMRSVYRLGDVERRLEKLPPKEHESLRATYERMLEKGAErfqVKPSgvpAMDHLYEQLPNFH--DV--LDDVKRQLal 97
Cdd:TIGR01243 394 MAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKM---VEPS---AIREVLVEVPNVRwsDIggLEEVKQEL-- 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   98 chdsRDALE-------------ITP---MLLLGPPGVGKTHFAREMAQllGTGLGFLSMSSltagwvlSGASSQWKGARP 161
Cdd:TIGR01243 466 ----REAVEwplkhpeifekmgIRPpkgVLLFGPPGTGKTLLAKAVAT--ESGANFIAVRG-------PEILSKWVGESE 532

                         170       180
                  ....*....|....*....|....
gi 124261099  162 GKVFETLVDGQYANPVMV-VDEID 184
Cdd:TIGR01243 533 KAIREIFRKARQAAPAIIfFDEID 556
 
Name Accession Description Interval E-value
RecA-like_Lon cd19500
lon protease homolog 2 peroxisomal; Lon protease (also known as Lon peptidase) is an ...
 79-249 1.30e-28

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: 109.19  E-value: 1.30e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  79 EQLPNFHDVLDDVKRQ-------LALCHDSRDALeitpMLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSG 151
Cdd:cd19500    6 KVLDADHYGLEDVKERileylavRKLKGSMKGPI----LCLVGPPGVGKTSLGKSIARALGRKFVRISLGGVRDEAEIRG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 152 ASSQWKGARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALYGLLEHDTAGSFTDEFAEVAIDASQVIWVATAN 231
Cdd:cd19500   82 HRRTYVGAMPGRIIQALKKAGTNNPVFLLDEIDKIGSSFRGDPASALLEVLDPEQNSTFSDHYLDVPFDLSKVLFIATAN 161

                        170
                 ....*....|....*...
gi 124261099 232 DARAIPEPILNRMNVFEV 249
Cdd:cd19500  162 SLDTIPGPLLDRMEIIEL 179
PRK10787 PRK10787
DNA-binding ATP-dependent protease La; Provisional
 79-246 4.18e-18

DNA-binding ATP-dependent protease La; Provisional


Pssm-ID: 182730 [Multi-domain]  Cd Length: 784  Bit Score: 85.38  E-value: 4.18e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  79 EQLPNFHDVLDDVKRQLA--LCHDSRDALEITPML-LLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSGASSQ 155
Cdd:PRK10787 318 EILDTDHYGLERVKDRILeyLAVQSRVNKIKGPILcLVGPPGVGKTSLGQSIAKATGRKYVRMALGGVRDEAEIRGHRRT 397

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 156 WKGARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALYGLLEHDTAGSFTDEFAEVAIDASQVIWVATANDARa 235
Cdd:PRK10787 398 YIGSMPGKLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPASALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSMN- 476

                        170
                 ....*....|.
gi 124261099 236 IPEPILNRMNV 246
Cdd:PRK10787 477 IPAPLLDRMEV 487
Lon COG0466
ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, ...
 85-249 3.60e-16

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


Pssm-ID: 440234 [Multi-domain]  Cd Length: 785  Bit Score: 79.29  E-value: 3.60e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  85 HDVLDDVK---------RQLA-------LChdsrdaleitpmlLLGPPGVGKTHFAREMAQLLGTGlgFLSMSsltagwv 148
Cdd:COG0466  327 HYGLEKVKerileylavRKLKkklkgpiLC-------------LVGPPGVGKTSLGKSIARALGRK--FVRIS------- 384

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 149 LSGAssqwK-------------GARPGKVFETLVDGQYANPVMVVDEIDKTGGEHAYDPLGALyglLE-------Hdtag 208
Cdd:COG0466  385 LGGV----RdeaeirghrrtyiGAMPGRIIQGLKKAGTKNPVFLLDEIDKMGSDFRGDPASAL---LEvldpeqnN---- 453

