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Conserved domains on  [gi|489203608|ref|WP_003112700|]
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AAA family ATPase [Pseudomonas aeruginosa]

Protein Classification

OLD family protein( domain architecture ID 1003243)

OLD (overcome lysogenization defect) family protein may function as an ATP-dependent endonuclease, similar to Bacteriophage P2 Old nuclease that acts preferentially on linear dsDNA, processively degrading it from 5'-3', releasing 5'-phosphomononucleotides

EC:  3.1.-.-
Gene Ontology:  GO:0005524|GO:0004527
PubMed:  2695400

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YbjD super family cl34639
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 4-355 1.51e-15

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


The actual alignment was detected with superfamily member COG3593:

Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 77.73  E-value: 1.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   4 QIVINNIQhiGYAELDVDLNaSGIICIVGKNGVGKTTLIKAI---LNLKSADTFSRTaspgIFKANSSMRCTygENSYEF 80
Cdd:COG3593    5 KIKIKNFR--SIKDLSIELS-DDLTVLVGENNSGKSSILEALrllLGPSSSRKFDEE----DFYLGDDPDLP--EIEIEL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  81 SFDSDINDLnsrspipeeLKSVIDVELPMPFGQRFNNYQNIMSADMD-----IRTALILGEYEVPVELISFLSDIyktNK 155
Cdd:COG3593   76 TFGSLLSRL---------LRLLLKEEDKEELEEALEELNEELKEALKalnelLSEYLKELLDGLDLELELSLDEL---ED 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 156 FNGLVEVSakggsyycipLDDDRYVREDHLSSGE--FFLISLYRKI-----KGRSKFIVIDEIDISLDAAAQAHLIGWLR 228
Cdd:COG3593  144 LLKSLSLR----------IEDGKELPLDRLGSGFqrLILLALLSALaelkrAPANPILLIEEPEAHLHPQAQRRLLKLLK 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 229 RFCtTEQVKVVFTTHSLALMRTLKDGELFYMEESEGKV---SVIPSSYNYIKSVLFGF----------KGWdryILTEDA 295
Cdd:COG3593  214 ELS-EKPNQVIITTHSPHLLSEVPLENIRRLRRDSGGTtstKLIDLDDEDLRKLLRYLgvtrsellfaRKV---ILVEGD 289

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489203608 296 MLKSLLEYvLANYCSGLFFSY--QIIHVGGGSNVVDLMRQNSTEGFfstpeNVISVLDGDQA 355
Cdd:COG3593  290 TEVILLPA-LARKLGKDLDEEgiSIIPVGGKSNLKPLAKLLKALGI-----PVAVLTDGDEA 345
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 4-355 1.51e-15

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 77.73  E-value: 1.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   4 QIVINNIQhiGYAELDVDLNaSGIICIVGKNGVGKTTLIKAI---LNLKSADTFSRTaspgIFKANSSMRCTygENSYEF 80
Cdd:COG3593    5 KIKIKNFR--SIKDLSIELS-DDLTVLVGENNSGKSSILEALrllLGPSSSRKFDEE----DFYLGDDPDLP--EIEIEL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  81 SFDSDINDLnsrspipeeLKSVIDVELPMPFGQRFNNYQNIMSADMD-----IRTALILGEYEVPVELISFLSDIyktNK 155
Cdd:COG3593   76 TFGSLLSRL---------LRLLLKEEDKEELEEALEELNEELKEALKalnelLSEYLKELLDGLDLELELSLDEL---ED 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 156 FNGLVEVSakggsyycipLDDDRYVREDHLSSGE--FFLISLYRKI-----KGRSKFIVIDEIDISLDAAAQAHLIGWLR 228
Cdd:COG3593  144 LLKSLSLR----------IEDGKELPLDRLGSGFqrLILLALLSALaelkrAPANPILLIEEPEAHLHPQAQRRLLKLLK 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 229 RFCtTEQVKVVFTTHSLALMRTLKDGELFYMEESEGKV---SVIPSSYNYIKSVLFGF----------KGWdryILTEDA 295
Cdd:COG3593  214 ELS-EKPNQVIITTHSPHLLSEVPLENIRRLRRDSGGTtstKLIDLDDEDLRKLLRYLgvtrsellfaRKV---ILVEGD 289

