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Conserved domains on  [gi|327200670|pdb|3QKS|A]
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Chain A, DNA double-strand break repair rad50 ATPase

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK03918 super family cl35229
DNA double-strand break repair ATPase Rad50;
1-195 2.69e-81

DNA double-strand break repair ATPase Rad50;


The actual alignment was detected with superfamily member PRK03918:

Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 258.84  E-value: 2.69e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYW--PLRIKDIKKDEFTKVGARDTYIDLIFEKD 78
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWghGSKPKGLKKDDFTRIGGSGTEIELKFEKN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        79 GTKYRITRRFLKGyssgeIHAMKRLVGNEwkhVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVR 158
Cdd:PRK03918  81 GRKYRIVRSFNRG-----ESYLKYLDGSE---VLEEGDSSVREWVERLIPYHVFLNAIYIRQGEIDAILESDESREKVVR 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
3QKS_A       159 EVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
Cdd:PRK03918 153 QILGLDDYENAYKNLGEVIKEIKRRIERLEKFIKRTE 189
 
Name Accession Description Interval E-value
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-195 2.69e-81

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 258.84  E-value: 2.69e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYW--PLRIKDIKKDEFTKVGARDTYIDLIFEKD 78
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWghGSKPKGLKKDDFTRIGGSGTEIELKFEKN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        79 GTKYRITRRFLKGyssgeIHAMKRLVGNEwkhVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVR 158
Cdd:PRK03918  81 GRKYRIVRSFNRG-----ESYLKYLDGSE---VLEEGDSSVREWVERLIPYHVFLNAIYIRQGEIDAILESDESREKVVR 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
3QKS_A       159 EVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
Cdd:PRK03918 153 QILGLDDYENAYKNLGEVIKEIKRRIERLEKFIKRTE 189
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-195 9.57e-29

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 106.25  E-value: 9.57e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        2 KLERVTVKNFRSHSDT-VVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGT 80
Cdd:COG0419   1 KLLRLRLENFRSYRDTeTIDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSKLRSDLINVGSEEASVELEFEHGGK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A       81 KYRITRrflkgyssgeihamkrlvgnewkhvtepsskaisafmeklipyniflnaiyiRQGQIDAILESD-EAREKVVRE 159
Cdd:COG0419  81 RYRIER----------------------------------------------------RQGEFAEFLEAKpSERKEALKR 108

                       170       180       190
                ....*....|....*....|....*....|....*.
3QKS_A      160 VLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
Cdd:COG0419 109 LLGLEIYEELKERLKELEEALESALEELAELQKLKQ 144
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-148 3.50e-24

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: 94.60  E-value: 3.50e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRS-HSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYW--PLRIKDIKKD-EFTKVGARDTYIDLIFEKD 78
Cdd:cd03240   1 IDKLSIRNIRSfHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYALTGelPPNSKGGAHDpKLIREGEVRAQVKLAFENA 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
3QKS_A       79 -GTKYRITRRFlkgyssgeihamkrlvgnewkhvtepsskaisafmeklipyNIFLNAIYIRQGQIDAILE 148
Cdd:cd03240  81 nGKKYTITRSL-----------------------------------------AILENVIFCHQGESNWPLL 110
AAA_23 pfam13476
AAA domain;
6-193 4.29e-17

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 75.61  E-value: 4.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A          6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKD--------EFTKVGARDTYIDLIFEK 77
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGggfvkgdiRIGLEGKGKAYVEITFEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         78 DGTK--YRITRRFLKGYSSGEIHAMKRLVGNEwkhvtepsSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREK 155
Cdd:pfam13476  81 NDGRytYAIERSRELSKKKGKTKKKEILEILE--------IDELQQFISELLKSDKIILPLLVFLGQEREEEFERKEKKE 152

                         170       180       190
                  ....*....|....*....|....*....|....*...
3QKS_A        156 VVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILAR 193
Cdd:pfam13476 153 RLEELEKALEEKEDEKKLLEKLLQLKEKKKELEELKEE 190
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 1-187 3.77e-13

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: 67.30  E-value: 3.77e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A           1 MKLERVTVKNFRSHSDT-VVEF--KEGINLIIGQNGSGKSSLLDAILVGLYWPLRIK---DIKKDEFTKVGARDTYIDLI 74
Cdd:TIGR00618    1 MKPLRLTLKNFGSYKGThTIDFtaLGPIFLICGKTGAGKTTLLDAITYALYGKLPRRsevIRSLNSLYAAPSEAAFAELE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A          75 FEKDGTKYRITR--RFLKGYSSGEIHAmKRLVGNEWKHVTePSSKAISAFMEKL-----IPYNIFLNAIYIRQGQIDAIL 147
Cdd:TIGR00618   81 FSLGTKIYRVHRtlRCTRSHRKTEQPE-QLYLEQKKGRGR-ILAAKKSETEEVIhdllkLDYKTFTRVVLLPQGEFAQFL 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
3QKS_A         148 -ESDEAREKVVREVLNLDKFET----AYKKLSELKKTINNRIKEY 187
Cdd:TIGR00618  159 kAKSKEKKELLMNLFPLDQYTQlalmEFAKKKSLHGKAELLTLRS 203
 