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 124261099 209 SFTDEFAEVAIDASQVIWVATANDARAIPEPILNRMNVFEV 249
Cdd:COG0466  454 TFSDHYLEVPFDLSKVMFIATANSLDTIPAPLLDRMEIIEL 494
AAA pfam00004
ATPase family associated with various cellular activities (AAA); AAA family proteins often ...
 110-247 1.23e-15

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: 72.24  E-value: 1.23e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVlsgassqwkGARPGKVFETLVDGQYANP-VMVVDEIDK--- 185
Cdd:pfam00004   1 LLLYGPPGTGKTTLAKAVAKELGAPFIEISGSELVSKYV---------GESEKRLRELFEAAKKLAPcVIFIDEIDAlag 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124261099  186 ----TGGEHAYDPLGALYGLLEhdtagsftdefaEVAIDASQVIWVATANDARAIPEPILNRMNVF 247
Cdd:pfam00004  72 srgsGGDSESRRVVNQLLTELD------------GFTSSNSKVIVIAATNRPDKLDPALLGRFDRI 125
AAA cd00009
The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily ...
 109-245 4.60e-09

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: 54.46  E-value: 4.60e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 109 PMLLLGPPGVGKTHFAREMAQLLGT-GLGF--LSMSSLTAGWVLSGAssqwkgARPGKVFETLVDGQYANP-VMVVDEID 184
Cdd:cd00009   21 NLLLYGPPGTGKTTLARAIANELFRpGAPFlyLNASDLLEGLVVAEL------FGHFLVRLLFELAEKAKPgVLFIDEID 94

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124261099 185 KTggehaydPLGALYGLLEH-DTAGSFTDEFAEVaidasQVIWVATANDARAIPEPILNRMN 245
Cdd:cd00009   95 SL-------SRGAQNALLRVlETLNDLRIDRENV-----RVIGATNRPLLGDLDRALYDRLD 144
RecA-like_protease cd19481
proteases similar to RecA; RecA-like NTPases. This family includes the NTP binding domain of ...
 110-249 5.54e-09

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: 54.60  E-value: 5.54e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSGAssqwkgARPGKVFETLvdGQYANPVMVVDEIDKTGGE 189
Cdd:cd19481   29 ILLYGPPGTGKTLLAKALAGELGLPLIVVKLSSLLSKYVGESE------KNLRKIFERA--RRLAPCILFIDEIDAIGRK 100

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124261099 190 HAYDPLG-----ALYGLLehdtagSFTDEFAEvaidASQVIWVATANDARAIPePILNRMNVFEV 249
Cdd:cd19481  101 RDSSGESgelrrVLNQLL------TELDGVNS----RSKVLVIAATNRPDLLD-PALLRPGRFDE 154
SpoVK COG0464
AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle ...
 5-253 5.66e-09

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: 56.84  E-value: 5.66e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   5 ATELVTVPTGLPRSGLPIAHMRSVYRLGDVERRLEKLPPKEHESLRATYERMLEKGAERFQVKPSGVPAMDHLYEQLpnF 84
Cdd:COG0464   79 LALLAALLSALELLLLGELLLLLLLLLLLLLLLLDLERALLELLRESAEALALAAPLVTYEDIGGLEEELLELREAI--L 156

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  85 HDV--LDDVKRQLA-------LCHDSRDALEITP---MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVlsGA 152
Cdd:COG0464  157 DDLggLEEVKEELRelvalplKRPELREEYGLPPprgLLLYGPPGTGKTLLARALAGELGLPLIEVDLSDLVSKYV--GE 234

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 153 SSqwKGARpgKVFETLVdgQYANPVMVVDEIDktggehaydplgALYGllehdTAGSFTDEFAEVAIDA---------SQ 223
Cdd:COG0464  235 TE--KNLR--EVFDKAR--GLAPCVLFIDEAD------------ALAG-----KRGEVGDGVGRRVVNTlltemeelrSD 291

                        250       260       270
                 ....*....|....*....|....*....|.
gi 124261099 224 VIWVATANDARAIPEPILNRMN-VFEVQMPD 253
Cdd:COG0464  292 VVVIAATNRPDLLDPALLRRFDeIIFFPLPD 322
RecA-like_ClpB_Hsp104-like cd19499
Chaperone protein ClpB/Hsp104 subfamily; Bacterial Caseinolytic peptidase B (ClpB) and ...
 110-245 1.54e-06