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489203608 296 MLKSLLEYvLANYCSGLFFSY--QIIHVGGGSNVVDLMRQNSTEGFfstpeNVISVLDGDQA 355
Cdd:COG3593  290 TEVILLPA-LARKLGKDLDEEgiSIIPVGGKSNLKPLAKLLKALGI-----PVAVLTDGDEA 345
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 27-249 6.70e-13

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 68.96  E-value: 6.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   27 IICIVGKNGVGKTTLIKAILNLKSADTFSRTASPGIFKANSSMRCTYG--------------------ENSYEFSFDSDI 86
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRNGGIGGIPSLlngidpkepiefeisefledGVRYRYGLDLER 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   87 NDLNSR-------------------------SPIPEELKSVIDVELPMPFG-QRFNNYQNIMSADMDIRT-------ALI 133
Cdd:pfam13304  81 EDVEEKlsskptllekrlllredseerepkfPPEAEELRLGLDVEERIELSlSELSDLISGLLLLSIISPlsfllllDEG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  134 LGEYEVPV--------------ELISFLSDIYKTNKFN-----------GLVEVSAKGGSYYCIPLDDDRYVREDHLSSG 188
Cdd:pfam13304 161 LLLEDWAVldlaadlalfpdlkELLQRLVRGLKLADLNlsdlgegieksLLVDDRLRERGLILLENGGGGELPAFELSDG 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489203608  189 E---FFLISLYRKIKGRSKFIVIDEIDISLDAAAQAHLIGWLRRfCTTEQVKVVFTTHSLALMR 249
Cdd:pfam13304 241 TkrlLALLAALLSALPKGGLLLIDEPESGLHPKLLRRLLELLKE-LSRNGAQLILTTHSPLLLD 303
ABC_NikE_OppD_transporters cd03257
ATP-binding cassette domain of nickel/oligopeptides specific transporters; The ABC transporter ...
 18-253 1.92e-06

ATP-binding cassette domain of nickel/oligopeptides specific transporters; The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.


Pssm-ID: 213224 [Multi-domain]  Cd Length: 228  Bit Score: 48.66  E-value: 1.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNLKSADTfsrtaspgifkanssmrctyGENSYEfsfDSDINDLNsrspipE 97
Cdd:cd03257   24 VSFSIKKGETLGLVGESGSGKSTLARAILGLLKPTS--------------------GSIIFD---GKDLLKLS------R 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  98 ELKSVIDVELPMPFgqrfnnyQNIMSA---DMDIRTALIlgeyevpvELISFLSDIYKTNKFNGLVEVSAKGgsyycIPL 174
Cdd:cd03257   75 RLRKIRRKEIQMVF-------QDPMSSlnpRMTIGEQIA--------EPLRIHGKLSKKEARKEAVLLLLVG-----VGL 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 175 DD---DRYVREdhLSSGEFFLISLYRKIKGRSKFIVIDEIDISLDAAAQAHLIGWLRRFCTTEQVKVVFTTHSLALMRTL 251
Cdd:cd03257  135 PEevlNRYPHE--LSGGQRQRVAIARALALNPKLLIADEPTSALDVSVQAQILDLLKKLQEELGLTLLFITHDLGVVAKI 212


                 ..
gi 489203608 252 KD 253
Cdd:cd03257  213 AD 214
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 26-48 1.12e-03

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 39.28  E-value: 1.12e-03
                           10        20
                   ....*....|....*....|...
gi 489203608    26 GIICIVGKNGVGKTTLIKAILNL 48
Cdd:smart00382   3 EVILIVGPPGSGKTTLARALARE 25
modC PRK11144
molybdenum ABC transporter ATP-binding protein ModC;
5-52 6.39e-03

molybdenum ABC transporter ATP-binding protein ModC;


Pssm-ID: 182993 [Multi-domain]  Cd Length: 352  Bit Score: 38.70  E-value: 6.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 489203608   5 IVINNIQHIGYAELDVD--LNASGIICIVGKNGVGKTTLIKAILNLKSAD 52
Cdd:PRK11144   2 LELNFKQQLGDLCLTVNltLPAQGITAIFGRSGAGKTSLINAISGLTRPQ 51
 
Name Accession Description Interval E-value
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 4-355 1.51e-15

Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM domains [Replication, recombination and repair];


Pssm-ID: 442812 [Multi-domain]  Cd Length: 359  Bit Score: 77.73  E-value: 1.51e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   4 QIVINNIQhiGYAELDVDLNaSGIICIVGKNGVGKTTLIKAI---LNLKSADTFSRTaspgIFKANSSMRCTygENSYEF 80
Cdd:COG3593    5 KIKIKNFR--SIKDLSIELS-DDLTVLVGENNSGKSSILEALrllLGPSSSRKFDEE----DFYLGDDPDLP--EIEIEL 75

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  81 SFDSDINDLnsrspipeeLKSVIDVELPMPFGQRFNNYQNIMSADMD-----IRTALILGEYEVPVELISFLSDIyktNK 155
Cdd:COG3593   76 TFGSLLSRL---------LRLLLKEEDKEELEEALEELNEELKEALKalnelLSEYLKELLDGLDLELELSLDEL---ED 143

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 156 FNGLVEVSakggsyycipLDDDRYVREDHLSSGE--FFLISLYRKI-----KGRSKFIVIDEIDISLDAAAQAHLIGWLR 228
Cdd:COG3593  144 LLKSLSLR----------IEDGKELPLDRLGSGFqrLILLALLSALaelkrAPANPILLIEEPEAHLHPQAQRRLLKLLK 213

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 229 RFCtTEQVKVVFTTHSLALMRTLKDGELFYMEESEGKV---SVIPSSYNYIKSVLFGF----------KGWdryILTEDA 295
Cdd:COG3593  214 ELS-EKPNQVIITTHSPHLLSEVPLENIRRLRRDSGGTtstKLIDLDDEDLRKLLRYLgvtrsellfaRKV---ILVEGD 289

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 489203608 296 MLKSLLEYvLANYCSGLFFSY--QIIHVGGGSNVVDLMRQNSTEGFfstpeNVISVLDGDQA 355
Cdd:COG3593  290 TEVILLPA-LARKLGKDLDEEgiSIIPVGGKSNLKPLAKLLKALGI-----PVAVLTDGDEA 345
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 27-249 6.70e-13

AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being of the abortive phage resistance system, in which case the family would be acting as the toxin for a type IV toxin-antitoxin resistance system.


Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 68.96  E-value: 6.70e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   27 IICIVGKNGVGKTTLIKAILNLKSADTFSRTASPGIFKANSSMRCTYG--------------------ENSYEFSFDSDI 86
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRNGGIGGIPSLlngidpkepiefeisefledGVRYRYGLDLER 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608   87 NDLNSR-------------------------SPIPEELKSVIDVELPMPFG-QRFNNYQNIMSADMDIRT-------ALI 133
Cdd:pfam13304  81 EDVEEKlsskptllekrlllredseerepkfPPEAEELRLGLDVEERIELSlSELSDLISGLLLLSIISPlsfllllDEG 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  134 LGEYEVPV--------------ELISFLSDIYKTNKFN-----------GLVEVSAKGGSYYCIPLDDDRYVREDHLSSG 188
Cdd:pfam13304 161 LLLEDWAVldlaadlalfpdlkELLQRLVRGLKLADLNlsdlgegieksLLVDDRLRERGLILLENGGGGELPAFELSDG 240

                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 489203608  189 E---FFLISLYRKIKGRSKFIVIDEIDISLDAAAQAHLIGWLRRfCTTEQVKVVFTTHSLALMR 249
Cdd:pfam13304 241 TkrlLALLAALLSALPKGGLLLIDEPESGLHPKLLRRLLELLKE-LSRNGAQLILTTHSPLLLD 303
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
17-269 5.14e-10

ATPase/GTPase, AAA15 family [General function prediction only];


