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Conserved domains on  [gi|1236078616|ref|WP_094884500|]
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MULTISPECIES: AAA family ATPase [Salmonella]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4938 super family cl34842
Predicted ATPase [General function prediction only];
334-534 4.91e-23

Predicted ATPase [General function prediction only];


The actual alignment was detected with superfamily member COG4938:

Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 98.89  E-value: 4.91e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 334 SAWDKLCLSQQNDSDLINKVSDWFSHrdklntnynIVRGrKFDIKVDpqfLDLKDNVFFCKIDSSQmLFPNQVGVGLTQI 413
Cdd:COG4938    84 AELENLEILDDKSKELLEQVEEWLEK---------IFPG-KVEVDAS---SDLVRLVFRPSGNGKR-IPLSNVGSGVSEL 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 414 APLIIA-ANIVQDG-LIAIEQPELHIHPALQLAVGDLF-THYPSDVKrpmFLVETHSEHILLRIlkRIRQTTDKELPesn 490
Cdd:COG4938   150 LPILLAlLSAAKPGsLLIIEEPEAHLHPKAQSALAELLaELANSGVQ---VIIETHSDYILNGL--RNLIKEGKLLD--- 221

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1236078616 491 ypvkPDFISVIVFEDNNGSTVTRKIDITDDGDFKQkWPKGFFEE 534
Cdd:COG4938   222 ----PDDVAVYFFERDGGGSELRRIEIDENGIISD-WPDGFFDE 260
COG4637 super family cl34796
Predicted ATPase [General function prediction only];
2-100 2.78e-12

Predicted ATPase [General function prediction only];


The actual alignment was detected with superfamily member COG4637:

Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 68.42  E-value: 2.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   2 KLTKLVLENFRSFKKrQEIDFSPVTLLLGPNSAGKTTILIALFYLQQILDREQCDPIyleamgnRRIDGFRSLVHNGD-- 79
Cdd:COG4637     1 MITRIRIKNFKSLRD-LELPLGPLTVLIGANGSGKSNLLDALRFLSDAARGGLQDAL-------ARRGGLEELLWRGPrt 72

                          90       100
                  ....*....|....*....|.
gi 1236078616  80 LNNVITIGIGFDPEQTIGVEY 100
Cdd:COG4637    73 ITEPIRLELEFAEEDERDLRY 93
AAA_21 super family cl37854
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-272 3.95e-03

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.


The actual alignment was detected with superfamily member pfam13304:

Pssm-ID: 433102 [Multi-domain]  Cd Length: 303  Bit Score: 39.30  E-value: 3.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616  25 VTLLLGPNSAGKTTILIALFYLQQILDREQcdPIYLEAMGNRRIDGFRSLVHNGDLNNVITIGIGFDPEQTIGVEY---- 100
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVI--GLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYgldl 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 101 -----KTYLEELGDVFDIHFIKMRDIADETEKVYVEFKIawsQLHRAAYIKSYAVSINNEFIGELSNDeytksslvnRLN 175
Cdd:pfam13304  79 eredvEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEE---LRLGLDVEERIELSLSELSDLISGLL---------LLS 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 176 FTHPLllpVDYNLWLEAIGKEGLDTIV-SEFEMSLNDLIPGLDRNKSGATErvRFVDYIFEEDKEKPMFPVFLKTKIGAL 254
Cdd:pfam13304 147 IISPL---SFLLLLDEGLLLEDWAVLDlAADLALFPDLKELLQRLVRGLKL--ADLNLSDLGEGIEKSLLVDDRLRERGL 221

                         250
                  ....*....|....*...
gi 1236078616 255 PQLGRTVDTNLKIFDISE 272
Cdd:pfam13304 222 ILLENGGGGELPAFELSD 239
 
Name Accession Description Interval E-value
COG4938 COG4938
Predicted ATPase [General function prediction only];
334-534 4.91e-23

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 98.89  E-value: 4.91e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 334 SAWDKLCLSQQNDSDLINKVSDWFSHrdklntnynIVRGrKFDIKVDpqfLDLKDNVFFCKIDSSQmLFPNQVGVGLTQI 413
Cdd:COG4938    84 AELENLEILDDKSKELLEQVEEWLEK---------IFPG-KVEVDAS---SDLVRLVFRPSGNGKR-IPLSNVGSGVSEL 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 414 APLIIA-ANIVQDG-LIAIEQPELHIHPALQLAVGDLF-THYPSDVKrpmFLVETHSEHILLRIlkRIRQTTDKELPesn 490
Cdd:COG4938   150 LPILLAlLSAAKPGsLLIIEEPEAHLHPKAQSALAELLaELANSGVQ---VIIETHSDYILNGL--RNLIKEGKLLD--- 221

