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Conserved domains on  [gi|873901339|ref|WP_048607772|]
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MULTISPECIES: helix-turn-helix transcriptional regulator [Providencia]

Protein Classification

XRE family transcriptional regulator( domain architecture ID 11443577)

XRE (Xenobiotic Response Element) family transcriptional regulator is a helix-turn-helix domain-containing transcriptional regulator with a peptidase S24 LexA-like domain

Gene Ontology:  GO:0003677
PubMed:  10473770|15808743|10556324

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 96-224 8.25e-28

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


:

Pssm-ID: 442176  Cd Length: 121  Bit Score: 102.35  E-value: 8.25e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339  96 VPFYkDIEFACGTGGSIDVDYNGFKLRFAkstlrkigaPTDGSTIICFPASGDSMEPVIPDGSAIAIDVSNKKIIDGKVY 175
Cdd:COG2932    1 VPLY-DGEASAGGGAFNEVEEPVDKLEFP---------GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 873901339 176 AIDQDGLKRLKMLYRKPGGKLIIRSYNRE--EYDDEEADENSVMIIGRMFW 224
Cdd:COG2932   71 VVRTDGELLVKRLQRRPDGKLRLISDNPAypPIEIPPEDADEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-76 1.53e-16

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


:

Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 71.95  E-value: 1.53e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 873901339   1 MSISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEEDKNDTLPPENE 76
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNpSLETLLKLAKALGVSLDELLGGADEELPEALLSEE 82
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 96-224 8.25e-28

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 102.35  E-value: 8.25e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339  96 VPFYkDIEFACGTGGSIDVDYNGFKLRFAkstlrkigaPTDGSTIICFPASGDSMEPVIPDGSAIAIDVSNKKIIDGKVY 175
Cdd:COG2932    1 VPLY-DGEASAGGGAFNEVEEPVDKLEFP---------GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 873901339 176 AIDQDGLKRLKMLYRKPGGKLIIRSYNRE--EYDDEEADENSVMIIGRMFW 224
Cdd:COG2932   71 VVRTDGELLVKRLQRRPDGKLRLISDNPAypPIEIPPEDADEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-76 1.53e-16

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 71.95  E-value: 1.53e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 873901339   1 MSISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEEDKNDTLPPENE 76
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNpSLETLLKLAKALGVSLDELLGGADEELPEALLSEE 82
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 141-202 2.71e-14

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 65.66  E-value: 2.71e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 873901339 141 ICFPASGDSMEPVIPDGSAIAIDvSNKKIIDGKVYAIDQDGLKRLKMLYRKPGGKLIIRSYN 202
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVD-PSDTPRDGDIVVARLDGELTVKRLQRRGGGRLRLISDN 61
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 2-95 1.71e-12

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 62.56  E-value: 1.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339   2 SISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEEDKNDTLPPENEwggi 80
Cdd:PRK09706   5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEpTGKNLFALAKALQCSPTWLLFGDEDKQPTPPVPLN---- 80

                         90
                 ....*....|....*
gi 873901339  81 kswdnkTPLDYDEVE 95
Cdd:PRK09706  81 ------QPVELSEDQ 89
Peptidase_S24 pfam00717
Peptidase S24-like;
103-223 1.36e-11

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 59.53  E-value: 1.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339  103 EFACGTGGSIDVDYNGFkLRFAKSTLRkigaptDGSTIICFPASGDSMEPVIPDGSAIAIDVSNkKIIDGKVYAIDQDGL 182
Cdd:pfam00717   5 RVAAGAPILAEEEIEGY-LPLPESLLS------PPGNLFALRVKGDSMEPGIPDGDLVLVDPSR-EARNGDIVVARLDGE 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 873901339  183 KRLKMLYRKpGGKLIIRSYNREEYDDEEADENSVMIIGRMF 223
Cdd:pfam00717  77 ATVKRLYRD-GGGIRLISLNPEYPPIELPAEDDVEIIGRVV 116
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 1.80e-11

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 57.56  E-value: 1.80e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 873901339   4 SERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWL 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNpSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-60 2.94e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.76  E-value: 2.94e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 873901339     6 RVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWL 60
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKpSLETLKKLAKALGVSLDEL 56
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-60 2.01e-09

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 51.77  E-value: 2.01e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 873901339    7 VKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWL 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 3-40 8.77e-06

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 41.88  E-value: 8.77e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 873901339    3 ISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKT 40
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKP 40
 
Name Accession Description Interval E-value
COG2932 COG2932
Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: ...
 96-224 8.25e-28

Phage repressor protein C, contains Cro/C1-type HTH and peptisase s24 domains [Mobilome: prophages, transposons];