Name Accession Description Interval E-value
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
1-195 2.69e-81

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 258.84  E-value: 2.69e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYW--PLRIKDIKKDEFTKVGARDTYIDLIFEKD 78
Cdd:PRK03918   1 MKIEELKIKNFRSHKSSVVEFDDGINLIIGQNGSGKSSILEAILVGLYWghGSKPKGLKKDDFTRIGGSGTEIELKFEKN 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        79 GTKYRITRRFLKGyssgeIHAMKRLVGNEwkhVTEPSSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVR 158
Cdd:PRK03918  81 GRKYRIVRSFNRG-----ESYLKYLDGSE---VLEEGDSSVREWVERLIPYHVFLNAIYIRQGEIDAILESDESREKVVR 152

                        170       180       190
                 ....*....|....*....|....*....|....*..
3QKS_A       159 EVLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
Cdd:PRK03918 153 QILGLDDYENAYKNLGEVIKEIKRRIERLEKFIKRTE 189
SbcC COG0419
DNA repair exonuclease SbcCD ATPase subunit [Replication, recombination and repair];
2-195 9.57e-29

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


Pssm-ID: 440188 [Multi-domain]  Cd Length: 204  Bit Score: 106.25  E-value: 9.57e-29
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        2 KLERVTVKNFRSHSDT-VVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARDTYIDLIFEKDGT 80
Cdd:COG0419   1 KLLRLRLENFRSYRDTeTIDFDDGLNLIVGPNGAGKSTILEAIRYALYGKARSRSKLRSDLINVGSEEASVELEFEHGGK 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A       81 KYRITRrflkgyssgeihamkrlvgnewkhvtepsskaisafmeklipyniflnaiyiRQGQIDAILESD-EAREKVVRE 159
Cdd:COG0419  81 RYRIER----------------------------------------------------RQGEFAEFLEAKpSERKEALKR 108

                       170       180       190
                ....*....|....*....|....*....|....*.
3QKS_A      160 VLNLDKFETAYKKLSELKKTINNRIKEYRDILARTE 195
Cdd:COG0419 109 LLGLEIYEELKERLKELEEALESALEELAELQKLKQ 144
PRK01156 PRK01156
chromosome segregation protein; Provisional
 1-190 2.89e-24

chromosome segregation protein; Provisional


Pssm-ID: 100796 [Multi-domain]  Cd Length: 895  Bit Score: 99.59  E-value: 2.89e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIkkDEFTKVGARDTYIDLIFEKDGT 80
Cdd:PRK01156   1 MIIKRIRLKNFLSHDDSEIEFDTGINIITGKNGAGKSSIVDAIRFALFTDKRTEKI--EDMIKKGKNNLEVELEFRIGGH 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        81 KYRITRRFLKGYSSGEIHAMKRLVGNewkhVTEPSSKAISAFMEK---LIPYNIFLNAIYIRQGQIDAILESDEA-REKV 156
Cdd:PRK01156  79 VYQIRRSIERRGKGSRREAYIKKDGS----IIAEGFDDTTKYIEKnilGISKDVFLNSIFVGQGEMDSLISGDPAqRKKI 154

                        170       180       190
                 ....*....|....*....|....*....|....
3QKS_A       157 VREVLNLDKFETAYKKLSELKKTINNRIKEYRDI 190
Cdd:PRK01156 155 LDEILEINSLERNYDKLKDVIDMLRAEISNIDYL 188
ABC_Rad50 cd03240
ATP-binding cassette domain of Rad50; The catalytic domains of Rad50 are similar to the ...
 3-148 3.50e-24

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: 94.60  E-value: 3.50e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRS-HSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYW--PLRIKDIKKD-EFTKVGARDTYIDLIFEKD 78
Cdd:cd03240   1 IDKLSIRNIRSfHERSEIEFFSPLTLIVGQNGAGKTTIIEALKYALTGelPPNSKGGAHDpKLIREGEVRAQVKLAFENA 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
3QKS_A       79 -GTKYRITRRFlkgyssgeihamkrlvgnewkhvtepsskaisafmeklipyNIFLNAIYIRQGQIDAILE 148
Cdd:cd03240  81 nGKKYTITRSL-----------------------------------------AILENVIFCHQGESNWPLL 110
PRK02224 PRK02224
DNA double-strand break repair Rad50 ATPase;
1-168 5.47e-18

DNA double-strand break repair Rad50 ATPase;


Pssm-ID: 179385 [Multi-domain]  Cd Length: 880  Bit Score: 81.24  E-value: 5.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKvGARDTYIDLIFEKDGT 80
Cdd:PRK02224   1 MRFDRVRLENFKCYADADLRLEDGVTVIHGVNGSGKSSLLEACFFALYGSKALDDTLDDVITI-GAEEAEIELWFEHAGG 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        81 KYRITRRFlkgYSSGEIHAMKRLVGNEWKHVTEpSSKAISAFMEKLIPYN--IFLNAIYIRQGQIDA-ILESDEAREKVV 157
Cdd:PRK02224  80 EYHIERRV---RLSGDRATTAKCVLETPEGTID-GARDVREEVTELLRMDaeAFVNCAYVRQGEVNKlINATPSDRQDMI 155