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 60.44  E-value: 5.14e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  17 ELDVDLNASG-----IICIVGKNGVGKTTLIKAILNLKSADTFSRTASPGI---FKANSSMR---------CTYGENSYE 79
Cdd:COG1106   16 ELTLSMVASGlrllrVNLIYGANASGKSNLLEALYFLRNLVLNSSQPGDKLvepFLLDSESKnepsefeilFLLDGVRYE 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  80 FSFDsdindLNSRSPIPEELK--SVIDVELPMPFGQRFNNYQNIMSADMDIRTALILGEYEVPV--ELISFLSDI----- 150
Cdd:COG1106   96 YGFE-----LDKERIISEWLYflSTAAQLNVPLLSPLYDWFDNNISLDTSSDGLTLLLKEDESLkeELLELLKIAdpgie 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 151 ---YKTNKFNGLVEVSAK---GGSYYCIPLDDdryvredhLSSGE---FFLISLYRKIKGRSKFIVIDEIDISLDAAAQA 221
Cdd:COG1106  171 dieVEEEEIEDLVERKLIfkhKGGNVPLPLSE--------ESDGTkrlLALAGALLDALAKGGVLLIDEIEASLHPSLLR 242

                        250       260       270       280       290
                 ....*....|....*....|....*....|....*....|....*....|..
gi 489203608 222 HLIGWLRRFCTTEQVKVVFTTHSLALMRTLKDG----ELFYMEESEGKVSVI 269
Cdd:COG1106  243 KLLKLFLDLANKNNAQLIFTTHSTELLDAFLELlrrdQIWFVEKDKDGASEL 294
ABC_NikE_OppD_transporters cd03257
ATP-binding cassette domain of nickel/oligopeptides specific transporters; The ABC transporter ...
 18-253 1.92e-06

ATP-binding cassette domain of nickel/oligopeptides specific transporters; The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE). The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE). The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis. The molecular mechanism of nickel uptake in many bacteria and most archaea is not known. Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides. The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.


Pssm-ID: 213224 [Multi-domain]  Cd Length: 228  Bit Score: 48.66  E-value: 1.92e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNLKSADTfsrtaspgifkanssmrctyGENSYEfsfDSDINDLNsrspipE 97
Cdd:cd03257   24 VSFSIKKGETLGLVGESGSGKSTLARAILGLLKPTS--------------------GSIIFD---GKDLLKLS------R 74

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  98 ELKSVIDVELPMPFgqrfnnyQNIMSA---DMDIRTALIlgeyevpvELISFLSDIYKTNKFNGLVEVSAKGgsyycIPL 174
Cdd:cd03257   75 RLRKIRRKEIQMVF-------QDPMSSlnpRMTIGEQIA--------EPLRIHGKLSKKEARKEAVLLLLVG-----VGL 134

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 175 DD---DRYVREdhLSSGEFFLISLYRKIKGRSKFIVIDEIDISLDAAAQAHLIGWLRRFCTTEQVKVVFTTHSLALMRTL 251
Cdd:cd03257  135 PEevlNRYPHE--LSGGQRQRVAIARALALNPKLLIADEPTSALDVSVQAQILDLLKKLQEELGLTLLFITHDLGVVAKI 212


                 ..
gi 489203608 252 KD 253
Cdd:cd03257  213 AD 214
COG4637 COG4637
Predicted ATPase [General function prediction only];
19-270 4.29e-06

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 48.77  E-value: 4.29e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  19 DVDLNASGIICIVGKNGVGKTTLIKAILNLKSA------DTFSR--------TASPGIFKANSSMRCTYGE-----NSYE 79
Cdd:COG4637   15 DLELPLGPLTVLIGANGSGKSNLLDALRFLSDAargglqDALARrggleellWRGPRTITEPIRLELEFAEederdLRYE 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  80 FSFDSDINDLNSRspIPEELKSVIDVELPMPF------GQRF-NNYQNIMSADMDIRTALILGEYEVPVELISFLSD--- 149
Cdd:COG4637   95 LELGLPEPGGRPE--VKEERLWLKRGSGGRPFldfrpkGRAVgGEPERLDSPESLLSQLGDPERFPELRALREALRSwrf 172

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 150 ---------------------------------IYKTNK----------------FNGLVEVSAKGGSYYcipL-----D 175
Cdd:COG4637  173 ydfhpaplrqpqpagrtpvlapdgsnlaavlatLRETHPerferilealrdafpgFEDIEVEPDEDGRVL---LefrekG 249

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 176 DDRYVREDHLSSGE--FF--LISLYRKIKGRskFIVIDEIDISLDAAAQAHLIGWLRRFCTTEQvkVVFTTHSLALMRTL 251
Cdd:COG4637  250 LDRPFPARELSDGTlrFLalLAALLSPRPPP--LLCIEEPENGLHPDLLPALAELLREASERTQ--VIVTTHSPALLDAL 325