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


Pssm-ID: 410907 [Multi-domain]  Cd Length: 178  Bit Score: 47.56  E-value: 1.54e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLL-GTGLGF--LSMSSLTagwvLSGASSQWKGARPG--------KVFETLVDGQYAnpVM 178
Cdd:cd19499   44 FLFLGPTGVGKTELAKALAELLfGDEDNLirIDMSEYM----EKHSVSRLIGAPPGyvgyteggQLTEAVRRKPYS--VV 117

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124261099 179 VVDEIDKTggehayDP--LGALYGLLEhdtAGSFTDEFAEVaIDASQVIWVATANdarAIPEPILNRMN 245
Cdd:cd19499  118 LLDEIEKA------HPdvQNLLLQVLD---DGRLTDSHGRT-VDFKNTIIIMTSN---HFRPEFLNRID 173
AAA_2 pfam07724
AAA domain (Cdc48 subfamily); This Pfam entry includes some of the AAA proteins not detected ...
 111-185 4.51e-06

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


Pssm-ID: 400187 [Multi-domain]  Cd Length: 168  Bit Score: 46.03  E-value: 4.51e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  111 LLLGPPGVGKTHFAREMAQLLGTGLGFLS---MSSLTAGWVLsgasSQWKGARPGKV-FE---TLVDGQYANPVMVV--D 181
Cdd:pfam07724   7 LFLGPTGVGKTELAKALAELLFGDERALIridMSEYMEEHSV----SRLIGAPPGYVgYEeggQLTEAVRRKPYSIVliD 82


                  ....
gi 124261099  182 EIDK 185
Cdd:pfam07724  83 EIEK 86
RecA-like_NVL_r1-like cd19518
first of two ATPase domains of NVL (nuclear VCP-like protein) and similar ATPase domains; NVL ...
 110-188 1.51e-05

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


Pssm-ID: 410926 [Multi-domain]  Cd Length: 169  Bit Score: 44.70  E-value: 1.51e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGwvLSGASSQwkgaRPGKVFETLVdgQYANPVMVVDEIDKTGG 188
Cdd:cd19518   37 VLLHGPPGCGKTMLANAIAGELKVPFLKISATEIVSG--VSGESEE----KIRELFDQAI--SNAPCIVFIDEIDAITP 107
AAA_5 pfam07728
AAA domain (dynein-related subfamily); This Pfam entry includes some of the AAA proteins not ...
 109-241 2.51e-05

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: 43.44  E-value: 2.51e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099  109 PMLLLGPPGVGKTHFAREMAQLLGTGLGF-------LSMSSLTAGWVLSGASSQW------KGARPGKVFetlvdgqyan 175
Cdd:pfam07728   1 GVLLVGPPGTGKTELAERLAAALSNRPVFyvqltrdTTEEDLFGRRNIDPGGASWvdgplvRAAREGEIA---------- 70

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124261099  176 pvmVVDEIDKTGGehayDPLGALYGLLEHDTAgSFTDEFAEVAIDASQVIWVATANDARAIPEPIL 241
Cdd:pfam07728  71 ---VLDEINRANP----DVLNSLLSLLDERRL-LLPDGGELVKAAPDGFRLIATMNPLDRGLNELS 128
RecA-like_Ycf46-like cd19507
ATPase domain of Ycf46 and similar ATPase domains; Ycf46 may play a role in the regulation of ...
 110-241 4.66e-05

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: 43.13  E-value: 4.66e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVlsGASSqwkgARPGKVFETLvdGQYANPVMVVDEIDKTgge 189
Cdd:cd19507   34 LLLVGIQGTGKSLTAKAIAGVWQLPLLRLDMGRLFGGLV--GESE----SRLRQMIQTA--EAIAPCVLWIDEIEKG--- 102