                        170
                 ....*....|.
3QKS_A       158 REVLNLDKFET 168
Cdd:PRK02224 156 DDLLQLGKLEE 166
AAA_23 pfam13476
AAA domain;
6-193 4.29e-17

AAA domain;


Pssm-ID: 463890 [Multi-domain]  Cd Length: 190  Bit Score: 75.61  E-value: 4.29e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A          6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKD--------EFTKVGARDTYIDLIFEK 77
Cdd:pfam13476   1 LTIENFRSFRDQTIDFSKGLTLITGPNGSGKTTILDAIKLALYGKTSRLKRKSGggfvkgdiRIGLEGKGKAYVEITFEN 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         78 DGTK--YRITRRFLKGYSSGEIHAMKRLVGNEwkhvtepsSKAISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREK 155
Cdd:pfam13476  81 NDGRytYAIERSRELSKKKGKTKKKEILEILE--------IDELQQFISELLKSDKIILPLLVFLGQEREEEFERKEKKE 152

                         170       180       190
                  ....*....|....*....|....*....|....*...
3QKS_A        156 VVREVLNLDKFETAYKKLSELKKTINNRIKEYRDILAR 193
Cdd:pfam13476 153 RLEELEKALEEKEDEKKLLEKLLQLKEKKKELEELKEE 190
YbjD COG3593
Predicted ATP-dependent endonuclease of the OLD family, contains P-loop ATPase and TOPRIM ...
 1-97 3.29e-14

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: 70.03  E-value: 3.29e-14
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVgLYWPLRIKDIKKDEF---TKVGARDTYIDLIFEK 77
Cdd:COG3593   1 MKLEKIKIKNFRSIKDLSIELSDDLTVLVGENNSGKSSILEALRL-LLGPSSSRKFDEEDFylgDDPDLPEIEIELTFGS 79

                        90       100
                ....*....|....*....|
3QKS_A       78 dgTKYRITRRFLKGYSSGEI 97
Cdd:COG3593  80 --LLSRLLRLLLKEEDKEEL 97
sbcc TIGR00618
exonuclease SbcC; All proteins in this family for which functions are known are part of an ...
 1-187 3.77e-13

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: 67.30  E-value: 3.77e-13
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A           1 MKLERVTVKNFRSHSDT-VVEF--KEGINLIIGQNGSGKSSLLDAILVGLYWPLRIK---DIKKDEFTKVGARDTYIDLI 74
Cdd:TIGR00618    1 MKPLRLTLKNFGSYKGThTIDFtaLGPIFLICGKTGAGKTTLLDAITYALYGKLPRRsevIRSLNSLYAAPSEAAFAELE 80

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A          75 FEKDGTKYRITR--RFLKGYSSGEIHAmKRLVGNEWKHVTePSSKAISAFMEKL-----IPYNIFLNAIYIRQGQIDAIL 147
Cdd:TIGR00618   81 FSLGTKIYRVHRtlRCTRSHRKTEQPE-QLYLEQKKGRGR-ILAAKKSETEEVIhdllkLDYKTFTRVVLLPQGEFAQFL 158

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
3QKS_A         148 -ESDEAREKVVREVLNLDKFET----AYKKLSELKKTINNRIKEY 187
Cdd:TIGR00618  159 kAKSKEKKELLMNLFPLDQYTQlalmEFAKKKSLHGKAELLTLRS 203
COG3950 COG3950
Predicted ATP-binding protein involved in virulence [General function prediction only];
1-61 3.78e-13

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


Pssm-ID: 443150 [Multi-domain]  Cd Length: 276  Bit Score: 66.17  E-value: 3.78e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
3QKS_A        1 MKLERVTVKNFRSHSDTVVEF--KEGINLIIGQNGSGKSSLLDAILVGLYWPL-RIKDIKKDEF 61
Cdd:COG3950   1 MRIKSLTIENFRGFEDLEIDFdnPPRLTVLVGENGSGKTTLLEAIALALSGLLsRLDDVKFRKL 64
RecF COG1195
Recombinational DNA repair ATPase RecF [Replication, recombination and repair];
2-43 6.69e-13

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


Pssm-ID: 440808 [Multi-domain]  Cd Length: 352  Bit Score: 65.95  E-value: 6.69e-13
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
3QKS_A        2 KLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAI 43
Cdd:COG1195   1 RLKRLSLTNFRNYESLELEFSPGINVLVGPNGQGKTNLLEAI 42
ABC_SMC6_euk cd03276
ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of ...
 3-47 1.82e-11

