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Conserved domains on  [gi|1609610544|gb|TGE90337|]
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Cro/Cl family transcriptional regulator [Rhizobium sp. SEMIA 4032]

Protein Classification

helix-turn-helix domain-containing protein( domain architecture ID 11467355)

helix-turn-helix (HTH) domain-containing protein with an XRE (Xenobiotic Response Element) family HTH domain, binds DNA and may function as a transcriptional regulator; similar to Cereibacter sphaeroides propionyl-CoA carboxylase regulator

CATH:  1.10.260.40
Gene Ontology:  GO:0003677
PubMed:  10473770|8831795|15808743|2644244
SCOP:  4000362

Graphical summary

 Zoom to residue level

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List of domain hits

 Name Accession Description Interval E-value
COG3800 COG3800
Predicted transcriptional regulator [General function prediction only];
19-470 0e+00

Predicted transcriptional regulator [General function prediction only];


:

Pssm-ID: 443013 [Multi-domain]  Cd Length: 447  Bit Score: 517.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544  19 ARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGESDRLVSAVREALKDPLFLNYEPGLQELK 98
Cdd:COG3800     1 LQLLAKLLGLSLSYLNLIENLKKNPRALLLLLLAELLLVDYDDLVSLLLDLLLALLALLLDSLLLDELPLELFGLLLALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544  99 LIAQNAPGFAHALLRAHQAYRQNSEqlvqlddRLGRGTAQVERTPYEEVRDFFHFVDNYVAEIDLLAEELAEELEIEGGE 178
Cdd:COG3800    81 AAAAAAAPAALAAALRAAAERAAAY-------ALGREGASAEPFPLEEVRDFFEAHDNYFPELDEAAEALAAELGLDPGD 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 179 TYGILAAHLRDRYGIHITRT--EAAGGLIRHFDPAGKTLALSSYMAAPTRCFQLALQIAQLHAGATVDRVLAGAGFRNTE 256
Cdd:COG3800   154 LYAALAERLRERHGITVRILplEALGGLLRRYDPHRRTLLLSERLDPAQRAFQLAHQLALLEQGDLIDALLASAGFSSEE 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 257 AAEICRIGLHNYFAAALILPYGQFHRAAQELRHDLELLAVRFGASLEQVAHRLSTLQRPGMKGVPIFFAKIDRAGNITKR 336
Cdd:COG3800   234 ARRLARIGLANYFAGALLMPYGRFLRAAEALRYDIELLARRFGVSFEQVCHRLTTLQRPGARGVPFFFLRVDRAGNISKR 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 337 HSATRLQFARFGAACPLWNIHQAFESSDRIVRQLAETPDGVRYLSIATQIEKAGAGFNTERPRYAIALGCEISHAQNFVY 416
Cdd:COG3800   314 FSATGFHFARFGGACPLWNVHEAFETPGRILTQLAEMPDGRRYLCIARTVSRPGGGYGAPGRRFAIGLGCEIRHAGRLVY 393

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1609610544 417 ADTLDLGNAASFKPIGISCRVCERVDCVQRAVPPLKRKLHFDHLSRGALPYSIA 470
Cdd:COG3800   394 ADGLDLDDPAAATPIGVGCRLCERPDCPQRAFPPLGRRLKVDENRRGVSPYRFA 447
 
Name Accession Description Interval E-value
COG3800 COG3800
Predicted transcriptional regulator [General function prediction only];
19-470 0e+00

Predicted transcriptional regulator [General function prediction only];