Pssm-ID: 442176  Cd Length: 121  Bit Score: 102.35  E-value: 8.25e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339  96 VPFYkDIEFACGTGGSIDVDYNGFKLRFAkstlrkigaPTDGSTIICFPASGDSMEPVIPDGSAIAIDVSNKKIIDGKVY 175
Cdd:COG2932    1 VPLY-DGEASAGGGAFNEVEEPVDKLEFP---------GLPPDNLFAVRVSGDSMEPTIRDGDIVLVDPSDTEIRDGGIY 70

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|.
gi 873901339 176 AIDQDGLKRLKMLYRKPGGKLIIRSYNRE--EYDDEEADENSVMIIGRMFW 224
Cdd:COG2932   71 VVRTDGELLVKRLQRRPDGKLRLISDNPAypPIEIPPEDADEIEIIGRVVW 121
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-76 1.53e-16

Transcriptional regulator, contains XRE-family HTH domain [Transcription];


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 71.95  E-value: 1.53e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 873901339   1 MSISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEEDKNDTLPPENE 76
Cdd:COG1396    6 KALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNpSLETLLKLAKALGVSLDELLGGADEELPEALLSEE 82
S24_LexA-like cd06529
Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of ...
 141-202 2.71e-14

Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the protein. In the presence of single-stranded DNA, the LexA, UmuD and MucA proteins interact with RecA, activating self cleavage, thus either derepressing transcription in the case of LexA or activating the lesion-bypass polymerase in the case of UmuD and MucA. The LexA proteins are serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases. LexA sequence homologs are found in almost all of the bacterial genomes sequenced to date, covering a large number of phyla, suggesting both, an ancient origin and a widespread distribution of lexA and the SOS response.


Pssm-ID: 119397 [Multi-domain]  Cd Length: 81  Bit Score: 65.66  E-value: 2.71e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 873901339 141 ICFPASGDSMEPVIPDGSAIAIDvSNKKIIDGKVYAIDQDGLKRLKMLYRKPGGKLIIRSYN 202
Cdd:cd06529    1 FALRVKGDSMEPTIPDGDLVLVD-PSDTPRDGDIVVARLDGELTVKRLQRRGGGRLRLISDN 61
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
1-65 1.50e-12

DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 60.63  E-value: 1.50e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 873901339   1 MSISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEE 65
Cdd:COG1476    3 KKLGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNpSLELALKIARALGVSLEELFSLEE 68
PRK09706 PRK09706
transcriptional repressor DicA; Reviewed
 2-95 1.71e-12

transcriptional repressor DicA; Reviewed


Pssm-ID: 182039 [Multi-domain]  Cd Length: 135  Bit Score: 62.56  E-value: 1.71e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339   2 SISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEEDKNDTLPPENEwggi 80
Cdd:PRK09706   5 TLGQRIRYRRKQLKLSQRSLAKAVKVSHVSISQWERDETEpTGKNLFALAKALQCSPTWLLFGDEDKQPTPPVPLN---- 80

                         90
                 ....*....|....*
gi 873901339  81 kswdnkTPLDYDEVE 95
Cdd:PRK09706  81 ------QPVELSEDQ 89
Peptidase_S24 pfam00717
Peptidase S24-like;
103-223 1.36e-11

Peptidase S24-like;


Pssm-ID: 425835  Cd Length: 116  Bit Score: 59.53  E-value: 1.36e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339  103 EFACGTGGSIDVDYNGFkLRFAKSTLRkigaptDGSTIICFPASGDSMEPVIPDGSAIAIDVSNkKIIDGKVYAIDQDGL 182
Cdd:pfam00717   5 RVAAGAPILAEEEIEGY-LPLPESLLS------PPGNLFALRVKGDSMEPGIPDGDLVLVDPSR-EARNGDIVVARLDGE 76

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|.
gi 873901339  183 KRLKMLYRKpGGKLIIRSYNREEYDDEEADENSVMIIGRMF 223
Cdd:pfam00717  77 ATVKRLYRD-GGGIRLISLNPEYPPIELPAEDDVEIIGRVV 116
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 4-60 1.80e-11

Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.


Pssm-ID: 238045 [Multi-domain]  Cd Length: 58  Bit Score: 57.56  E-value: 1.80e-11
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 873901339   4 SERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWL 60
Cdd:cd00093    1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNpSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
6-60 2.94e-11

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 56.76  E-value: 2.94e-11
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 873901339     6 RVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWL 60
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKpSLETLKKLAKALGVSLDEL 56
Peptidase_S24_S26 cd06462
The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal ...
 142-221 1.63e-09

The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the transport of proteins across membranes in all living organisms. All members in this superfamily are unique serine proteases that carry out catalysis using a serine/lysine dyad instead of the prototypical serine/histidine/aspartic acid triad found in most serine proteases.