ATP-binding cassette domain of eukaryotic SM6 proteins; The structural maintenance of chromosomes (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: 213243 [Multi-domain]  Cd Length: 198  Bit Score: 60.30  E-value: 1.82e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
3QKS_A        3 LERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
Cdd:cd03276   1 IESITLKNFMCHRHLQIEFGPRVNFIVGNNGSGKSAILTALTIGL 45
recF PRK00064
recombination protein F; Reviewed
 1-43 2.34e-11

recombination protein F; Reviewed


Pssm-ID: 234608 [Multi-domain]  Cd Length: 361  Bit Score: 61.71  E-value: 2.34e-11
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAI 43
Cdd:PRK00064   1 MYLTRLSLTDFRNYEELDLELSPGVNVLVGENGQGKTNLLEAI 43
ABC_sbcCD cd03279
ATP-binding cassette domain of sbcCD; SbcCD and other Mre11/Rad50 (MR) complexes are ...
 1-88 3.62e-11

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: 59.98  E-value: 3.62e-11
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        1 MKLERVTVKNFRS-HSDTVVEF----KEGINLIIGQNGSGKSSLLDAILVGLYW--PLRIKDIKKDEFTKVGARDTYIDL 73
Cdd:cd03279   1 MKPLKLELKNFGPfREEQVIDFtgldNNGLFLICGPTGAGKSTILDAITYALYGktPRYGRQENLRSVFAPGEDTAEVSF 80

                        90
                ....*....|....*
3QKS_A       74 IFEKDGTKYRITRRF 88
Cdd:cd03279  81 TFQLGGKKYRVERSR 95
COG4637 COG4637
Predicted ATPase [General function prediction only];
2-43 5.16e-11

Predicted ATPase [General function prediction only];


Pssm-ID: 443675 [Multi-domain]  Cd Length: 371  Bit Score: 60.71  E-value: 5.16e-11
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
3QKS_A        2 KLERVTVKNFRSHSDTVVEFkEGINLIIGQNGSGKSSLLDAI 43
Cdd:COG4637   1 MITRIRIKNFKSLRDLELPL-GPLTVLIGANGSGKSNLLDAL 41
ABC_SMC5_euk cd03277
ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of ...
 5-71 8.25e-11

ATP-binding cassette domain of eukaryotic SMC5 proteins; The structural maintenance of chromosomes (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: 213244 [Multi-domain]  Cd Length: 213  Bit Score: 58.76  E-value: 8.25e-11
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
3QKS_A        5 RVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPL----RIKDIKkdEFTKVGARDTYI 71
Cdd:cd03277   5 RIKLENFVTYDETEFRPGPSLNMIIGPNGSGKSSIVCAICLGLGGKPkllgRAKKVG--EFVKRGCDEGTI 73
AAA_15 pfam13175
AAA ATPase domain; This family of domains contain a P-loop motif that is characteriztic of the ...
 1-43 2.07e-10

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: 59.15  E-value: 2.07e-10
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
3QKS_A          1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAI 43
Cdd:pfam13175   1 MKIKSIIIKNFRCLKDTEIDLDEDLTVLIGKNNSGKSSILEAL 43
ABC_SMC_head cd03239
The SMC head domain belongs to the ATP-binding cassette superfamily; The structural ...
 3-77 2.63e-10

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: 56.93  E-value: 2.63e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRSHSD-TVVEFKEGINLIIGQNGSGKSSLLDAILVGL---YWPLRIKDIKKD--EFTKVGARDTYIDLIFE 76
Cdd:cd03239   1 IKQITLKNFKSYRDeTVVGGSNSFNAIVGPNGSGKSNIVDAICFVLggkAAKLRRGSLLFLagGGVKAGINSASVEITFD 80


                .
3QKS_A       77 K 77
Cdd:cd03239  81 K 81
COG1106 COG1106
ATPase/GTPase, AAA15 family [General function prediction only];
3-188 6.97e-10

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


Pssm-ID: 440723 [Multi-domain]  Cd Length: 330  Bit Score: 57.36  E-value: 6.97e-10
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRS-HSDTVVEFKEG------INLIIGQNGSGKSSLLDAILVgLYWPLRIKDIKKDEFTKVGARD------- 68
Cdd:COG1106   2 LISFSIENFRSfKDELTLSMVASglrllrVNLIYGANASGKSNLLEALYF-LRNLVLNSSQPGDKLVEPFLLDsesknep 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A       69 TYIDLIFEKDGTKYRItrrflkgyssgEIHAMKRLVGNEWKHVTEPSSKAISAFMEKLipYNIFLNAIYI--RQGQIDAI 146
Cdd:COG1106  81 SEFEILFLLDGVRYEY-----------GFELDKERIISEWLYFLSTAAQLNVPLLSPL--YDWFDNNISLdtSSDGLTLL 147

                       170       180       190       200
                ....*....|....*....|....*....|....*....|..
3QKS_A      147 LESDEAREKVVREVLNldKFETAYKKLsELKKTINNRIKEYR 188
Cdd:COG1106 148 LKEDESLKEELLELLK--IADPGIEDI-EVEEEEIEDLVERK 186
ABC_RecF cd03242
ATP-binding cassette domain of RecF; RecF is a recombinational DNA repair ATPase that ...
 3-79 3.81e-09

