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Conserved domains on  [gi|124487005|ref|NP_001074692|]
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DNA endonuclease RBBP8 [Mus musculus]

Protein Classification

DNA endonuclease RBBP8( domain architecture ID 10564642)

DNA endonuclease RBBP8 similar to human RBBP8 that cooperates with the MRE11-RAD50-NBN complex in DNA-end resection, the first step of double-strand break (DSB) repair through the homologous recombination pathway

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
CtIP_N pfam10482
Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that ...
 20-139 4.05e-63

Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.


:

Pssm-ID: 463107 [Multi-domain]  Cd Length: 120  Bit Score: 208.37  E-value: 4.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005   20 FKELWTKLKEYHDKEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLCDRCAVTEEHM 99
Cdd:pfam10482   1 FEELLNKLKEIHDKEVQGLQAKVSELKKERCLDAQRLEELFSKNQQLREQQKALQENIKVLENRLRAGLCDRCAVTQELA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 124487005  100 HKKQQEFENIRQQNLKLITELMNEKNTLQEENKKLSEQLQ 139
Cdd:pfam10482  81 KKKQQEFENSQLQSLQHITILTNEMNTLKDENRKLKEELK 120
SAE2 pfam08573
DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing ...
 793-856 1.89e-13

DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity.


:

Pssm-ID: 462525  Cd Length: 108  Bit Score: 67.39  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  793 EVVRKKEERRKLLGHTCKEC--EIYYA------------------------------DLPAEERE--------KKLASC- 831
Cdd:pfam08573   4 EVVRGKDERKCLPGCTCPCCcgDYFRAmaplpgrlrqkeedqklledylgdeayklgTMSAEEREellveaktRKLANKy 83

                          90       100
                  ....*....|....*....|....*
gi 124487005  832 SRHRFRYIPPNTPENFWEVGFPSTQ 856
Cdd:pfam08573  84 GRHRHHFERAPTPPGFWRTDFPSTQ 108
 
Name Accession Description Interval E-value
CtIP_N pfam10482
Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that ...
 20-139 4.05e-63

Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.


Pssm-ID: 463107 [Multi-domain]  Cd Length: 120  Bit Score: 208.37  E-value: 4.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005   20 FKELWTKLKEYHDKEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLCDRCAVTEEHM 99
Cdd:pfam10482   1 FEELLNKLKEIHDKEVQGLQAKVSELKKERCLDAQRLEELFSKNQQLREQQKALQENIKVLENRLRAGLCDRCAVTQELA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 124487005  100 HKKQQEFENIRQQNLKLITELMNEKNTLQEENKKLSEQLQ 139
Cdd:pfam10482  81 KKKQQEFENSQLQSLQHITILTNEMNTLKDENRKLKEELK 120
SAE2 pfam08573
DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing ...
 793-856 1.89e-13

DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity.


Pssm-ID: 462525  Cd Length: 108  Bit Score: 67.39  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  793 EVVRKKEERRKLLGHTCKEC--EIYYA------------------------------DLPAEERE--------KKLASC- 831
Cdd:pfam08573   4 EVVRGKDERKCLPGCTCPCCcgDYFRAmaplpgrlrqkeedqklledylgdeayklgTMSAEEREellveaktRKLANKy 83

                          90       100
                  ....*....|....*....|....*
gi 124487005  832 SRHRFRYIPPNTPENFWEVGFPSTQ 856
Cdd:pfam08573  84 GRHRHHFERAPTPPGFWRTDFPSTQ 108
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
14-152 1.92e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 45.14  E-value: 1.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  14 ADASNDFKELWTKLKEYHD-KEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRD---QQKVLQETIKILEDRLRAGLC 89
Cdd:COG4717  105 EELEAELEELREELEKLEKlLQLLPLYQELEALEAELAELPERLEELEERLEELREleeELEELEAELAELQEELEELLE 184

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124487005  90 DRCAVTEEHMHKKQQEFENIRQQnlklITELMNEKNTLQEENKKLSEQLQQKMENGQQDQVAE 152
Cdd:COG4717  185 QLSLATEEELQDLAEELEELQQR----LAELEEELEEAQEELEELEEELEQLENELEAAALEE 243
PRK12704 PRK12704
phosphodiesterase; Provisional
 21-153 9.89e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 42.84  E-value: 9.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  21 KELWTKLKEYHDKEVQGLQVKVTKL-----KKERILDaQRLEEFFTKNQQLRDQQKVLQETIKILEdrlraglcdrcavt 95
Cdd:PRK12704  63 KEEIHKLRNEFEKELRERRNELQKLekrllQKEENLD-RKLELLEKREEELEKKEKELEQKQQELE-------------- 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 124487005  96 eehmhKKQQEFENIRQQNLKLITELMNekntLQEENKKlsEQLQQKMENGQQDQVAEL 153
Cdd:PRK12704 128 -----KKEEELEELIEEQLQELERISG----LTAEEAK--EILLEKVEEEARHEAAVL 174
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 18-153 1.36e-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: 42.74  E-value: 1.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005    18 NDFKELWTKLKEyHDKEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLCDRCAVTEE 97
Cdd:TIGR02168  246 EELKEAEEELEE-LTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQ 324