                        330       340
                 ....*....|....*....|
gi 489203608 252 KDGELFYME-ESEGKVSVIP 270
Cdd:COG4637  326 EPEEVLVLErEDDGETRIRR 345
AAA_23 pfam13476
AAA domain;
5-45 4.70e-06

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 47.11  E-value: 4.70e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 489203608    5 IVINNIQhiGYAELDVDLNaSGIICIVGKNGVGKTTLIKAI 45
Cdd:pfam13476   1 LTIENFR--SFRDQTIDFS-KGLTLITGPNGSGKTTILDAI 38
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 18-48 1.30e-05

ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 44.93  E-value: 1.30e-05
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNL 48
Cdd:cd00267   18 VSLTLKAGEIVALVGPNGSGKSTLLRAIAGL 48
ABC_DR_subfamily_A cd03230
ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily ...
 4-52 1.49e-05

ATP-binding cassette domain of the drug resistance transporter and related proteins, subfamily A; This family of ATP-binding proteins belongs to a multi-subunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity. In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins. Eukaryotic systems of the ABCA subfamily display ABC domains that are quite similar to this family. The ATP-binding domain shows the highest similarity between all members of the ABC transporter family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213197 [Multi-domain]  Cd Length: 173  Bit Score: 45.08  E-value: 1.49e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 489203608   4 QIVINNIqhigyaelDVDLNASGIICIVGKNGVGKTTLIKAILNLKSAD 52
Cdd:cd03230   13 KTALDDI--------SLTVEKGEIYGLLGPNGAGKTTLIKIILGLLKPD 53
ABC_TM1139_LivF_branched cd03224
ATP-binding cassette domain of branched-chain amino acid transporter; LivF (TM1139) is part of ...
 12-48 2.33e-05

ATP-binding cassette domain of branched-chain amino acid transporter; LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids. The E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ). ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.


Pssm-ID: 213191 [Multi-domain]  Cd Length: 222  Bit Score: 45.50  E-value: 2.33e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 489203608  12 HIGYAEL----DVDL--NASGIICIVGKNGVGKTTLIKAILNL 48
Cdd:cd03224    7 NAGYGKSqilfGVSLtvPEGEIVALLGRNGAGKTTLLKTIMGL 49
ABCF_EF-3 cd03221
ATP-binding cassette domain of elongation factor 3, subfamily F; Elongation factor 3 (EF-3) is ...
 18-62 8.55e-05

ATP-binding cassette domain of elongation factor 3, subfamily F; Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth. EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site. The reaction requires ATP hydrolysis. EF-3 contains two ATP nucleotide binding sequence (NBS) motifs. NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.


Pssm-ID: 213188 [Multi-domain]  Cd Length: 144  Bit Score: 42.44  E-value: 8.55e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNLKSADTFSRTASPGI 62
Cdd:cd03221   19 ISLTINPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTV 63
ABC_Metallic_Cations cd03235
ATP-binding cassette domain of the metal-type transporters; This family includes transporters ...
 18-48 8.84e-05

ATP-binding cassette domain of the metal-type transporters; This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc. The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor. The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri. Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.


Pssm-ID: 213202 [Multi-domain]  Cd Length: 213  Bit Score: 43.68  E-value: 8.84e-05
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNL 48
Cdd:cd03235   18 VSFEVKPGEFLAIVGPNGAGKSTLLKAILGL 48
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
15-45 1.48e-04

Recombinational DNA repair ATPase RecF [Replication, recombination and repair];


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 43.60  E-value: 1.48e-04
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489203608  15 YAELDVDLNAsGIICIVGKNGVGKTTLIKAI 45
Cdd:COG1195   13 YESLELEFSP-GINVLVGPNGQGKTNLLEAI 42
ABC_tran pfam00005
ABC transporter; ABC transporters for a large family of proteins responsible for translocation ...
 18-48 2.09e-04

ABC transporter; ABC transporters for a large family of proteins responsible for translocation of a variety of compounds across biological membranes. ABC transporters are the largest family of proteins in many completely sequenced bacteria. ABC transporters are composed of two copies of this domain and two copies of a transmembrane domain pfam00664. These four domains may belong to a single polypeptide or belong in different polypeptide chains.