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: 55.00  E-value: 3.81e-09
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
3QKS_A        3 LERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAIlvGLYWPLRIKDIKKD-EFTKVGARDTYIDLIFEKDG 79
Cdd:cd03242   1 LKSLELRNFRNYAELELEFEPGVTVLVGENAQGKTNLLEAI--SLLATGKSHRTSRDkELIRWGAEEAKISAVLERQG 76
ABC_SMC_barmotin cd03278
ATP-binding cassette domain of barmotin, a member of the SMC protein family; Barmotin is a ...
 3-83 4.07e-09

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: 54.01  E-value: 4.07e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRSHSD-TVVEFKEGINLIIGQNGSGKSSLLDAILvglyWPL---RIKDIKKDEFTkvgardtyiDLIFekD 78
Cdd:cd03278   1 LKKLELKGFKSFADkTTIPFPPGLTAIVGPNGSGKSNIIDAIR----WVLgeqSAKSLRGEKMS---------DVIF--A 65


                ....*
3QKS_A       79 GTKYR 83
Cdd:cd03278  66 GSETR 70
46 PHA02562
endonuclease subunit; Provisional
 2-86 2.51e-08

endonuclease subunit; Provisional


Pssm-ID: 222878 [Multi-domain]  Cd Length: 562  Bit Score: 53.09  E-value: 2.51e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         2 KLERVTVKNFRSHSDTVVEF---KEGINLIIGQNGSGKSSLLDAILVGLYW-PLRikDIKKDEF-TKVGARDTYIDLIFE 76
Cdd:PHA02562   3 KFKKIRYKNILSVGNQPIEIqldKVKKTLITGKNGAGKSTMLEALTFALFGkPFR--DIKKGQLiNSINKKDLLVELWFE 80

                         90
                 ....*....|
3QKS_A        77 KDGTKYRITR 86
Cdd:PHA02562  81 YGEKEYYIKR 90
recf TIGR00611
recF protein; All proteins in this family for which functions are known are DNA binding ...
 1-43 2.89e-08

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: 52.74  E-value: 2.89e-08
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
3QKS_A          1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAI 43
Cdd:TIGR00611   1 MYLSRLELTDFRNYDAVDLELSPGVNVIVGPNGQGKTNLLEAI 43
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
1-44 4.95e-08

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 52.08  E-value: 4.95e-08
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
3QKS_A        1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAIL 44
Cdd:COG4717   1 MKIKELEIYGFGKFRDRTIEFSPGLNVIYGPNEAGKSTLLAFIR 44
AAA_29 pfam13555
P-loop containing region of AAA domain;
3-54 1.43e-07

P-loop containing region of AAA domain;


Pssm-ID: 433304 [Multi-domain]  Cd Length: 61  Bit Score: 46.82  E-value: 1.43e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
3QKS_A          3 LERVTVKNFRSHSDTVVEFKE-GINLIIGQNGSGKSSLLDAILVGLYWPLRIK 54
Cdd:pfam13555   1 LTRLQLINWGTFDGHTIPIDPrGNTLLTGPSGSGKSTLLDAIQTLLVPAKRAR 53
SMC_N pfam02463
RecF/RecN/SMC N terminal domain; This domain is found at the N terminus of SMC proteins. The ...
 2-44 7.66e-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: 48.81  E-value: 7.66e-07
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....
3QKS_A           2 KLERVTVKNFRSHSDTVV-EFKEGINLIIGQNGSGKSSLLDAIL 44
Cdd:pfam02463    1 YLKRIEIEGFKSYAKTVIlPFSPGFTAIVGPNGSGKSNILDAIL 44
ABC_SMC1_euk cd03275
ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of ...
 3-146 1.08e-06

ATP-binding cassette domain of eukaryotic SMC1 proteins; The structural maintenance of chromosomes (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: 213242 [Multi-domain]  Cd Length: 247  Bit Score: 47.57  E-value: 1.08e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRSHSDT-VVEFKEGINLIIGQNGSGKSSLLDAILVGL---YWPLRIKDIK----KDEFTKVGARDTYIDLI 74
Cdd:cd03275   1 LKRLELENFKSYKGRhVIGPFDRFTCIIGPNGSGKSNLMDAISFVLgekSSHLRSKNLKdliyRARVGKPDSNSAYVTAV 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
3QKS_A       75 FEKDGTKYR-ITRRFLKGYSSGEIHamKRLVgnewkhvtepSSKAISAFMEKLipyNIFLNA--IYIRQGQIDAI 146
Cdd:cd03275  81 YEDDDGEEKtFRRIITGGSSSYRIN--GKVV----------SLKEYNEELEKI---NILVKArnFLVFQGDVESI 140
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 1-44 1.96e-06

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 47.62  E-value: 1.96e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
3QKS_A        1 MKLERVTVKNFRSHSD-TVVEFKEGINLIIGQNGSGKSSLLDAIL 44
Cdd:COG1196   1 MRLKRLELAGFKSFADpTTIPFEPGITAIVGPNGSGKSNIVDAIR 45
ABC_Class2 cd03227
ATP-binding cassette domain of non-transporter proteins; ABC-type Class 2 contains systems ...
 5-75 2.84e-06