Pssm-ID: 119396 [Multi-domain]  Cd Length: 84  Bit Score: 53.04  E-value: 1.63e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339 142 CFPASGDSMEPVIPDGSAIAIDVSNKKIIDGKVYAIDQDGLKRL-KMLYRKPG-GKLIIRSYNREEYDDEEADENSVMII 219
Cdd:cd06462    2 ALRVEGDSMEPTIPDGDLVLVDKSSYEPKRGDIVVFRLPGGELTvKRVIGLPGeGHYFLLGDNPNSPDSRIDGPPELDIV 81


                 ..
gi 873901339 220 GR 221
Cdd:cd06462   82 GV 83
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 7-60 2.01e-09

Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and CI. Within the protein Swiss:Q5F9C2, the full protein fold incorporates a helix-turn-helix motif, but the function of this member is unlikely to be that of a DNA-binding regulator, the function of most other members, so is not necessarily characteriztic of the whole family.


Pssm-ID: 460181 [Multi-domain]  Cd Length: 55  Bit Score: 51.77  E-value: 2.01e-09
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 873901339    7 VKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWL 60
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREpSLETLKKLAEALGVSLDEL 55
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 1-67 5.97e-08

Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain CBS pair) [Transcription];


Pssm-ID: 442838 [Multi-domain]  Cd Length: 95  Bit Score: 49.25  E-value: 5.97e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 873901339   1 MSISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKtKRPRF--LPELAAALRCSVSWLVTGEEDK 67
Cdd:COG3620   16 DTLGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGK-RDPTVstLEKIAEALGKELSAVLVVDDGK 83
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 3-59 2.22e-07

Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and HTH domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441418 [Multi-domain]  Cd Length: 70  Bit Score: 46.85  E-value: 2.22e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 873901339   3 ISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSW 59
Cdd:COG1813   13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATpSLDTLRKLEKALGISLAE 70
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 5-66 4.68e-07

Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. This family contains many example antitoxins from bacterial toxin-antitoxin systems. These antitoxins are likely to be DNA-binding domains.


Pssm-ID: 463728 [Multi-domain]  Cd Length: 64  Bit Score: 45.74  E-value: 4.68e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 873901339    5 ERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK-RPRFLPELAAALRCSVSWLVTGEED 66
Cdd:pfam12844   2 ERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVpPAETLYKIAELLGVPANWLLQGEGE 64
couple_hipB TIGR03070
transcriptional regulator, y4mF family; Members of this family belong to a clade of ...
 3-40 8.77e-06

transcriptional regulator, y4mF family; Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems. [Regulatory functions, DNA interactions]


Pssm-ID: 213767 [Multi-domain]  Cd Length: 58  Bit Score: 41.88  E-value: 8.77e-06
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 873901339    3 ISERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKT 40
Cdd:TIGR03070   3 IGILVRARRKALGLTQADLADLAGVGLRFIRDLENGKP 40
PRK13355 PRK13355
bifunctional HTH-domain containing protein/aminotransferase; Provisional
 4-64 1.27e-05

bifunctional HTH-domain containing protein/aminotransferase; Provisional


Pssm-ID: 237361 [Multi-domain]  Cd Length: 517  Bit Score: 45.50  E-value: 1.27e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 873901339   4 SERVKNKRILLGLTQTELAET-------VGTTQqsIEQLESGKTkRPR--FLPELAAALRCSVSWLVTGE 64
Cdd:PRK13355   5 AERLKQAMKARGLKQEDLVHAaeargvkLGKSH--ISQYVSGKT-GPRrdVLPFLAAILGVSEDWLLGGE 71
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
5-41 2.86e-04

DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 37.99  E-value: 2.86e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 873901339   5 ERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTK 41
Cdd:COG2944    9 EEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRK 45
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 15-56 3.35e-04

Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433309 [Multi-domain]  Cd Length: 64  Bit Score: 37.89  E-value: 3.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 873901339   15 GLTQTELAETVGTTQQSIEQLESGKTKRPR--FLPELAAALRCS 56
Cdd:pfam13560  14 GLSQEALARRLGVSRSTLSRLETGRRGRPSpaVVERLARALGVD 57
PRK08154 PRK08154
anaerobic benzoate catabolism transcriptional regulator; Reviewed
 5-74 1.25e-03

anaerobic benzoate catabolism transcriptional regulator; Reviewed


Pssm-ID: 236167 [Multi-domain]  Cd Length: 309  Bit Score: 39.17  E-value: 1.25e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 873901339   5 ERVKNKRILLGLTQTELAETVGTTQQSIEQLESGKTKRP-RFLPELAAALRCSVSWLVTGEedknDTLPPE 74
Cdd:PRK08154  31 ERVRTLRARRGMSRKVLAQASGVSERYLAQLESGQGNVSiLLLRRVARALGCSLADLLGDV----DTSSPD 97
 
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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