Pssm-ID: 394964 [Multi-domain]  Cd Length: 150  Bit Score: 41.48  E-value: 2.09e-04
                          10        20        30
                  ....*....|....*....|....*....|.
gi 489203608   18 LDVDLNASGIICIVGKNGVGKTTLIKAILNL 48
Cdd:pfam00005   4 VSLTLNPGEILALVGPNGAGKSTLLKLIAGL 34
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 158-253 3.23e-04

ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules. The nucleotide-binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213179 [Multi-domain]  Cd Length: 157  Bit Score: 41.08  E-value: 3.23e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608 158 GLVEVSAKGGSYYCIPLDDDRYVREDHLSSGEFFLISLYRKIKGRSKFIVIDEIDISLDAAAQAHLIGWLRRFCtTEQVK 237
Cdd:cd00267   54 GEILIDGKDIAKLPLEELRRRIGYVPQLSGGQRQRVALARALLLNPDLLLLDEPTSGLDPASRERLLELLRELA-EEGRT 132

                         90
                 ....*....|....*.
gi 489203608 238 VVFTTHSLALMRTLKD 253
Cdd:cd00267  133 VIIVTHDPELAELAAD 148
AAA_13 pfam13166
AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA ...
 178-303 5.16e-04

AAA domain; This family of domains contain a P-loop motif that is characteriztic of the AAA superfamily. Many of the proteins in this family are conjugative transfer proteins. This family includes the PrrC protein that is thought to be the active component of the anticodon nuclease.


Pssm-ID: 463796 [Multi-domain]  Cd Length: 712  Bit Score: 42.36  E-value: 5.16e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  178 RYVRED------HLSSGE-------FFLISLYRKI--KGRSKFIVIDEIDISLDAAAQAHLIGWLRRFCTTEQVKVVF-T 241
Cdd:pfam13166 487 RIIRKGgsqaaeTLSEGErtaiaflYFLKSLKDSDndIGKDKIVVIDDPVSSLDSNHLFIVFSLIRTRTEKTNAKQVFiL 566

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 489203608  242 THSLALMRTLK---------DGELFYMEESEGKVSVIP----------SSYNYI-KSVLFGFKGWDRYILTEDAMLKsLL 301
Cdd:pfam13166 567 THNFYFFKEVTnwfdnkrkkKNERFYILKKDGNSSKIKeydrllnpieSEYHYLfKEVYRASENDDHFYGMPNVARR-IL 645


                  ..
gi 489203608  302 EY 303
Cdd:pfam13166 646 ET 647
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
4-45 1.02e-03

DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 40.38  E-value: 1.02e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 489203608   4 QIVINNIQhiGYAELD-VDLNAsGIICIVGKNGVGKTTLIKAI 45
Cdd:COG0419    4 RLRLENFR--SYRDTEtIDFDD-GLNLIVGPNGAGKSTILEAI 43
AAA smart00382
ATPases associated with a variety of cellular activities; AAA - ATPases associated with a ...
 26-48 1.12e-03

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


Pssm-ID: 214640 [Multi-domain]  Cd Length: 148  Bit Score: 39.28  E-value: 1.12e-03
                           10        20
                   ....*....|....*....|...
gi 489203608    26 GIICIVGKNGVGKTTLIKAILNL 48
Cdd:smart00382   3 EVILIVGPPGSGKTTLARALARE 25
Uup COG0488
ATPase components of ABC transporters with duplicated ATPase domains [General function ...
 18-46 1.56e-03

ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only];


Pssm-ID: 440254 [Multi-domain]  Cd Length: 520  Bit Score: 40.82  E-value: 1.56e-03
                         10        20
                 ....*....|....*....|....*....
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAIL 46
Cdd:COG0488  334 LSLRIDRGDRIGLIGPNGAGKSTLLKLLA 362
ABC_BcrA_bacitracin_resist cd03268
ATP-binding cassette domain of the bacitracin-resistance transporter; The BcrA subfamily ...
 18-53 1.60e-03

ATP-binding cassette domain of the bacitracin-resistance transporter; The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance. Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis. The synthesis of bacitracin is non-ribosomally catalyzed by a multi-enzyme complex BcrABC. Bacitracin has potent antibiotic activity against gram-positive bacteria. The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin. The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC. B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.