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: 45.43  E-value: 2.84e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
3QKS_A        5 RVTVKNFRSH-SDTVVEFKEG-INLIIGQNGSGKSSLLDAILVGLYwpLRIKDIKKDEFTKVGARDTYIDLIF 75
Cdd:cd03227   1 KIVLGRFPSYfVPNDVTFGEGsLTIITGPNGSGKSTILDAIGLALG--GAQSATRRRSGVKAGCIVAAVSAEL 71
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
1-48 4.21e-06

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 46.45  E-value: 4.21e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
3QKS_A         1 MKLERVTVKN---FrsHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLY 48
Cdd:COG4913    1 FRLQRLQLINwgtF--DGVHTIDFDGRGTLLTGDNGSGKSTLLDAIQTLLV 49
recF PRK14079
recombination protein F; Provisional
 1-91 5.31e-06

recombination protein F; Provisional


Pssm-ID: 184491 [Multi-domain]  Cd Length: 349  Bit Score: 45.93  E-value: 5.31e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A         1 MKLERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYWPLRIKDIkkDEFTKVGARDTYIDLIFEKDGT 80
Cdd:PRK14079   1 MRLLSLRQLNYRNLAPPTLAFPPGVTAVVGENAAGKTNLLEAIYLALTGELPNGRL--ADLVRFGEGEAWVHAEVETGGG 78

                         90
                 ....*....|.
3QKS_A        81 KYRITRRFLKG 91
Cdd:PRK14079  79 LSRLEVGLGPG 89
COG4938 COG4938
Predicted ATPase [General function prediction only];
3-97 1.27e-05

Predicted ATPase [General function prediction only];


Pssm-ID: 443965 [Multi-domain]  Cd Length: 277  Bit Score: 44.57  E-value: 1.27e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        3 LERVTVKNFRSHSDTVVEFKeGINLIIGQNGSGKSSLLDAILvGLYW------------PLRIKDIKKDEFTKVGARDTY 70
Cdd:COG4938   1 IKSISIKNFGPFKEAELELK-PLTLLIGPNGSGKSTLIQALL-LLLQsnfiylpaersgPARLYPSLVRELSDLGSRGEY 78

                        90       100       110
                ....*....|....*....|....*....|....*..
3QKS_A       71 ----------IDLIFEKDGTKYRITRRFLKGYSSGEI 97
Cdd:COG4938  79 tadflaelenLEILDDKSKELLEQVEEWLEKIFPGKV 115
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 3-47 1.67e-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: 44.67  E-value: 1.67e-05
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*.
3QKS_A           3 LERVTVKNFRSHSD-TVVEFKEGINLIIGQNGSGKSSLLDAILVGL 47
Cdd:TIGR02169    2 IERIELENFKSFGKkKVIPFSKGFTVISGPNGSGKSNIGDAILFAL 47
ABC_RecN cd03241
ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC ...
 3-44 2.32e-05

ATP-binding cassette domain of RecN; RecN ATPase involved in DNA repair; similar to ABC (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 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 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: 213208 [Multi-domain]  Cd Length: 276  Bit Score: 43.73  E-value: 2.32e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|..
3QKS_A        3 LERVTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAIL 44
Cdd:cd03241   1 LLELSIKNFALIEELELDFEEGLTVLTGETGAGKSILLDALS 42
ABC_SMC3_euk cd03272
ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of ...
 5-43 5.49e-05

ATP-binding cassette domain of eukaryotic SMC3 proteins; The structural maintenance of chromosomes (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: 213239 [Multi-domain]  Cd Length: 243  Bit Score: 42.63  E-value: 5.49e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
3QKS_A        5 RVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAI 43
Cdd:cd03272   3 QVIIQGFKSYKDQTViePFSPKHNVVVGRNGSGKSNFFAAI 43
YydB COG5293
Uncharacterized conserved protein YydD, contains DUF2326 domain [Function unknown];
1-190 6.46e-05

Uncharacterized conserved protein YydD, contains DUF2326 domain [Function unknown];


Pssm-ID: 444096 [Multi-domain]  Cd Length: 572  Bit Score: 43.01  E-value: 6.46e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A        1 MKLERVTVKNFRSHSdtvVEFKEGINLIIGQ-----------NGSGKSSLLDAI--LVGlywplriKDIKKDEFTKVGA- 66
Cdd:COG5293   1 MMLKKLYSNLPRFKP---IEFNPGLNVILGEisspendkdstNGVGKSTLLELIdfCLG-------ADKDKKRFLKHEDe 70

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A       67 -RDTYIDLIFEKDGTKYRITRRF-------LKGYSSGEIHA------MKRLVGNE---WKHVTEPS-SKAISAFM----- 123
Cdd:COG5293  71 lGDHTFFLEFELDGKDLTIRRSVsdpkkisLCGDGYEWDHEkvsleeAKALLEELlfgLPALKGPSfRSLLGYFLrrqgd 150