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1236078616 491 ypvkPDFISVIVFEDNNGSTVTRKIDITDDGDFKQkWPKGFFEE 534
Cdd:COG4938   222 ----PDDVAVYFFERDGGGSELRRIEIDENGIISD-WPDGFFDE 260
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-100 2.78e-12

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 68.42  E-value: 2.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   2 KLTKLVLENFRSFKKrQEIDFSPVTLLLGPNSAGKTTILIALFYLQQILDREQCDPIyleamgnRRIDGFRSLVHNGD-- 79
Cdd:COG4637     1 MITRIRIKNFKSLRD-LELPLGPLTVLIGANGSGKSNLLDALRFLSDAARGGLQDAL-------ARRGGLEELLWRGPrt 72

                          90       100
                  ....*....|....*....|.
gi 1236078616  80 LNNVITIGIGFDPEQTIGVEY 100
Cdd:COG4637    73 ITEPIRLELEFAEEDERDLRY 93
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-45 1.22e-11

ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 64.17  E-value: 1.22e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1236078616   3 LTKLVLENFRSFKKRQEIDF-SPVTLLLGPNSAGKTTILIALFY 45
Cdd:cd03240     1 IDKLSIRNIRSFHERSEIEFfSPLTLIVGQNGAGKTTIIEALKY 44
recF PRK00064
recombination protein F; Reviewed
 1-46 2.43e-09

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 59.02  E-value: 2.43e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1236078616   1 MKLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:PRK00064    1 MYLTRLSLTDFRNYE-ELDLELSPgVNVLVGENGQGKTNLLEAIYLL 46
AAA_23 pfam13476
AAA domain;
6-45 5.17e-08

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 53.27  E-value: 5.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1236078616   6 LVLENFRSFKKrQEIDFS-PVTLLLGPNSAGKTTILIALFY 45
Cdd:pfam13476   1 LTIENFRSFRD-QTIDFSkGLTLITGPNGSGKTTILDAIKL 40
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-471 1.03e-07

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


Pssm-ID: 433011 [Multi-domain]  Cd Length: 392  Bit Score: 54.14  E-value: 1.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   1 MKLTKLVLENFRSFKKrQEIDFSP-VTLLLGPNSAGKTTILIAL-FYLQQILDREQCDPIYLEAMGNRRID-GFRSLVHN 77
Cdd:pfam13175   1 MKIKSIIIKNFRCLKD-TEIDLDEdLTVLIGKNNSGKSSILEALdIFLNNKEKFFEDDFLVLYLKDVIKIDkEDLNIFEN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616  78 GDLNNVITIGIgfdpeqtigveykTYLEELGDVFDIHFIKMRDIADETEKVYVEFKiawsqlhrAAYIKSYAVSINNEFI 157
Cdd:pfam13175  80 ISFSIDIEIDV-------------EFLLILFGYLEIKKKYLCLASKGKAKEYEKTL--------HPKGANKADLLLELKI 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 158 GELSNDEYTKSSLVNRLNFTHPLLLPVDynlwleaigKEGLDTIVSEFEMSLNDLIPGLDRNKSGATERVRFVDYIFEED 237
Cdd:pfam13175 139 SDLKKYLKQFKIYIYNNYYLDEKKNVFD---------KKSKYELPSLKEEFLNSEKEEIKVDKEDLKKLINELEKSINYH 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 238 KEKPMFPVFLKtkigALPQLGRTVDTNLKifDISEPVeyfnrdiitrvltqvftspLDKLNDYLKASVSIGPLRIIPDSS 317
Cdd:pfam13175 210 ENVLENLQIKK----LLISADRNASDEDS--EKINSL-------------------LGALKQRIFEEALQEELELTEKLK 264

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 318 FTPNPYPEQDGwfdgtsawdklCLSQQNDSDLINKVSDWfshrdkLNTNYNIVRGRKFDIKVDPQFLDLKDNvffckids 397
Cdd:pfam13175 265 ETQNKLKEIDK-----------TLAEELKNILFKKIDKL------KDFGYPPFLNPEIEIKKDDEDLPLNKN-------- 319