Pssm-ID: 213235 [Multi-domain]  Cd Length: 208  Bit Score: 39.51  E-value: 1.60e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNLKSADT 53
Cdd:cd03268   19 ISLHVKKGEIYGFLGPNGAGKTTTMKIILGLIKPDS 54
MK0520 COG2401
ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction ...
 2-48 2.18e-03

ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only];


Pssm-ID: 441957 [Multi-domain]  Cd Length: 222  Bit Score: 39.56  E-value: 2.18e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 489203608   2 NFQIVINNIQHIGYAELDVDLNASGIICIVGKNGVGKTTLIKAILNL 48
Cdd:COG2401   33 AFGVELRVVERYVLRDLNLEIEPGEIVLIVGASGSGKSTLLRLLAGA 79
Uup COG0488
ATPase components of ABC transporters with duplicated ATPase domains [General function ...
 28-62 3.00e-03

ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only];


Pssm-ID: 440254 [Multi-domain]  Cd Length: 520  Bit Score: 39.66  E-value: 3.00e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 489203608  28 ICIVGKNGVGKTTLIKAILNLKSADTFSRTASPGI 62
Cdd:COG0488   27 IGLVGRNGAGKSTLLKILAGELEPDSGEVSIPKGL 61
ABC_cobalt_CbiO_domain2 cd03226
Second domain of the ATP-binding cassette component of cobalt transport system; Domain II of ...
 18-45 4.36e-03

Second domain of the ATP-binding cassette component of cobalt transport system; Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota. The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed. The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways. Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO. Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.


Pssm-ID: 213193 [Multi-domain]  Cd Length: 205  Bit Score: 38.39  E-value: 4.36e-03
                         10        20
                 ....*....|....*....|....*...
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAI 45
Cdd:cd03226   19 LSLDLYAGEIIALTGKNGAGKTTLAKIL 46
CcmA COG1131
ABC-type multidrug transport system, ATPase component [Defense mechanisms];
19-48 4.38e-03

ABC-type multidrug transport system, ATPase component [Defense mechanisms];


Pssm-ID: 440746 [Multi-domain]  Cd Length: 236  Bit Score: 38.51  E-value: 4.38e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 489203608  19 DVDLN-ASG-IICIVGKNGVGKTTLIKAILNL 48
Cdd:COG1131   18 GVSLTvEPGeIFGLLGPNGAGKTTTIRMLLGL 49
modC PRK11144
molybdenum ABC transporter ATP-binding protein ModC;
5-52 6.39e-03

molybdenum ABC transporter ATP-binding protein ModC;


Pssm-ID: 182993 [Multi-domain]  Cd Length: 352  Bit Score: 38.70  E-value: 6.39e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 489203608   5 IVINNIQHIGYAELDVD--LNASGIICIVGKNGVGKTTLIKAILNLKSAD 52
Cdd:PRK11144   2 LELNFKQQLGDLCLTVNltLPAQGITAIFGRSGAGKTSLINAISGLTRPQ 51
ABCC_MRP_Like cd03228
ATP-binding cassette domain of multidrug resistance protein-like transporters; The MRP ...
 18-48 7.00e-03

ATP-binding cassette domain of multidrug resistance protein-like transporters; The MRP (Multidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export. They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins. The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities. The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD). ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213195 [Multi-domain]  Cd Length: 171  Bit Score: 37.36  E-value: 7.00e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489203608  18 LDVDLNASGIICIVGKNGVGKTTLIKAILNL 48
Cdd:cd03228   21 VSLTIKPGEKVAIVGPSGSGKSTLLKLLLRL 51
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 15-45 8.86e-03

ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage. When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task. This CD represents the nucleotide binding domain of RecF. RecF belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family. ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.


Pssm-ID: 213209 [Multi-domain]  Cd Length: 270  Bit Score: 37.66  E-value: 8.86e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 489203608  15 YAELDVDLNAsGIICIVGKNGVGKTTLIKAI 45
Cdd:cd03242   12 YAELELEFEP-GVTVLVGENAQGKTNLLEAI 41
 
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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