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
3QKS_A      124 ---------------EKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFETAYKKLSELKKTINNRIKEYR 188
Cdd:COG5293 151 dfkdplqlfstaqkdADWKLYLAYLLGLDWDLAAEKYELKEEIKELKKLRKALKDELIGSVVKSISELRAEILELEEEIE 230


                ..
3QKS_A      189 DI 190
Cdd:COG5293 231 KL 232
ABC_ATPase cd00267
ATP-binding cassette transporter nucleotide-binding domain; ABC transporters are a large ...
 2-50 1.14e-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: 40.69  E-value: 1.14e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
3QKS_A        2 KLERVTVKNFRSH--SDTVVEFKEG-INLIIGQNGSGKSSLLDAILvGLYWP 50
Cdd:cd00267   1 EIENLSFRYGGRTalDNVSLTLKAGeIVALVGPNGSGKSTLLRAIA-GLLKP 51
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 2-43 1.39e-04

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: 41.97  E-value: 1.39e-04
                           10        20        30        40
                   ....*....|....*....|....*....|....*....|...
3QKS_A           2 KLERVTVKNFRSHSD-TVVEFKEGINLIIGQNGSGKSSLLDAI 43
Cdd:TIGR02168    1 RLKKLELAGFKSFADpTTINFDKGITGIVGPNGCGKSNIVDAI 43
AAA_21 pfam13304
AAA domain, putative AbiEii toxin, Type IV TA system; Several members are annotated as being ...
 25-91 2.31e-04

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: 40.84  E-value: 2.31e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
3QKS_A         25 INLIIGQNGSGKSSLLDAILVGLYWPLRIKDIKKDEFTKVGARD--TYIDLIFEKDGTKYRITRRFLKG 91
Cdd:pfam13304   1 INVLIGPNGSGKSNLLEALRFLADFDALVIGLTDERSRNGGIGGipSLLNGIDPKEPIEFEISEFLEDG 69
ABCD_peroxisomal_ALDP cd03223
ATP-binding cassette domain of peroxisomal transporter, subfamily D; Peroxisomal ATP-binding ...
 1-52 2.54e-04

ATP-binding cassette domain of peroxisomal transporter, subfamily D; Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome. The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation. To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes. X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family. The disease is characterized by a striking and unpredictable variation in phenotypic expression. Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asymptomatic).


Pssm-ID: 213190 [Multi-domain]  Cd Length: 166  Bit Score: 39.83  E-value: 2.54e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*.
3QKS_A        1 MKLERVTVKNFRSH---SDTVVEFKEGIN-LIIGQNGSGKSSLLdAILVGLyWPLR 52
Cdd:cd03223   1 IELENLSLATPDGRvllKDLSFEIKPGDRlLITGPSGTGKSSLF-RALAGL-WPWG 54
ABC_SMC4_euk cd03274
ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of ...
 3-44 2.77e-04

ATP-binding cassette domain of eukaryotic SMC4 proteins; The structural maintenance of chromosomes (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: 213241 [Multi-domain]  Cd Length: 212  Bit Score: 40.36  E-value: 2.77e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
3QKS_A        3 LERVTVKNFRSHSDTVV--EFKEGINLIIGQNGSGKSSLLDAIL 44
Cdd:cd03274   3 ITKLVLENFKSYAGEQVigPFHKSFSAIVGPNGSGKSNVIDSML 46
DUF2813 pfam11398
Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which ...
 1-43 5.51e-04

Protein of unknown function (DUF2813); This entry contains YjbD from Escherichia coli, which is annotated as a nucleotide triphosphate hydrolase.


Pssm-ID: 431868 [Multi-domain]  Cd Length: 372  Bit Score: 40.03  E-value: 5.51e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
3QKS_A          1 MKLERVTVKNFRSHSDTVVEFKEgINLIIGQNGSGKSSLLDAI 43
Cdd:pfam11398   1 MHLERIEVVGFRGINRLSLHFDQ-LTVLIGENAWGKSSLLDAL 42
ABC_tran pfam00005
ABC transporter; ABC transporters for a large family of proteins responsible for translocation ...
 28-85 6.45e-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: 38.78  E-value: 6.45e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
3QKS_A         28 IIGQNGSGKSSLLDAILvGLYWP------LRIKDIKKDEFTKVGARdtyIDLIFEKDGTKYRIT 85
Cdd:pfam00005  16 LVGPNGAGKSTLLKLIA-GLLSPtegtilLDGQDLTDDERKSLRKE---IGYVFQDPQLFPRLT 75
ABC_SMC2_euk cd03273
ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of ...
 1-44 9.79e-04

ATP-binding cassette domain of eukaryotic SMC2 proteins; The structural maintenance of chromosomes (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: 213240 [Multi-domain]  Cd Length: 251  Bit Score: 38.82  E-value: 9.79e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
3QKS_A        1 MKLERVTVKNFRSHSD-TVVE-FKEGINLIIGQNGSGKSSLLDAIL 44
Cdd:cd03273   1 MHIKEIILDGFKSYATrTVISgFDPQFNAITGLNGSGKSNILDAIC 46
ABCC_MRP_domain1 cd03250
ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C; This ...
 19-44 1.09e-03

ATP-binding cassette domain 1 of multidrug resistance-associated protein, subfamily C; This subfamily is also known as MRP (multidrug resistance-associated protein). Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear. The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.