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 124261099 190 haydpLGALYGLLEHDTA----GSFTDEFAEvaiDASQVIWVATANDARAIPEPIL 241
Cdd:cd19507  103 -----FSNADSKGDSGTSsrvlGTFLTWLQE---KKKPVFVVATANNVQSLPPELL 150
RecA-like_VPS4-like cd19509
ATPase domain of VPS4, ATAD1, K, KTNA1, Spastin, FIGL-1 and similar ATPase domains; This ...
 110-244 5.33e-05

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


Pssm-ID: 410917 [Multi-domain]  Cd Length: 163  Bit Score: 43.11  E-value: 5.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVlsGASSqwKGARpgKVFEtlVDGQYANPVMVVDEIDKTGGE 189
Cdd:cd19509   35 ILLYGPPGTGKTLLARAVASESGSTFFSISASSLVSKWV--GESE--KIVR--ALFA--LARELQPSIIFIDEIDSLLSE 106

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 190 haydplgalYGLLEHDTAGSFTDEF-----AEVAIDASQVIWVATANDARAIPEPILNRM 244
Cdd:cd19509  107 ---------RGSGEHEASRRVKTEFlvqmdGVLNKPEDRVLVLGATNRPWELDEAFLRRF 157
RecA-like_KTNA1 cd19522
Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is ...
 110-190 6.13e-05

Katanin p60 ATPase-containing subunit A1; Katanin p60 ATPase-containing subunit A1 (KTNA1) is the catalytic subunit of the Katanin complex which is severs microtubules in an ATP-dependent manner, and is implicated in multiple aspects of microtubule dynamics. In addition to the p60 catalytic ATPase subunit, Katanin contains an accessory subunit (p80 or p80-like). The microtubule-severing activity of the ATPase is essential for female meiotic spindle assembly, and male gamete production; and the katanin complex severing microtubules is under tight regulation during the transition from the meiotic to mitotic stage to allow proper embryogenesis. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410930 [Multi-domain]  Cd Length: 170  Bit Score: 43.05  E-value: 6.13e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTagwvlsgasSQWKGARPgKVFETLVDGQ--YANPVMVVDEIDK-- 185
Cdd:cd19522   36 VLMVGPPGTGKTLLAKAVATECGTTFFNVSSSTLT---------SKYRGESE-KLVRLLFEMArfYAPTTIFIDEIDSic 105


                 ....*....
gi 124261099 186 ----TGGEH 190
Cdd:cd19522  106 srrgTSEEH 114
RecA-like_Figl-1 cd19525
ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; ...
 110-190 1.75e-04

ATPase domain of Fidgetin-Like 1 (FIGL-1); FIGL-1 may participate in DNA repair in the nucleus; it may be involved in DNA double-strand break repair via homologous recombination. Caenorhabditis elegans FIGL-1 is a nuclear protein and controls the mitotic progression in the germ line and mouse FIGL-1 may be involved in the control of male meiosis. human FIGL-1 has been shown to be a centrosome protein involved in ciliogenesis perhaps as a microtubule-severing protein. This subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410933 [Multi-domain]  Cd Length: 186  Bit Score: 41.90  E-value: 1.75e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSGassqwkgarpgkvfETLVDGQYA------NPVMVVDEI 183
Cdd:cd19525   58 ILLFGPPGTGKTLIGKCIASQSGATFFSISASSLTSKWVGEG--------------EKMVRALFSvarckqPAVIFIDEI 123

                         90
                 ....*....|..
gi 124261099 184 D-----KTGGEH 190
Cdd:cd19525  124 DsllsqRGEGEH 135
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 109-185 2.18e-04

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: 40.82  E-value: 2.18e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   109 PMLLLGPPGVGKTHFAREMAQLLG-TGLGFLsmsSLTAGWVLSGASSQWKGARPGKVFETLVDGQYA-----------NP 176
Cdd:smart00382   4 VILIVGPPGSGKTTLARALARELGpPGGGVI---YIDGEDILEEVLDQLLLIIVGGKKASGSGELRLrlalalarklkPD 80


