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Conserved domains on  [gi|485765987|ref|WP_001390651|]
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helix-turn-helix domain-containing protein, partial [Escherichia coli]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
COG4584 super family cl27787
Transposase [Mobilome: prophages, transposons];
1-85 3.20e-23

Transposase [Mobilome: prophages, transposons];


The actual alignment was detected with superfamily member COG4584:

Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 91.05  E-value: 3.20e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485765987   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPP-KYTPRPAVASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78


                 ....*.
gi 485765987  80 VIAREI 85
Cdd:COG4584   79 RIWEEL 84
 
Name Accession Description Interval E-value
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-85 3.20e-23

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 91.05  E-value: 3.20e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485765987   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPP-KYTPRPAVASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78


                 ....*.
gi 485765987  80 VIAREI 85
Cdd:COG4584   79 RIWEEL 84
transpos_IS21 NF033546
IS21 family transposase;
10-85 2.15e-22

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 87.26  E-value: 2.15e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 485765987  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ--AKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYK-IPATVIAREI 85
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRraGLDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEEL 79
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 9-73 2.13e-07

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 46.25  E-value: 2.13e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485765987    9 EIKILHKQ-GMSSRAIARELGISRNTVKRYLQAKSEPPKYTPRPAVASLLDE-YRDYIRQR---IADAHP 73
Cdd:pfam15978 190 RLKILVEDeGLSLREIAKELGVDIKTVKRYARKLGLLHPWTKVKKRDRELSSsDREKHRKEwleLIRNYP 259
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 3-38 1.01e-05

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 38.46  E-value: 1.01e-05
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 485765987  3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd00569   7 TPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
transpos_IS630 NF033545
IS630 family transposase;
8-73 1.24e-05

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 41.09  E-value: 1.24e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 485765987   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLQ---------AKSEPPKYTPRpavaSLLDEYRDYIRQRIADAHP 73
Cdd:NF033545   3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKrfnegglegLLDKPRPGRPR----KLLSEQQAELLALLLEEPP 73
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 6-38 1.91e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 38.28  E-value: 1.91e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 485765987    6 TVMEIKILHK--QGMSSRAIARELGISRNTVKRYL 38
Cdd:smart00421  5 TPREREVLRLlaEGLTNKEIAERLGISEKTVKTHL 39
transpos_IS1 NF033558
IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family ...
 17-51 6.86e-05

IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family elements usually through a translational frameshift mechanism.


Pssm-ID: 468085 [Multi-domain]  Cd Length: 199  Bit Score: 38.79  E-value: 6.86e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 485765987  17 GMSSRAIARELGISRNTVKRYLQaKSEPPKYTPRP 51
Cdd:NF033558  55 GMGFRAIARVLGVSHNTVLRWLK-KLGPRQVTPEP 88
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
9-39 1.02e-03

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 35.85  E-value: 1.02e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 485765987   9 EIKILHKQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:PRK13413 164 KIKKLLDKGTSKSEIARKLGVSRTTLARFLK 194
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 9-39 3.29e-03

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 34.07  E-value: 3.29e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 485765987    9 EIKILHK-QGMSSRAIARELGISRNTVKRYLQ 39
Cdd:TIGR02985 120 EIFILSRfEGLSNKEIAEELGISVKTVEYHIT 151
 
Name Accession Description Interval E-value
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-85 3.20e-23

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 91.05  E-value: 3.20e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485765987   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPP-KYTPRPAVASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78


                 ....*.
gi 485765987  80 VIAREI 85
Cdd:COG4584   79 RIWEEL 84
transpos_IS21 NF033546
IS21 family transposase;
10-85 2.15e-22

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 87.26  E-value: 2.15e-22
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 485765987  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ--AKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYK-IPATVIAREI 85
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRraGLDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEEL 79
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 9-73 2.13e-07

Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins type D.


Pssm-ID: 379756  Cd Length: 360  Bit Score: 46.25  E-value: 2.13e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485765987    9 EIKILHKQ-GMSSRAIARELGISRNTVKRYLQAKSEPPKYTPRPAVASLLDE-YRDYIRQR---IADAHP 73
Cdd:pfam15978 190 RLKILVEDeGLSLREIAKELGVDIKTVKRYARKLGLLHPWTKVKKRDRELSSsDREKHRKEwleLIRNYP 259
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
9-41 4.12e-06

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 39.65  E-value: 4.12e-06
                         10        20        30
                 ....*....|....*....|....*....|...
gi 485765987   9 EIKILHKQGMSSRAIARELGISRNTVKRYLQAK 41
Cdd:pfam02796 13 EVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 3-36 8.59e-06

Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is likely to be DNA-binding.


Pssm-ID: 433591 [Multi-domain]  Cd Length: 44  Bit Score: 39.03  E-value: 8.59e-06
                         10        20        30
                 ....*....|....*....|....*....|....
gi 485765987   3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKR 36
Cdd:pfam13936  6 SLEEREEIARLLAEGLSLREIARRLGRSPSTISR 39
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 3-38 1.01e-05

Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a C-terminal DNA-binding domain (HTH_Hin) and a catalytic domain.