Pssm-ID: 213217 [Multi-domain]  Cd Length: 204  Bit Score: 38.60  E-value: 1.09e-03
                        10        20
                ....*....|....*....|....*..
3QKS_A       19 VEFKEG-INLIIGQNGSGKSSLLDAIL 44
Cdd:cd03250  26 LEVPKGeLVAIVGPVGSGKSSLLSALL 52
PRK13539 PRK13539
cytochrome c biogenesis protein CcmA; Provisional
 27-71 1.73e-03

cytochrome c biogenesis protein CcmA; Provisional


Pssm-ID: 237421 [Multi-domain]  Cd Length: 207  Bit Score: 37.93  E-value: 1.73e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
3QKS_A        27 LIIGQNGSGKSSLLdAILVGLYWPL--RIK-DIKKDEFTKVGARDTYI 71
Cdd:PRK13539  32 VLTGPNGSGKTTLL-RLIAGLLPPAagTIKlDGGDIDDPDVAEACHYL 78
COG3910 COG3910
Predicted ATPase [General function prediction only];
20-47 5.25e-03

Predicted ATPase [General function prediction only];


Pssm-ID: 443116 [Multi-domain]  Cd Length: 239  Bit Score: 36.67  E-value: 5.25e-03
                        10        20
                ....*....|....*....|....*...
3QKS_A       20 EFKEGINLIIGQNGSGKSSLLDAILVGL 47
Cdd:COG3910  34 EFHPPVTFFVGENGSGKSTLLEAIAVAA 61
CcmA COG4133
ABC-type transport system involved in cytochrome c biogenesis, ATPase component ...
 27-52 5.38e-03

ABC-type transport system involved in cytochrome c biogenesis, ATPase component [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 443308 [Multi-domain]  Cd Length: 206  Bit Score: 36.30  E-value: 5.38e-03
                        10        20
                ....*....|....*....|....*.
3QKS_A       27 LIIGQNGSGKSSLLDaILVGLYWPLR 52
Cdd:COG4133  32 ALTGPNGSGKTTLLR-ILAGLLPPSA 56
SunT COG2274
ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase ...
 23-50 5.54e-03

ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms];


Pssm-ID: 441875 [Multi-domain]  Cd Length: 711  Bit Score: 37.12  E-value: 5.54e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
3QKS_A       23 EGINL---------IIGQNGSGKSSLLDaILVGLYWP 50
Cdd:COG2274 492 DNISLtikpgervaIVGRSGSGKSTLLK-LLLGLYEP 527
ZnuC COG1121
ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism]; ...
 2-47 7.44e-03

ABC-type Mn2+/Zn2+ transport system, ATPase component [Inorganic ion transport and metabolism];


Pssm-ID: 440738 [Multi-domain]  Cd Length: 245  Bit Score: 36.22  E-value: 7.44e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*
3QKS_A        2 KLERVTVkNFRSHsdTVVEfkeGINL---------IIGQNGSGKSSLLDAILvGL 47
Cdd:COG1121   8 ELENLTV-SYGGR--PVLE---DVSLtippgefvaIVGPNGAGKSTLLKAIL-GL 55
ABCC_bacteriocin_exporters cd03245
ATP-binding cassette domain of bacteriocin exporters, subfamily C; Many non-lantibiotic ...
 28-50 8.44e-03

ATP-binding cassette domain of bacteriocin exporters, subfamily C; Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2. A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.


Pssm-ID: 213212 [Multi-domain]  Cd Length: 220  Bit Score: 36.03  E-value: 8.44e-03
                        10        20
                ....*....|....*....|...
3QKS_A       28 IIGQNGSGKSSLLdAILVGLYWP 50
Cdd:cd03245  35 IIGRVGSGKSTLL-KLLAGLYKP 56
TIGR00157 TIGR00157
ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and ...
 6-56 8.85e-03

ribosome small subunit-dependent GTPase A; Members of this protein were designated YjeQ and are now designated RsgA (ribosome small subunit-dependent GTPase A). The strongest motif in the alignment of these proteins is GXSGVGKS[ST], a classic P-loop for nucleotide binding. This protein has been shown to cleave GTP and remain bound to GDP. A role as a regulator of translation has been suggested. The Aquifex aeolicus ortholog is split into consecutive open reading frames. Consequently, this model was build in fragment mode (-f option). [Protein synthesis, Translation factors]


Pssm-ID: 272934 [Multi-domain]  Cd Length: 245  Bit Score: 35.85  E-value: 8.85e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
3QKS_A          6 VTVKNFRSHSDTVVEFKEGINLIIGQNGSGKSSLLDAILVGLYwpLRIKDI 56
Cdd:TIGR00157 103 TSSKNQDGLKELIEALQNRISVFAGQSGVGKSSLINALDPSVK--QQVNDI 151
 
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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