Pssm-ID: 443013 [Multi-domain]  Cd Length: 447  Bit Score: 517.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544  19 ARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGESDRLVSAVREALKDPLFLNYEPGLQELK 98
Cdd:COG3800     1 LQLLAKLLGLSLSYLNLIENLKKNPRALLLLLLAELLLVDYDDLVSLLLDLLLALLALLLDSLLLDELPLELFGLLLALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544  99 LIAQNAPGFAHALLRAHQAYRQNSEqlvqlddRLGRGTAQVERTPYEEVRDFFHFVDNYVAEIDLLAEELAEELEIEGGE 178
Cdd:COG3800    81 AAAAAAAPAALAAALRAAAERAAAY-------ALGREGASAEPFPLEEVRDFFEAHDNYFPELDEAAEALAAELGLDPGD 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 179 TYGILAAHLRDRYGIHITRT--EAAGGLIRHFDPAGKTLALSSYMAAPTRCFQLALQIAQLHAGATVDRVLAGAGFRNTE 256
Cdd:COG3800   154 LYAALAERLRERHGITVRILplEALGGLLRRYDPHRRTLLLSERLDPAQRAFQLAHQLALLEQGDLIDALLASAGFSSEE 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 257 AAEICRIGLHNYFAAALILPYGQFHRAAQELRHDLELLAVRFGASLEQVAHRLSTLQRPGMKGVPIFFAKIDRAGNITKR 336
Cdd:COG3800   234 ARRLARIGLANYFAGALLMPYGRFLRAAEALRYDIELLARRFGVSFEQVCHRLTTLQRPGARGVPFFFLRVDRAGNISKR 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 337 HSATRLQFARFGAACPLWNIHQAFESSDRIVRQLAETPDGVRYLSIATQIEKAGAGFNTERPRYAIALGCEISHAQNFVY 416
Cdd:COG3800   314 FSATGFHFARFGGACPLWNVHEAFETPGRILTQLAEMPDGRRYLCIARTVSRPGGGYGAPGRRFAIGLGCEIRHAGRLVY 393

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1609610544 417 ADTLDLGNAASFKPIGISCRVCERVDCVQRAVPPLKRKLHFDHLSRGALPYSIA 470
Cdd:COG3800   394 ADGLDLDDPAAATPIGVGCRLCERPDCPQRAFPPLGRRLKVDENRRGVSPYRFA 447
ScfRs pfam09856
Short-chain fatty acyl coenzyme A regulators; This family includes short-chain fatty acid ...
 311-467 1.26e-91

Short-chain fatty acyl coenzyme A regulators; This family includes short-chain fatty acid regulators such as RAMB (regulator of acetate metabolism B), PCCR (Propionyl-CoA carboxylase regulator), PrpR (Propionate regulator). RamB is a negative transcriptional regulator of genes involved in acetate metabolism of C. glutamicum. It is responsible for expression control of the AK, PTA, ICL, and MS genes and, thus, for the proper adaptation to acetate as carbon and energy source. Nucleotide sequence analysis indicate the RamB protein consists of 469 aa with a putative HTH motif at the N terminus. PCCR prevents the accumulation of propionyl-CoA by controlling expression of the gene encoding propionyl-CoA carboxylase, which is responsible for propionyl-CoA consumption by Rhodobacter sphaeroides. Many other Proteobacteria and Actinomycetales contain one or several PccR homologs that group into distinct clades on the basis of the pathway of acyl-CoA metabolism that they control. PrpR is a transcriptional activator controlling prpDBC2 operon which encodes enzymes 2-methylcitrate dehydratase (PrpD2), 2-methylisocitrate lyase (PrpB2) and 2-methylcitrate synthase (PrpC2). They are essential for growth with propionate as carbon source. The regulatory protein belongs to the HTH_XRE regulator family. It has a length of 441 amino acids and an N-terminal lamda repressor-like DNA-binding domain.


Pssm-ID: 430882 [Multi-domain]  Cd Length: 157  Bit Score: 275.17  E-value: 1.26e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 311 TLQRPGMKGVPIFFAKIDRAGNITKRHSATRLQFARFGAACPLWNIHQAFESSDRIVRQLAETPDGVRYLSIATQIEKAG 390
Cdd:pfam09856   1 TLQRPGARGVPFFFVRVDRAGNISKRFSATGFPFARFGGACPLWNVHEAFATPGRILTQLAEMPDGRRYLTIARTVTRPG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1609610544 391 AGFNTERPRYAIALGCEISHAQNFVYADTLDLGNAASFKPIGISCRVCERVDCVQRAVPPLKRKLHFDHLSRGALPY 467
Cdd:pfam09856  81 GGFGAPPRRFAIGLGCEAEHAARLVYADGLDLDDPAAATPIGVGCRLCERPDCPQRAFPPLGRPLRVDENRRGVSPY 157
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-66 7.78e-12

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: 60.26  E-value: 7.78e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1609610544   9 GRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAEL 66
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-66 9.05e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 54.06  E-value: 9.05e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1609610544   11 KVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAEL 66
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
 
Name Accession Description Interval E-value
COG3800 COG3800
Predicted transcriptional regulator [General function prediction only];
19-470 0e+00