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 398 sqmlfpnqvGVGLTQIAPLII---------AANIVQDGLIAIEQPELHIHPALQLAVGDLFTHYPSDVKRpMFLVETHSE 468
Cdd:pfam13175 320 ---------GSGVQRLILLIFfiaeaerkeDEIEEKNVILAIEEPEAHLHPQAQRVLIKLLKELANDNKT-QVIITTHSP 389


                  ...
gi 1236078616 469 HIL 471
Cdd:pfam13175 390 HII 392
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-46 5.33e-06

recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273173 [Multi-domain]  Cd Length: 365  Bit Score: 48.89  E-value: 5.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1236078616   1 MKLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:TIGR00611   1 MYLSRLELTDFRNYD-AVDLELSPgVNVIVGPNGQGKTNLLEAIYYL 46
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-272 3.95e-03

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: 39.30  E-value: 3.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616  25 VTLLLGPNSAGKTTILIALFYLQQILDREQcdPIYLEAMGNRRIDGFRSLVHNGDLNNVITIGIGFDPEQTIGVEY---- 100
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVI--GLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYgldl 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 101 -----KTYLEELGDVFDIHFIKMRDIADETEKVYVEFKIawsQLHRAAYIKSYAVSINNEFIGELSNDeytksslvnRLN 175
Cdd:pfam13304  79 eredvEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEE---LRLGLDVEERIELSLSELSDLISGLL---------LLS 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 176 FTHPLllpVDYNLWLEAIGKEGLDTIV-SEFEMSLNDLIPGLDRNKSGATErvRFVDYIFEEDKEKPMFPVFLKTKIGAL 254
Cdd:pfam13304 147 IISPL---SFLLLLDEGLLLEDWAVLDlAADLALFPDLKELLQRLVRGLKL--ADLNLSDLGEGIEKSLLVDDRLRERGL 221

                         250
                  ....*....|....*...
gi 1236078616 255 PQLGRTVDTNLKIFDISE 272
Cdd:pfam13304 222 ILLENGGGGELPAFELSD 239
 
Name Accession Description Interval E-value
COG4938 COG4938
Predicted ATPase [General function prediction only];
334-534 4.91e-23

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 98.89  E-value: 4.91e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 334 SAWDKLCLSQQNDSDLINKVSDWFSHrdklntnynIVRGrKFDIKVDpqfLDLKDNVFFCKIDSSQmLFPNQVGVGLTQI 413
Cdd:COG4938    84 AELENLEILDDKSKELLEQVEEWLEK---------IFPG-KVEVDAS---SDLVRLVFRPSGNGKR-IPLSNVGSGVSEL 149

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 414 APLIIA-ANIVQDG-LIAIEQPELHIHPALQLAVGDLF-THYPSDVKrpmFLVETHSEHILLRIlkRIRQTTDKELPesn 490
Cdd:COG4938   150 LPILLAlLSAAKPGsLLIIEEPEAHLHPKAQSALAELLaELANSGVQ---VIIETHSDYILNGL--RNLIKEGKLLD--- 221

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 1236078616 491 ypvkPDFISVIVFEDNNGSTVTRKIDITDDGDFKQkWPKGFFEE 534
Cdd:COG4938   222 ----PDDVAVYFFERDGGGSELRRIEIDENGIISD-WPDGFFDE 260
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-100 2.78e-12

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 68.42  E-value: 2.78e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   2 KLTKLVLENFRSFKKrQEIDFSPVTLLLGPNSAGKTTILIALFYLQQILDREQCDPIyleamgnRRIDGFRSLVHNGD-- 79
Cdd:COG4637     1 MITRIRIKNFKSLRD-LELPLGPLTVLIGANGSGKSNLLDALRFLSDAARGGLQDAL-------ARRGGLEELLWRGPrt 72

                          90       100
                  ....*....|....*....|.
gi 1236078616  80 LNNVITIGIGFDPEQTIGVEY 100
Cdd:COG4637    73 ITEPIRLELEFAEEDERDLRY 93
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-45 1.22e-11

ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains. The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence. This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.