Pssm-ID: 259851 [Multi-domain]  Cd Length: 42  Bit Score: 38.46  E-value: 1.01e-05
                        10        20        30
                ....*....|....*....|....*....|....*.
gi 485765987  3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd00569   7 TPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
transpos_IS630 NF033545
IS630 family transposase;
8-73 1.24e-05

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 41.09  E-value: 1.24e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 485765987   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLQ---------AKSEPPKYTPRpavaSLLDEYRDYIRQRIADAHP 73
Cdd:NF033545   3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKrfnegglegLLDKPRPGRPR----KLLSEQQAELLALLLEEPP 73
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 6-38 1.91e-05

helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 38.28  E-value: 1.91e-05
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 485765987    6 TVMEIKILHK--QGMSSRAIARELGISRNTVKRYL 38
Cdd:smart00421  5 TPREREVLRLlaEGLTNKEIAERLGISEKTVKTHL 39
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 9-40 3.06e-05

DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 441799 [Multi-domain]  Cd Length: 131  Bit Score: 39.11  E-value: 3.06e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 485765987   9 EIKILH--KQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:COG2197   74 EREVLRllAEGLSNKEIAERLGISERTVKTHVSN 107
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 13-75 4.28e-05

CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein Csa3, CARF domain is part of the Pathway/BioSystem: CRISPR-Cas system


Pssm-ID: 442641 [Multi-domain]  Cd Length: 325  Bit Score: 39.83  E-value: 4.28e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 485765987  13 LHKQGMSSRAIARELGISRNTVKRYLQAKSE-------PPKYTPRPavASLLDEYRDYIRQRIADAHPYK 75
Cdd:COG3415   34 LLAEGLSVREIAERLGVSRSTVYRWLKRYREgglaglkDRPRGGRP--SKLSDEQRERLLELLREKSPDQ 101
SfsB COG3423
Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription];
13-58 4.32e-05

Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription];


Pssm-ID: 442649 [Multi-domain]  Cd Length: 69  Bit Score: 37.51  E-value: 4.32e-05
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 485765987 13 LHKQGMSSRAIARELGISRNTVKRYLQAKSepPKYtpRPAVASLLD 58
Cdd:COG3423  16 LRKRGTSLAALAREAGLSSSTLSNALTRPW--PKG--ERAIAEALG 57
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
16-39 6.49e-05

ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 38.92  E-value: 6.49e-05
                         10        20
                 ....*....|....*....|....
gi 485765987  16 QGMSSRAIARELGISRNTVKRYLQ 39
Cdd:COG2909  136 EGLSNKEIAERLFISVNTVKTHLR 159
transpos_IS1 NF033558
IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family ...
 17-51 6.86e-05

IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family elements usually through a translational frameshift mechanism.


Pssm-ID: 468085 [Multi-domain]  Cd Length: 199  Bit Score: 38.79  E-value: 6.86e-05
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 485765987  17 GMSSRAIARELGISRNTVKRYLQaKSEPPKYTPRP 51
Cdd:NF033558  55 GMGFRAIARVLGVSHNTVLRWLK-KLGPRQVTPEP 88
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
6-40 1.47e-04

DNA-binding transcriptional regulator, CsgD family [Transcription];


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 38.20  E-value: 1.47e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 485765987   6 TVMEIKILH--KQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:COG2771  129 TPREREVLRllAEGLTLKEIARILGISERTVRTHLKR 165
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 9-38 1.53e-04

C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental nitrate or nitrite is present under anerobic conditions. FixJ is involved in the transcriptional activation of nitrogen fixation genes. The group also includes small proteins which lack an N-terminal signaling domain, such as Bacillus subtilis GerE. GerE is dimeric and acts in conjunction with sigmaK as an activator or a repressor modulating the expression of various genes in particular those encoding the spore-coat. These LuxR family regulators may share a similar organization of their target binding sites. For example the LuxR dimer binds the lux box, a 20bp inverted repeat, GerE dimers bind two 12bp consensus sequences in inverted orientation having the central four bases overlap, and the NarL dimer binds two 7bp inverted repeats separated by 2 bp.


Pssm-ID: 99777 [Multi-domain]  Cd Length: 57  Bit Score: 35.97  E-value: 1.53e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 485765987  9 EIKILH--KQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd06170   5 EREVLRllAEGKTNKEIADILGISEKTVKTHL 36
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
10-39 2.85e-04

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 37.54  E-value: 2.85e-04
                         10        20        30
                 ....*....|....*....|....*....|
gi 485765987  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:COG3677   68 AIRLLLNGISLRQIARVLGVSYKTVWRWLH 97
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 9-38 4.13e-04

Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell division, chromosome partitioning, Transcription];


Pssm-ID: 444607 [Multi-domain]  Cd Length: 76  Bit Score: 35.32  E-value: 4.13e-04
                        10        20        30
                ....*....|....*....|....*....|..
gi 485765987  9 EIKILHK--QGMSSRAIARELGISRNTVKRYL 38
Cdd:COG5905  17 EREVLELlaEGLTNKEIARQLFISEKTVKNHV 48
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 11-58 8.52e-04

Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to DNA.