Predicted transcriptional regulator [General function prediction only];


Pssm-ID: 443013 [Multi-domain]  Cd Length: 447  Bit Score: 517.96  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544  19 ARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGESDRLVSAVREALKDPLFLNYEPGLQELK 98
Cdd:COG3800     1 LQLLAKLLGLSLSYLNLIENLKKNPRALLLLLLAELLLVDYDDLVSLLLDLLLALLALLLDSLLLDELPLELFGLLLALL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544  99 LIAQNAPGFAHALLRAHQAYRQNSEqlvqlddRLGRGTAQVERTPYEEVRDFFHFVDNYVAEIDLLAEELAEELEIEGGE 178
Cdd:COG3800    81 AAAAAAAPAALAAALRAAAERAAAY-------ALGREGASAEPFPLEEVRDFFEAHDNYFPELDEAAEALAAELGLDPGD 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 179 TYGILAAHLRDRYGIHITRT--EAAGGLIRHFDPAGKTLALSSYMAAPTRCFQLALQIAQLHAGATVDRVLAGAGFRNTE 256
Cdd:COG3800   154 LYAALAERLRERHGITVRILplEALGGLLRRYDPHRRTLLLSERLDPAQRAFQLAHQLALLEQGDLIDALLASAGFSSEE 233

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 257 AAEICRIGLHNYFAAALILPYGQFHRAAQELRHDLELLAVRFGASLEQVAHRLSTLQRPGMKGVPIFFAKIDRAGNITKR 336
Cdd:COG3800   234 ARRLARIGLANYFAGALLMPYGRFLRAAEALRYDIELLARRFGVSFEQVCHRLTTLQRPGARGVPFFFLRVDRAGNISKR 313

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 337 HSATRLQFARFGAACPLWNIHQAFESSDRIVRQLAETPDGVRYLSIATQIEKAGAGFNTERPRYAIALGCEISHAQNFVY 416
Cdd:COG3800   314 FSATGFHFARFGGACPLWNVHEAFETPGRILTQLAEMPDGRRYLCIARTVSRPGGGYGAPGRRFAIGLGCEIRHAGRLVY 393

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1609610544 417 ADTLDLGNAASFKPIGISCRVCERVDCVQRAVPPLKRKLHFDHLSRGALPYSIA 470
Cdd:COG3800   394 ADGLDLDDPAAATPIGVGCRLCERPDCPQRAFPPLGRRLKVDENRRGVSPYRFA 447
ScfRs pfam09856
Short-chain fatty acyl coenzyme A regulators; This family includes short-chain fatty acid ...
 311-467 1.26e-91

Short-chain fatty acyl coenzyme A regulators; This family includes short-chain fatty acid regulators such as RAMB (regulator of acetate metabolism B), PCCR (Propionyl-CoA carboxylase regulator), PrpR (Propionate regulator). RamB is a negative transcriptional regulator of genes involved in acetate metabolism of C. glutamicum. It is responsible for expression control of the AK, PTA, ICL, and MS genes and, thus, for the proper adaptation to acetate as carbon and energy source. Nucleotide sequence analysis indicate the RamB protein consists of 469 aa with a putative HTH motif at the N terminus. PCCR prevents the accumulation of propionyl-CoA by controlling expression of the gene encoding propionyl-CoA carboxylase, which is responsible for propionyl-CoA consumption by Rhodobacter sphaeroides. Many other Proteobacteria and Actinomycetales contain one or several PccR homologs that group into distinct clades on the basis of the pathway of acyl-CoA metabolism that they control. PrpR is a transcriptional activator controlling prpDBC2 operon which encodes enzymes 2-methylcitrate dehydratase (PrpD2), 2-methylisocitrate lyase (PrpB2) and 2-methylcitrate synthase (PrpC2). They are essential for growth with propionate as carbon source. The regulatory protein belongs to the HTH_XRE regulator family. It has a length of 441 amino acids and an N-terminal lamda repressor-like DNA-binding domain.