                   ....*....
gi 124261099   177 VMVVDEIDK 185
Cdd:smart00382  81 VLILDEITS 89
CDC48 TIGR01243
AAA family ATPase, CDC48 subfamily; This subfamily of the AAA family ATPases includes two ...
 22-184 3.82e-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: 42.20  E-value: 3.82e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   22 IAHMRSVYRLGDVERRLEKLPPKEHESLRATYERMLEKGAErfqVKPSgvpAMDHLYEQLPNFH--DV--LDDVKRQLal 97
Cdd:TIGR01243 394 MAALRRFIREGKINFEAEEIPAEVLKELKVTMKDFMEALKM---VEPS---AIREVLVEVPNVRwsDIggLEEVKQEL-- 465

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099   98 chdsRDALE-------------ITP---MLLLGPPGVGKTHFAREMAQllGTGLGFLSMSSltagwvlSGASSQWKGARP 161
Cdd:TIGR01243 466 ----REAVEwplkhpeifekmgIRPpkgVLLFGPPGTGKTLLAKAVAT--ESGANFIAVRG-------PEILSKWVGESE 532

                         170       180
                  ....*....|....*....|....
gi 124261099  162 GKVFETLVDGQYANPVMV-VDEID 184
Cdd:TIGR01243 533 KAIREIFRKARQAAPAIIfFDEID 556
RPT1 COG1222
ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein ...
 84-141 3.97e-04

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


Pssm-ID: 440835 [Multi-domain]  Cd Length: 326  Bit Score: 41.53  E-value: 3.97e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124261099  84 FHDV--LDDVKRQLalchdsRDALE-------------ITP---MLLLGPPGVGKTHFAREMAQllGTGLGFLSMS 141
Cdd:COG1222   77 FDDIggLDEQIEEI------REAVElplknpelfrkygIEPpkgVLLYGPPGTGKTLLAKAVAG--ELGAPFIRVR 144
COG1223 COG1223
Predicted ATPase, AAA+ superfamily [General function prediction only];
110-325 7.31e-04

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


Pssm-ID: 440836 [Multi-domain]  Cd Length: 246  Bit Score: 40.64  E-value: 7.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVLSGAssqwkgARPGKVFEtlvdgqYAN--PVMV-VDEIDKT 186
Cdd:COG1223   38 ILFYGPPGTGKTMLAEALAGELKLPLLTVRLDSLIGSYLGETA------RNLRKLFD------FARraPCVIfFDEFDAI 105

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 187 GGEHAYDplgalyglleHDTAgsftdEFAEV------AID--ASQVIWVATANDARAIPEPILNRMN-VFEVQMPDaaaa 257
Cdd:COG1223  106 AKDRGDQ----------NDVG-----EVKRVvnallqELDglPSGSVVIAATNHPELLDSALWRRFDeVIEFPLPD---- 166

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124261099 258 RAIAARLYRgiradhDWGSRFaPEPGDDVLDAMAELAP----REMRRAWMTAFGNAKLAGRAAVEPRDLPEA 325
Cdd:COG1223  167 KEERKEILE------LNLKKF-PLPFELDLKKLAKKLEglsgADIEKVLKTALKKAILEDREKVTKEDLEEA 231
RecA-like_HslU cd19498
ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease ...
 106-185 7.33e-04

ATP-dependent protease ATPase subunit HslU; HslU is a component of the ATP-dependent protease HslVU. In HslVU, HslU ATPase serves to unfold and translocate protein substrate, and the HslV protease degrades the unfolded proteins. This RecA-like_HslU subfamily belongs to the RecA-like NTPase family which includes the NTP binding domain of F1 and V1 H(+)ATPases, DnaB and related helicases as well as bacterial RecA and related eukaryotic and archaeal recombinases. The RecA-like NTPase family also includes bacterial conjugation proteins and related DNA transfer proteins involved in type II and type IV secretion.