Pssm-ID: 213207 [Multi-domain]  Cd Length: 204  Bit Score: 64.17  E-value: 1.22e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1236078616   3 LTKLVLENFRSFKKRQEIDF-SPVTLLLGPNSAGKTTILIALFY 45
Cdd:cd03240     1 IDKLSIRNIRSFHERSEIEFfSPLTLIVGQNGAGKTTIIEALKY 44
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-46 4.68e-11

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 62.33  E-value: 4.68e-11
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1236078616   2 KLTKLVLENFRSFKKRQEIDFS-PVTLLLGPNSAGKTTILIALFYL 46
Cdd:COG0419     1 KLLRLRLENFRSYRDTETIDFDdGLNLIVGPNGAGKSTILEAIRYA 46
COG4938 COG4938
Predicted ATPase [General function prediction only];
3-109 5.12e-10

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 60.37  E-value: 5.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   3 LTKLVLENFRSFKKrQEIDFSPVTLLLGPNSAGKTTILIALFYLQQIldreqcDPIYLEA-------MGNRRIDGFRSLV 75
Cdd:COG4938     1 IKSISIKNFGPFKE-AELELKPLTLLIGPNGSGKSTLIQALLLLLQS------NFIYLPAersgparLYPSLVRELSDLG 73

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1236078616  76 HNGD-----LNNVITIGIGFDPEQTIGVEYKTYLEELGD 109
Cdd:COG4938    74 SRGEytadfLAELENLEILDDKSKELLEQVEEWLEKIFP 112
recF PRK00064
recombination protein F; Reviewed
 1-46 2.43e-09

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 59.02  E-value: 2.43e-09
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1236078616   1 MKLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:PRK00064    1 MYLTRLSLTDFRNYE-ELDLELSPgVNVLVGENGQGKTNLLEAIYLL 46
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-43 3.42e-08

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: 55.39  E-value: 3.42e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1236078616   1 MKLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIAL 43
Cdd:COG3593     1 MKLEKIKIKNFRSIK-DLSIELSDdLTVLVGENNSGKSSILEAL 43
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-46 4.86e-08

Predicted ATP-binding protein involved in virulence [General function prediction only];


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 54.62  E-value: 4.86e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1236078616   1 MKLTKLVLENFRSFKKRqEIDFSP---VTLLLGPNSAGKTTILIALFYL 46
Cdd:COG3950     1 MRIKSLTIENFRGFEDL-EIDFDNpprLTVLVGENGSGKTTLLEAIALA 48
AAA_23 pfam13476
AAA domain;
6-45 5.17e-08

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 53.27  E-value: 5.17e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1236078616   6 LVLENFRSFKKrQEIDFS-PVTLLLGPNSAGKTTILIALFY 45
Cdd:pfam13476   1 LTIENFRSFRD-QTIDFSkGLTLITGPNGSGKTTILDAIKL 40
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-46 5.99e-08

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 54.78  E-value: 5.99e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1236078616   2 KLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:COG1195     1 RLKRLSLTNFRNYE-SLELEFSPgINVLVGPNGQGKTNLLEAIYLL 45
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-471 1.03e-07

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


Pssm-ID: 433011 [Multi-domain]  Cd Length: 392  Bit Score: 54.14  E-value: 1.03e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   1 MKLTKLVLENFRSFKKrQEIDFSP-VTLLLGPNSAGKTTILIAL-FYLQQILDREQCDPIYLEAMGNRRID-GFRSLVHN 77
Cdd:pfam13175   1 MKIKSIIIKNFRCLKD-TEIDLDEdLTVLIGKNNSGKSSILEALdIFLNNKEKFFEDDFLVLYLKDVIKIDkEDLNIFEN 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616  78 GDLNNVITIGIgfdpeqtigveykTYLEELGDVFDIHFIKMRDIADETEKVYVEFKiawsqlhrAAYIKSYAVSINNEFI 157
Cdd:pfam13175  80 ISFSIDIEIDV-------------EFLLILFGYLEIKKKYLCLASKGKAKEYEKTL--------HPKGANKADLLLELKI 138

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 158 GELSNDEYTKSSLVNRLNFTHPLLLPVDynlwleaigKEGLDTIVSEFEMSLNDLIPGLDRNKSGATERVRFVDYIFEED 237
Cdd:pfam13175 139 SDLKKYLKQFKIYIYNNYYLDEKKNVFD---------KKSKYELPSLKEEFLNSEKEEIKVDKEDLKKLINELEKSINYH 209