Pssm-ID: 430882 [Multi-domain]  Cd Length: 157  Bit Score: 275.17  E-value: 1.26e-91
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 311 TLQRPGMKGVPIFFAKIDRAGNITKRHSATRLQFARFGAACPLWNIHQAFESSDRIVRQLAETPDGVRYLSIATQIEKAG 390
Cdd:pfam09856   1 TLQRPGARGVPFFFVRVDRAGNISKRFSATGFPFARFGGACPLWNVHEAFATPGRILTQLAEMPDGRRYLTIARTVTRPG 80

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1609610544 391 AGFNTERPRYAIALGCEISHAQNFVYADTLDLGNAASFKPIGISCRVCERVDCVQRAVPPLKRKLHFDHLSRGALPY 467
Cdd:pfam09856  81 GGFGAPPRRFAIGLGCEAEHAARLVYADGLDLDDPAAATPIGVGCRLCERPDCPQRAFPPLGRPLRVDENRRGVSPY 157
Peptidase_M78 pfam06114
IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, ...
 188-310 2.13e-23

IrrE N-terminal-like domain; This entry includes the catalytic domain of the protein ImmA, which is a metallopeptidase containing an HEXXH zinc-binding motif from peptidase family M78. ImmA is encoded on a conjugative transposon. Conjugating bacteria are able to transfer conjugative transposons that can, for example, confer resistance to antibiotics. The transposon is integrated into the chromosome, but during conjugation excises itself and then moves to the recipient bacterium and re-integrate into its chromosome. Typically a conjugative tranposon encodes only the proteins required for this activity and the proteins that regulate it. During exponential growth, the ICEBs1 transposon of Bacillus subtilis is inactivated by the immunity repressor protein ImmR, which is encoded by the transposon and represses the genes for excision and transfer. Cleavage of ImmR relaxes repression and allows transfer of the transposon. ImmA has been shown to be essential for the cleavage of ImmR. This domain is also found in in metalloprotease IrrE, a central regulator of DNA damage repair in Deinococcaceae, HTH-type transcriptional regulators RamB and PrpC.


Pssm-ID: 399250  Cd Length: 122  Bit Score: 94.79  E-value: 2.13e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544 188 RDRYGIHITRT--EAAGGLIRHFDPAGKTLALSSYMAAPTRCFQLALQIAQLHAGATVDRVLAGAGFRNTEAAEICRigl 265
Cdd:pfam06114   1 AERLGIRVFFLplGAEDGDGRRFDRHTPVIFLNENLSPTRQRFTLAHELGHLLLHEGGDTLSDQFDFKTAEAREREA--- 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1609610544 266 hNYFAAALILPYGQFHRAAQELRHDLEL-LAVRFGASLEQVAHRLS 310
Cdd:pfam06114  78 -NIFAAALLMPYEAFLAAAETLRYDLELlLAERFGVSYEAVAHRLS 122
HipB COG1396
Transcriptional regulator, contains XRE-family HTH domain [Transcription];
1-83 2.71e-17

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


Pssm-ID: 441006 [Multi-domain]  Cd Length: 83  Bit Score: 76.57  E-value: 2.71e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1609610544   1 MATEKLFIGRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGESDRLVSAVRE 80
Cdd:COG1396     1 MSTLKKALGERLRELRKARGLTQEELAERLGVSRSTISRIERGRRNPSLETLLKLAKALGVSLDELLGGADEELPEALLS 80


                  ...
gi 1609610544  81 ALK 83
Cdd:COG1396    81 EEE 83
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 9-66 7.78e-12

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: 60.26  E-value: 7.78e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1609610544   9 GRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAEL 66
Cdd:cd00093     1 GERLKELRKEKGLTQEELAEKLGVSRSTISRIENGKRNPSLETLEKLAKALGVSLDEL 58
HTH_19 pfam12844
Helix-turn-helix domain; Members of this family contains a DNA-binding helix-turn-helix domain. ...
 9-72 1.69e-10

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: 56.53  E-value: 1.69e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1609610544   9 GRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGESD 72
Cdd:pfam12844   1 GERLRKAREERGLTQEELAERLGISRSQLSAIENGKSVPPAETLYKIAELLGVPANWLLQGEGE 64
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-66 9.05e-10

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 54.06  E-value: 9.05e-10
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*.
gi 1609610544   11 KVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAEL 66
Cdd:smart00530   1 RLKELREEKGLTQEELAEKLGVSRSTLSRIENGKRKPSLETLKKLAKALGVSLDEL 56
XRE COG1476
DNA-binding transcriptional regulator, XRE-family HTH domain [Transcription];
8-70 3.65e-09