Pssm-ID: 410906 [Multi-domain]  Cd Length: 183  Bit Score: 40.06  E-value: 7.33e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 106 EITP--MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLT-AGWVlsgassqwkGARPGKVFETLVDGqyanpVMVVDE 182
Cdd:cd19498   43 EVTPknILMIGPTGVGKTEIARRLAKLAGAPFIKVEATKFTeVGYV---------GRDVESIIRDLVEG-----IVFIDE 108


                 ...
gi 124261099 183 IDK 185
Cdd:cd19498  109 IDK 111
RecA-like_ATAD1 cd19520
ATPase domain of ATPase family AAA domain-containing protein 1 and similar ATPase domains; ...
 110-249 8.31e-04

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


Pssm-ID: 410928 [Multi-domain]  Cd Length: 166  Bit Score: 39.72  E-value: 8.31e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 110 MLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVlsGASSQWKGArpgkVFETLVDGQYAnpVMVVDEIDKTGGE 189
Cdd:cd19520   38 VLLYGPPGCGKTMLAKATAKEAGARFINLQVSSLTDKWY--GESQKLVAA----VFSLASKLQPS--IIFIDEIDSFLRQ 109

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124261099 190 HAYDplgalygllEHDTAGSFTDEFAEV-----AIDASQVIWVATANDARAIPEPILNRM-NVFEV 249
Cdd:cd19520  110 RSST---------DHEATAMMKAEFMSLwdglsTDGNCRVIVMGATNRPQDLDEAILRRMpKRFHI 166
PRK13342 PRK13342
recombination factor protein RarA; Reviewed
 110-146 1.00e-03

recombination factor protein RarA; Reviewed


Pssm-ID: 237355 [Multi-domain]  Cd Length: 413  Bit Score: 40.45  E-value: 1.00e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 124261099 110 MLLLGPPGVGKTHFAREMAQllGTGLGFLSMSSLTAG 146
Cdd:PRK13342  39 MILWGPPGTGKTTLARIIAG--ATDAPFEALSAVTSG 73
SpoIIIAA COG3854
Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome ...
 111-135 1.76e-03

Stage III sporulation protein SpoIIIAA [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443063  Cd Length: 309  Bit Score: 39.75  E-value: 1.76e-03
                         10        20
                 ....*....|....*....|....*
gi 124261099 111 LLLGPPGVGKTHFAREMAQLLGTGL 135
Cdd:COG3854  144 LIISPPGCGKTTLLRDIARVLSDGL 168
RecA-like_CDC48_NLV2_r1-like cd19503
first of two ATPase domains of CDC48 and NLV2, and similar ATPase domains; CDC48 in yeast and ...
 104-184 1.83e-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: 38.43  E-value: 1.83e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 104 ALEITP---MLLLGPPGVGKTHFAREMAQLLGTGLgflsmssltagWVLSGAS--SQWKGARPGKVFETLVDGQYANP-V 177
Cdd:cd19503   28 ALGLKPprgVLLHGPPGTGKTLLARAVANEAGANF-----------LSISGPSivSKYLGESEKNLREIFEEARSHAPsI 96


                 ....*..
gi 124261099 178 MVVDEID 184
Cdd:cd19503   97 IFIDEID 103
RarA COG2256
Replication-associated recombination protein RarA (DNA-dependent ATPase) [Replication, ...
 107-146 2.06e-03

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


Pssm-ID: 441857 [Multi-domain]  Cd Length: 439  Bit Score: 39.65  E-value: 2.06e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 124261099 107 ITPMLLLGPPGVGKTHFAREMAQllGTGLGFLSMSSLTAG 146
Cdd:COG2256   49 LSSMILWGPPGTGKTTLARLIAN--ATDAEFVALSAVTSG 86
McrB COG1401
5-methylcytosine-specific restriction endonuclease McrBC, GTP-binding regulatory subunit McrB ...
 103-132 3.45e-03

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


Pssm-ID: 441011 [Multi-domain]  Cd Length: 477  Bit Score: 38.98  E-value: 3.45e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 124261099 103 DALEITPMLLL-GPPGVGKTHFAREMAQLLG 132
Cdd:COG1401  216 AALKTKKNVILaGPPGTGKTYLARRLAEALG 246
Kti12 COG4088
tRNA uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein) ...
 107-132 4.01e-03

tRNA uridine 5-carbamoylmethylation protein Kti12 (Killer toxin insensitivity protein) [Translation, ribosomal structure and biogenesis, Defense mechanisms];