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 238 KEKPMFPVFLKtkigALPQLGRTVDTNLKifDISEPVeyfnrdiitrvltqvftspLDKLNDYLKASVSIGPLRIIPDSS 317
Cdd:pfam13175 210 ENVLENLQIKK----LLISADRNASDEDS--EKINSL-------------------LGALKQRIFEEALQEELELTEKLK 264

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 318 FTPNPYPEQDGwfdgtsawdklCLSQQNDSDLINKVSDWfshrdkLNTNYNIVRGRKFDIKVDPQFLDLKDNvffckids 397
Cdd:pfam13175 265 ETQNKLKEIDK-----------TLAEELKNILFKKIDKL------KDFGYPPFLNPEIEIKKDDEDLPLNKN-------- 319

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 398 sqmlfpnqvGVGLTQIAPLII---------AANIVQDGLIAIEQPELHIHPALQLAVGDLFTHYPSDVKRpMFLVETHSE 468
Cdd:pfam13175 320 ---------GSGVQRLILLIFfiaeaerkeDEIEEKNVILAIEEPEAHLHPQAQRVLIKLLKELANDNKT-QVIITTHSP 389


                  ...
gi 1236078616 469 HIL 471
Cdd:pfam13175 390 HII 392
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-52 1.76e-07

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 53.12  E-value: 1.76e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1236078616   3 LTKLVLENFRSFKKRQEIDF-------SPVTLLLGPNSAGKTTILIALFYLQQILDR 52
Cdd:COG1106     2 LISFSIENFRSFKDELTLSMvasglrlLRVNLIYGANASGKSNLLEALYFLRNLVLN 58
ABC_sbcCD cd03279
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ...
 1-79 3.45e-07

ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.


Pssm-ID: 213246 [Multi-domain]  Cd Length: 213  Bit Score: 51.12  E-value: 3.45e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616   1 MKLTKLVLENFRSFKKRQEIDFS-----PVTLLLGPNSAGKTTILIALFYlqqildreqcdPIYLEAMGNRRIDGFRSLV 75
Cdd:cd03279     1 MKPLKLELKNFGPFREEQVIDFTgldnnGLFLICGPTGAGKSTILDAITY-----------ALYGKTPRYGRQENLRSVF 69


                  ....
gi 1236078616  76 HNGD 79
Cdd:cd03279    70 APGE 73
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 2-46 9.11e-07

RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The SMC (structural maintenance of chromosomes) superfamily proteins have ATP-binding domains at the N- and C-termini, and two extended coiled-coil domains separated by a hinge in the middle. The eukaryotic SMC proteins form two kind of heterodimers: the SMC1/SMC3 and the SMC2/SMC4 types. These heterodimers constitute an essential part of higher order complexes, which are involved in chromatin and DNA dynamics. This family also includes the RecF and RecN proteins that are involved in DNA metabolism and recombination.


Pssm-ID: 426784 [Multi-domain]  Cd Length: 1161  Bit Score: 51.90  E-value: 9.11e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1236078616    2 KLTKLVLENFRSFKKRQEIDFSP-VTLLLGPNSAGKTTILIA-LFYL 46
Cdd:pfam02463    1 YLKRIEIEGFKSYAKTVILPFSPgFTAIVGPNGSGKSNILDAiLFVL 47
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-46 2.86e-06

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: 48.83  E-value: 2.86e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1236078616   3 LTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:cd03242     1 LKSLELRNFRNYA-ELELEFEPgVTVLVGENAQGKTNLLEAISLL 44
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-46 5.33e-06

recF protein; All proteins in this family for which functions are known are DNA binding proteins that assist the filamentation of RecA onto DNA for the initiation of recombination or recombinational repair. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 273173 [Multi-domain]  Cd Length: 365  Bit Score: 48.89  E-value: 5.33e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1236078616   1 MKLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:TIGR00611   1 MYLSRLELTDFRNYD-AVDLELSPgVNVIVGPNGQGKTNLLEAIYYL 46
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-54 1.43e-05

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 47.84  E-value: 1.43e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1236078616   1 MKLTKLVLENFRSFKkRQEIDFSP-VTLLLGPNSAGKTTILIALFY-LQQILDREQ 54
Cdd:COG4717     1 MKIKELEIYGFGKFR-DRTIEFSPgLNVIYGPNEAGKSTLLAFIRAmLLERLEKEA 55
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 1-45 1.44e-05

exonuclease SbcC; All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University). [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 129705 [Multi-domain]  Cd Length: 1042  Bit Score: 48.04  E-value: 1.44e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*...
gi 1236078616    1 MKLTKLVLENFRSFKKRQEIDFSPVT---LLLGPNSAGKTTILIALFY 45
Cdd:TIGR00618    1 MKPLRLTLKNFGSYKGTHTIDFTALGpifLICGKTGAGKTTLLDAITY 48
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 3-43 2.02e-05

ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function. Barmotin belongs to the SMC protein family. SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains. Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences. In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (formerly known as Rad18).