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 124487005    98 HMHKKQQ--EFENIRQQNLKLITELMNEKNTLQEENKKLSEQLQQkMENGQQDQVAEL 153
Cdd:TIGR02168  325 LEELESKldELAEELAELEEKLEELKEELESLEAELEELEAELEE-LESRLEELEEQL 381
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 39-144 7.30e-03

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 39.48  E-value: 7.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  39 QVKVTKLKKERILDAQRLEEfftknQQLRDQQKVLQETIKILEDRLRaglcdrcavteEHMHKKQQEFENIRQQNLKLIT 118
Cdd:cd16269  199 EIEAERAKAEAAEQERKLLE-----EQQRELEQKLEDQERSYEEHLR-----------QLKEKMEEERENLLKEQERALE 262

                         90       100
                 ....*....|....*....|....*..
gi 124487005 119 ELMNE-KNTLQEENKKLSEQLQQKMEN 144
Cdd:cd16269  263 SKLKEqEALLEEGFKEQAELLQEEIRS 289
 
Name Accession Description Interval E-value
CtIP_N pfam10482
Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that ...
 20-139 4.05e-63

Tumour-suppressor protein CtIP N-terminal domain; CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control. This N-terminal domain carries a coiled-coil region and is essential for homodimerization of the protein. The C-terminal domain is family pfam08573.


Pssm-ID: 463107 [Multi-domain]  Cd Length: 120  Bit Score: 208.37  E-value: 4.05e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005   20 FKELWTKLKEYHDKEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLCDRCAVTEEHM 99
Cdd:pfam10482   1 FEELLNKLKEIHDKEVQGLQAKVSELKKERCLDAQRLEELFSKNQQLREQQKALQENIKVLENRLRAGLCDRCAVTQELA 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 124487005  100 HKKQQEFENIRQQNLKLITELMNEKNTLQEENKKLSEQLQ 139
Cdd:pfam10482  81 KKKQQEFENSQLQSLQHITILTNEMNTLKDENRKLKEELK 120
SAE2 pfam08573
DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing ...
 793-856 1.89e-13

DNA endonuclease activator SAE2/CtIP C-terminus; SAE2 is a protein involved in repairing meiotic and mitotic double-strand breaks in DNA. It has been shown to negatively regulate DNA damage checkpoint signalling. SAE2 is homologous to the CtIP proteins in mammals and an homologous protein in plants. Crucial sequence motifs that are highly conserved are the CxxC and the RHR motifs in this C-terminal part of the protein. In budding yeast, genetic evidence suggests that the SAE2 protein is essential for the processing of hairpin DNA intermediates and meiotic double-strand breaks by Mre11/Rad50 complexes. SAE2 binds DNA and exhibits endonuclease activity on single-stranded DNA independently of Mre11/Rad50 complexes, but hairpin DNA structures are cleaved cooperatively in the presence of Mre11/Rad50 or Mre11/Rad50/Xrs2. Hairpin structures are not processed at the tip by SAE2 but rather at single-stranded DNA regions adjacent to the hairpin. The catalytic activities of SAE2 are important for its biological functions. Although proteins containing this domain were described as endonucleases, it is now known that they actually function as endonuclease activators. This domain contains highly conserved residues at its 15-residue extreme that are indispensable for MRN (Mre11-Rad50-Nbs1) complex activation, through the stimulation of Mre11 endonuclease activity.


Pssm-ID: 462525  Cd Length: 108  Bit Score: 67.39  E-value: 1.89e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  793 EVVRKKEERRKLLGHTCKEC--EIYYA------------------------------DLPAEERE--------KKLASC- 831
Cdd:pfam08573   4 EVVRGKDERKCLPGCTCPCCcgDYFRAmaplpgrlrqkeedqklledylgdeayklgTMSAEEREellveaktRKLANKy 83

                          90       100
                  ....*....|....*....|....*
gi 124487005  832 SRHRFRYIPPNTPENFWEVGFPSTQ 856
Cdd:pfam08573  84 GRHRHHFERAPTPPGFWRTDFPSTQ 108
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
14-152 1.92e-04

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


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 45.14  E-value: 1.92e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  14 ADASNDFKELWTKLKEYHD-KEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRD---QQKVLQETIKILEDRLRAGLC 89
Cdd:COG4717  105 EELEAELEELREELEKLEKlLQLLPLYQELEALEAELAELPERLEELEERLEELREleeELEELEAELAELQEELEELLE 184

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124487005  90 DRCAVTEEHMHKKQQEFENIRQQnlklITELMNEKNTLQEENKKLSEQLQQKMENGQQDQVAE 152
Cdd:COG4717  185 QLSLATEEELQDLAEELEELQQR----LAELEEELEEAQEELEELEEELEQLENELEAAALEE 243
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
34-154 5.79e-04