Pssm-ID: 443264 [Multi-domain]  Cd Length: 179  Bit Score: 37.78  E-value: 4.01e-03
                         10        20
                 ....*....|....*....|....*...
gi 124261099 107 ITPMLLL--GPPGVGKTHFAREMAQLLG 132
Cdd:COG4088    2 DSPMLLIltGPPGSGKTTFAKALAQRLY 29
MoxR COG0714
MoxR-like ATPase [General function prediction only]; MoxR-like ATPase is part of the Pathway ...
 109-186 4.34e-03

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


Pssm-ID: 440478 [Multi-domain]  Cd Length: 292  Bit Score: 38.22  E-value: 4.34e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 109 PMLLLGPPGVGKTHFAREMAQLLGTGLGFL-----SM-SSLTAGWVLSGASSQWKgARPGKVFETLVdgqyanpvmVVDE 182
Cdd:COG0714   33 HLLLEGVPGVGKTTLAKALARALGLPFIRIqftpdLLpSDILGTYIYDQQTGEFE-FRPGPLFANVL---------LADE 102


                 ....
gi 124261099 183 IDKT 186
Cdd:COG0714  103 INRA 106
RNA_helicase pfam00910
RNA helicase; This family includes RNA helicases thought to be involved in duplex unwinding ...
 111-184 5.38e-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: 36.04  E-value: 5.38e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124261099  111 LLLGPPGVGKTHFAREMAQLLGTGLGFLsmssltAGWVLSGASSQwkgarpgKVFetlvDGQYANPVMVVDEID 184
Cdd:pfam00910   2 WLYGPPGCGKSTLAKYLARALLKKLGLP------KDSVYSRNPDD-------DFW----DGYTGQPVVIIDDFG 58
RecA-like_FtsH cd19501
ATP-dependent zinc metalloprotease FtsH; FtsH ATPase is a processive, ATP-dependent zinc ...
 111-189 6.80e-03

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: 36.83  E-value: 6.80e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124261099 111 LLLGPPGVGKTHFAREMAQllGTGLGFLSM--SSLTAGWVLSGASsqwkgaRPGKVFETLvdGQYANPVMVVDEIDKTGG 188
Cdd:cd19501   41 LLVGPPGTGKTLLAKAVAG--EAGVPFFSIsgSDFVEMFVGVGAS------RVRDLFEQA--KKNAPCIVFIDEIDAVGR 110


                 .
gi 124261099 189 E 189
Cdd:cd19501  111 K 111
RepA_RSF1010_like cd01125
Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family ...
 108-149 7.28e-03

Hexameric Replicative Helicase RepA of plasmid RSF1010 and related proteins; This family includes the homo-hexameric replicative helicase RepA encoded by plasmid RSF1010. RSF1010 is found in most Gram-negative bacteria and some Gram-positive bacteria . The RepA protein of Plasmid RSF1010 is a 5'-3' DNA helicase which can utilize ATP, dATP, GTP and dGTP (and CTP and dCTP to a lesser extent).


Pssm-ID: 410870  Cd Length: 238  Bit Score: 37.36  E-value: 7.28e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 124261099 108 TPMLLLGPPGVGKTHFAREMAQLLGTGLGFLSMSSLTAGWVL 149
Cdd:cd01125    2 TLGMLVGPPGSGKSFLALDLAVAVATGRDWLGERRVKQGRVV 43
ruvB TIGR00635
Holliday junction DNA helicase, RuvB subunit; All proteins in this family for which functions ...
 110-135 8.42e-03

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


Pssm-ID: 129721 [Multi-domain]  Cd Length: 305  Bit Score: 37.66  E-value: 8.42e-03
                          10        20
                  ....*....|....*....|....*.
gi 124261099  110 MLLLGPPGVGKTHFAREMAQLLGTGL 135
Cdd:TIGR00635  33 LLLYGPPGLGKTTLAHIIANEMGVNL 58
 
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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