Pssm-ID: 213245 [Multi-domain]  Cd Length: 197  Bit Score: 45.53  E-value: 2.02e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1236078616   3 LTKLVLENFRSFKKRQEIDFSP-VTLLLGPNSAGKTTILIAL 43
Cdd:cd03278     1 LKKLELKGFKSFADKTTIPFPPgLTAIVGPNGSGKSNIIDAI 42
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 5-79 4.59e-05

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 46.60  E-value: 4.59e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616    5 KLVLENFRSFKKRQEIDFSP-VTLLLGPNSAGKTTILIALfylqqildreqcdpiyLEAMGNRRIDGFRS-----LVHNG 78
Cdd:TIGR02169    4 RIELENFKSFGKKKVIPFSKgFTVISGPNGSGKSNIGDAI----------------LFALGLSSSKAMRAerlsdLISNG 67


                   .
gi 1236078616   79 D 79
Cdd:TIGR02169   68 K 68
rad50 TIGR00606
rad50; All proteins in this family for which functions are known are involvedin recombination, ...
 2-46 9.01e-05

rad50; All proteins in this family for which functions are known are involvedin recombination, recombinational repair, and/or non-homologous end joining.They are components of an exonuclease complex with MRE11 homologs. This family is distantly related to the SbcC family of bacterial proteins.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).


Pssm-ID: 129694 [Multi-domain]  Cd Length: 1311  Bit Score: 45.42  E-value: 9.01e-05
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 1236078616    2 KLTKLVLENFRSF----KKRQEIDF-SPVTLLLGPNSAGKTTILIALFYL 46
Cdd:TIGR00606    2 KFLKMSILGVRSFgiedKDKQIIDFfSPLTILVGPNGAGKTTIIECLKYI 51
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-44 3.35e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 43.51  E-value: 3.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1236078616   1 MKLTKLVLENFRSFKKrQEIDFSP-VTLLLGPNSAGKTTILIALF 44
Cdd:PRK03918    1 MKIEELKIKNFRSHKS-SVVEFDDgINLIIGQNGSGKSSILEAIL 44
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 5-46 4.37e-04

ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems involved in cellular processes other than transport. These families are characterized by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2). No known transmembrane proteins or domains are associated with these proteins.


Pssm-ID: 213194 [Multi-domain]  Cd Length: 162  Bit Score: 41.19  E-value: 4.37e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1236078616   5 KLVLENFRSFKKRQEIDFSP--VTLLLGPNSAGKTTILIALFYL 46
Cdd:cd03227     1 KIVLGRFPSYFVPNDVTFGEgsLTIITGPNGSGKSTILDAIGLA 44
AAA_27 pfam13514
AAA domain; This domain is found in a number of double-strand DNA break proteins. This domain ...
 1-43 5.45e-04

AAA domain; This domain is found in a number of double-strand DNA break proteins. This domain contains a P-loop motif.


Pssm-ID: 433272 [Multi-domain]  Cd Length: 207  Bit Score: 41.39  E-value: 5.45e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1236078616   1 MKLTKLVLENFRSFKKRQeIDFSP----VTLLLGPNSAGKTTILIAL 43
Cdd:pfam13514   1 MRIRRLDLERYGPFTDRS-LDFPAggpdLHLIYGPNEAGKSTALRAI 46
AAA_29 pfam13555
P-loop containing region of AAA domain;
3-46 6.71e-04

P-loop containing region of AAA domain;


Pssm-ID: 433304 [Multi-domain]  Cd Length: 61  Bit Score: 37.96  E-value: 6.71e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1236078616   3 LTKLVLENFRSFKKRQ-EIDFSPVTLLLGPNSAGKTTILIALFYL 46
Cdd:pfam13555   1 LTRLQLINWGTFDGHTiPIDPRGNTLLTGPSGSGKSTLLDAIQTL 45
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
1-46 1.21e-03