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 43.35  E-value: 5.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  34 EVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLcDRCAVTEEHMHKKQQEFENIRQQn 113
Cdd:COG4372   39 ELDKLQEELEQLREELEQAREELEQLEEELEQARSELEQLEEELEELNEQLQAAQ-AELAQAQEELESLQEEAEELQEE- 116

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|.
gi 124487005 114 lklITELMNEKNTLQEENKKLSEQlQQKMENGQQDQVAELA 154
Cdd:COG4372  117 ---LEELQKERQDLEQQRKQLEAQ-IAELQSEIAEREEELK 153
PRK12704 PRK12704
phosphodiesterase; Provisional
 21-153 9.89e-04

phosphodiesterase; Provisional


Pssm-ID: 237177 [Multi-domain]  Cd Length: 520  Bit Score: 42.84  E-value: 9.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  21 KELWTKLKEYHDKEVQGLQVKVTKL-----KKERILDaQRLEEFFTKNQQLRDQQKVLQETIKILEdrlraglcdrcavt 95
Cdd:PRK12704  63 KEEIHKLRNEFEKELRERRNELQKLekrllQKEENLD-RKLELLEKREEELEKKEKELEQKQQELE-------------- 127

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 124487005  96 eehmhKKQQEFENIRQQNLKLITELMNekntLQEENKKlsEQLQQKMENGQQDQVAEL 153
Cdd:PRK12704 128 -----KKEEELEELIEEQLQELERISG----LTAEEAK--EILLEKVEEEARHEAAVL 174
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 18-153 1.36e-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: 42.74  E-value: 1.36e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005    18 NDFKELWTKLKEyHDKEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLCDRCAVTEE 97
Cdd:TIGR02168  246 EELKEAEEELEE-LTAELQELEEKLEELRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQ 324

                           90       100       110       120       130
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 124487005    98 HMHKKQQ--EFENIRQQNLKLITELMNEKNTLQEENKKLSEQLQQkMENGQQDQVAEL 153
Cdd:TIGR02168  325 LEELESKldELAEELAELEEKLEELKEELESLEAELEELEAELEE-LESRLEELEEQL 381
PRK10246 PRK10246
exonuclease subunit SbcC; Provisional
 33-157 4.29e-03

exonuclease subunit SbcC; Provisional


Pssm-ID: 182330 [Multi-domain]  Cd Length: 1047  Bit Score: 40.94  E-value: 4.29e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005   33 KEVQGLQVKVTKLKKERILDAQRLEE----FFTKNQQLRDQQKV--LQETIKILE---DRLRAGL-CDRCAVTEEHMHKK 102
Cdd:PRK10246  440 KRLAQLQVAIQNVTQEQTQRNAALNEmrqrYKEKTQQLADVKTIceQEARIKDLEaqrAQLQAGQpCPLCGSTSHPAVEA 519

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 124487005  103 QQEFENIRQQNLKLitELMNEKNTLQEENKKLSEQLQQKMENGQQD--QVAELACEE 157
Cdd:PRK10246  520 YQALEPGVNQSRLD--ALEKEVKKLGEEGAALRGQLDALTKQLQRDesEAQSLRQEE 574
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 22-140 5.70e-03

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: 40.44  E-value: 5.70e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005    22 ELWTKLKEYHdKEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAGLCDRCAVTEEhMHK 101
Cdd:TIGR02169  340 ELEREIEEER-KRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEE-LQR 417

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|..
gi 124487005   102 KQQEFENIRQQNLKL---ITELMNEKNTLQEENKKLSEQLQQ 140
Cdd:TIGR02169  418 LSEELADLNAAIAGIeakINELEEEKEDKALEIKKQEWKLEQ 459
GBP_C cd16269
Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal ...
 39-144 7.30e-03

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.


Pssm-ID: 293879 [Multi-domain]  Cd Length: 291  Bit Score: 39.48  E-value: 7.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  39 QVKVTKLKKERILDAQRLEEfftknQQLRDQQKVLQETIKILEDRLRaglcdrcavteEHMHKKQQEFENIRQQNLKLIT 118
Cdd:cd16269  199 EIEAERAKAEAAEQERKLLE-----EQQRELEQKLEDQERSYEEHLR-----------QLKEKMEEERENLLKEQERALE 262

                         90       100
                 ....*....|....*....|....*..
gi 124487005 119 ELMNE-KNTLQEENKKLSEQLQQKMEN 144
Cdd:cd16269  263 SKLKEqEALLEEGFKEQAELLQEEIRS 289
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 33-158 9.86e-03

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 39.53  E-value: 9.86e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487005  33 KEVQGLQVKVTKLKKERILDAQRLEEFFTKNQQLRDQQKVLQETIKILEDRLRAgLCDRCAVTEEHMHKKQQEFENIRQQ 112
Cdd:COG1196  288 AEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEE-LEEELEEAEEELEEAEAELAEAEEA 366

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*.
gi 124487005 113 NLKLITELMNEKNTLQEENKKLSEQLQQKMENGQQDQVAELACEEN 158
Cdd:COG1196  367 LLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEAL 412
 
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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