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


Pssm-ID: 441085 [Multi-domain]  Cd Length: 68  Bit Score: 52.93  E-value: 3.65e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1609610544   8 IGRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGE 70
Cdd:COG1476     5 LGNRLKELRKERGLTQEELAELLGVSRQTISAIENGKYNPSLELALKIARALGVSLEELFSLE 67
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 12-66 1.55e-08

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: 50.62  E-value: 1.55e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1609610544  12 VRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAEL 66
Cdd:pfam01381   1 LKELREELGLSQEELAEKLGVSRSTISKIENGKREPSLETLKKLAEALGVSLDEL 55
aMBF1 COG1813
Archaeal ribosome-binding protein aMBF1, putative translation factor, contains Zn-ribbon and ...
 8-65 4.12e-08

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: 49.94  E-value: 4.12e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1609610544   8 IGRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAE 65
Cdd:COG1813    13 YGERIREAREARGLSQEELAEKLGVSESTIRRIERGEATPSLDTLRKLEKALGISLAE 70
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 8-67 1.44e-07

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: 48.29  E-value: 1.44e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1609610544   8 IGRKVRGLRENARATQAQFAERLGISASYLNQIENNQRP-VSASVLVTLVEKFQLDMAELA 67
Cdd:pfam13560   2 LGARLRRLRERAGLSQEALARRLGVSRSTLSRLETGRRGrPSPAVVERLARALGVDGAERA 62
AF2118 COG3620
Predicted transcriptional regulator, contains an XRE-type HTH domain (archaeal members contain ...
 8-75 2.86e-06

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: 45.40  E-value: 2.86e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1609610544   8 IGRKVRGLRENARATQAQFAERLGISASYLNQIENNQRPVSASVLVTLVEKFQLDMAELATGESDRLV 75
Cdd:COG3620    18 LGEALRLMRKELGLSQLPVAELVGVSQSDILRIESGKRDPTVSTLEKIAEALGKELSAVLVVDDGKLV 85
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
3-58 2.25e-05

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 42.23  E-value: 2.25e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1609610544   3 TEKLFIGRKVRGLRENARATQAQFAERLGISASYLNQIENNQR--PVSASVLVTLVEK 58
Cdd:COG2944     2 TKKPLTPEEIRALRERLGLSQAEFAALLGVSVSTVRRWEQGRRkpSGAALKLLRLLEK 59
VapI COG3093
Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense ...
 22-55 8.04e-05

Plasmid maintenance system antidote protein VapI, contains XRE-type HTH domain [Defense mechanisms];


Pssm-ID: 442327 [Multi-domain]  Cd Length: 87  Bit Score: 41.33  E-value: 8.04e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1609610544  22 TQAQFAERLGISASYLNQIENNQRPVSASVLVTL 55
Cdd:COG3093    24 SQTELAKALGVSRQRISEILNGKRAITADTALRL 57
RodZ COG1426
Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell ...
 8-45 1.57e-04

Cytoskeletal protein RodZ, contains Xre-like HTH and DUF4115 domains [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 441035 [Multi-domain]  Cd Length: 71  Bit Score: 39.79  E-value: 1.57e-04
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1609610544   8 IGRKVRGLRENARATQAQFAERLGISASYLNQIENNQR 45
Cdd:COG1426     6 IGELLRQAREAKGLSLEDVAERTKISVSYLEAIEEGDF 43
ImmA COG2856
Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, ...
 267-324 2.92e-03

Zn-dependent peptidase ImmA, M78 family [Posttranslational modification, protein turnover, chaperones];


Pssm-ID: 442104  Cd Length: 105  Bit Score: 37.33  E-value: 2.92e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1609610544 267 NYFAAALILPYGQFHRAAQE-LRHDLELLAVRFGASLEQVAHRLSTLQRPGMKGVPIFF 324
Cdd:COG2856    46 NAFAAELLMPEEALRELLKEkLSEDLEELAKRFGVSEEALLYRLKELGLIDEPGLGLIL 104
YdaS COG4197
DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];
23-58 9.28e-03

DNA-binding transcriptional regulator YdaS, prophage-encoded, Cro superfamily [Transcription];


Pssm-ID: 443351  Cd Length: 68  Bit Score: 34.89  E-value: 9.28e-03
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1609610544  23 QAQFAERLGISASYLNQIENNQRPVSASvLVTLVEK 58
Cdd:COG4197    11 QSALARALGVSQQAVSQWLNGKRRVPAE-RCLAIER 45
 
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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