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 41.82  E-value: 1.21e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 1236078616    1 MKLTKLVLENFRSFKKRQEIDFSP-VTLLLGPNSAGKTTILIALFYL 46
Cdd:COG4913      1 FRLQRLQLINWGTFDGVHTIDFDGrGTLLTGDNGSGKSTLLDAIQTL 47
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 427-524 2.93e-03

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: 39.99  E-value: 2.93e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 427 LIAIEQPELHIHPALQLAVGDLFTHYPSdvKRPMFLVETHSEHILLRIlkrirqttdkelpesnypvkpDFISVIVFEDN 506
Cdd:COG3593   190 ILLIEEPEAHLHPQAQRRLLKLLKELSE--KPNQVIITTHSPHLLSEV---------------------PLENIRRLRRD 246

                          90
                  ....*....|....*...
gi 1236078616 507 NGSTVTRKIDITDDGDFK 524
Cdd:COG3593   247 SGGTTSTKLIDLDDEDLR 264
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-272 3.95e-03

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: 39.30  E-value: 3.95e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616  25 VTLLLGPNSAGKTTILIALFYLQQILDREQcdPIYLEAMGNRRIDGFRSLVHNGDLNNVITIGIGFDPEQTIGVEY---- 100
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVI--GLTDERSRNGGIGGIPSLLNGIDPKEPIEFEISEFLEDGVRYRYgldl 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 101 -----KTYLEELGDVFDIHFIKMRDIADETEKVYVEFKIawsQLHRAAYIKSYAVSINNEFIGELSNDeytksslvnRLN 175
Cdd:pfam13304  79 eredvEEKLSSKPTLLEKRLLLREDSEEREPKFPPEAEE---LRLGLDVEERIELSLSELSDLISGLL---------LLS 146

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 176 FTHPLllpVDYNLWLEAIGKEGLDTIV-SEFEMSLNDLIPGLDRNKSGATErvRFVDYIFEEDKEKPMFPVFLKTKIGAL 254
Cdd:pfam13304 147 IISPL---SFLLLLDEGLLLEDWAVLDlAADLALFPDLKELLQRLVRGLKL--ADLNLSDLGEGIEKSLLVDDRLRERGL 221

                         250
                  ....*....|....*...
gi 1236078616 255 PQLGRTVDTNLKIFDISE 272
Cdd:pfam13304 222 ILLENGGGGELPAFELSD 239
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 382-471 4.16e-03

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: 39.30  E-value: 4.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1236078616 382 QFLDLKDNVFFCKIDSSQMLFPNQVGVGLTQIAPLIIA--ANIVQDGLIAIEQPELHIHPALQLAVGDLFTHYPSdvKRP 459
Cdd:pfam13304 213 DDRLRERGLILLENGGGGELPAFELSDGTKRLLALLAAllSALPKGGLLLIDEPESGLHPKLLRRLLELLKELSR--NGA 290

                          90
                  ....*....|..
gi 1236078616 460 MFLVETHSEHIL 471
Cdd:pfam13304 291 QLILTTHSPLLL 302
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 2-43 4.55e-03

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 40.04  E-value: 4.55e-03
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
gi 1236078616    2 KLTKLVLENFRSFKKRQEIDFSP-VTLLLGPNSAGKTTILIAL 43
Cdd:TIGR02168    1 RLKKLELAGFKSFADPTTINFDKgITGIVGPNGCGKSNIVDAI 43
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1-43 4.93e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 39.92  E-value: 4.93e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1236078616   1 MKLTKLVLENFRSFKKRQEIDFSP-VTLLLGPNSAGKTTILIAL 43
Cdd:COG1196     1 MRLKRLELAGFKSFADPTTIPFEPgITAIVGPNGSGKSNIVDAI 44
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 3-43 5.08e-03

The SMC head domain belongs to the ATP-binding cassette superfamily; The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms. SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair, and epigenetic silencing of gene expression.


Pssm-ID: 213206 [Multi-domain]  Cd Length: 178  Bit Score: 38.06  E-value: 5.08e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1236078616   3 LTKLVLENFRSFKKRQEIDFS-PVTLLLGPNSAGKTTILIAL 43
Cdd:cd03239     1 IKQITLKNFKSYRDETVVGGSnSFNAIVGPNGSGKSNIVDAI 42
 
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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