Pssm-ID: 433211 [Multi-domain]  Cd Length: 63  Bit Score: 34.05  E-value: 8.52e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 485765987  11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEPPKYTPRPAVASLLD 58
Cdd:pfam13443  4 KLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALG 51
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
9-39 1.02e-03

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 35.85  E-value: 1.02e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 485765987   9 EIKILHKQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:PRK13413 164 KIKKLLDKGTSKSEIARKLGVSRTTLARFLK 194
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-44 1.27e-03

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: 33.68  E-value: 1.27e-03
                        10        20        30
                ....*....|....*....|....*....|....
gi 485765987 11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEP 44
Cdd:cd00093   6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNP 39
PRK10651 PRK10651
transcriptional regulator NarL; Provisional
 6-35 1.44e-03

transcriptional regulator NarL; Provisional


Pssm-ID: 182619 [Multi-domain]  Cd Length: 216  Bit Score: 35.39  E-value: 1.44e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 485765987   6 TVMEIKILHK--QGMSSRAIARELGISRNTVK 35
Cdd:PRK10651 157 TPRERDILKLiaQGLPNKMIARRLDITESTVK 188
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-73 1.51e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 33.75  E-value: 1.51e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 485765987  6 TVMEIKILHKQ-GMSSRAIARELGISRNTVKRYLQAKSEPPkytprPAVASLLdeyrdyirqRIADAHP 73
Cdd:COG2944   7 TPEEIRALRERlGLSQAEFAALLGVSVSTVRRWEQGRRKPS-----GAALKLL---------RLLEKHP 61
HTH_31 pfam13560
Helix-turn-helix domain; This domain is a helix-turn-helix domain that probably binds to DNA.
 17-61 1.58e-03

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: 33.66  E-value: 1.58e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*
gi 485765987  17 GMSSRAIARELGISRNTVKRYLQAKSEPPkytPRPAVASLLDEYR 61
Cdd:pfam13560 14 GLSQEALARRLGVSRSTLSRLETGRRGRP---SPAVVERLARALG 55
HTH_23 pfam13384
Homeodomain-like domain;
13-40 1.65e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 33.40  E-value: 1.65e-03
                         10        20
                 ....*....|....*....|....*...
gi 485765987  13 LHKQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:pfam13384 13 LLAEGLSVKEIAELLGVSRRTVYRWLKR 40
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
14-43 1.84e-03

DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 35.10  E-value: 1.84e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 485765987  14 HKQGMSSRAIARELGISRNTVKRYLQ-AKSE 43
Cdd:COG2390    7 YVEGLTQREIAERLGISRRTVSRLLAeAREE 37
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
8-38 2.06e-03

Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 34.03  E-value: 2.06e-03
                        10        20        30
                ....*....|....*....|....*....|.
gi 485765987  8 MEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:COG2522  19 LLAKELVERGLSQSEIAKLLGITQAAVSQYL 49
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-44 3.02e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 32.49  E-value: 3.02e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 485765987   11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEP 44
Cdd:smart00530  4 ELREEKGLTQEELAEKLGVSRSTLSRIENGKRKP 37
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 16-39 3.03e-03

Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif.


Pssm-ID: 400535 [Multi-domain]  Cd Length: 54  Bit Score: 32.43  E-value: 3.03e-03
                         10        20
                 ....*....|....*....|....
gi 485765987  16 QGMSSRAIARELGISRNTVKRYLQ 39
Cdd:pfam08281 25 EGLSYAEIAELLGISEGTVKSRLS 48
Phage_antitermQ pfam06530
Phage antitermination protein Q; This family consists of several phage antitermination protein ...
 17-40 3.15e-03

Phage antitermination protein Q; This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream.


Pssm-ID: 428991  Cd Length: 118  Bit Score: 33.76  E-value: 3.15e-03
                          10        20
                  ....*....|....*....|....
gi 485765987   17 GMSSRAIARELGISRNTVKRYLQA 40
Cdd:pfam06530  78 GMSKRAIARKLKCSEGEIRKKLQT 101
Sig70_bacteroi1 TIGR02985
RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors ...
 9-39 3.29e-03

RNA polymerase sigma-70 factor, Bacteroides expansion family 1; This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.


Pssm-ID: 274376 [Multi-domain]  Cd Length: 161  Bit Score: 34.07  E-value: 3.29e-03
                          10        20        30
                  ....*....|....*....|....*....|..
gi 485765987    9 EIKILHK-QGMSSRAIARELGISRNTVKRYLQ 39
Cdd:TIGR02985 120 EIFILSRfEGLSNKEIAEELGISVKTVEYHIT 151
CxxCG_CxxCG_HTH TIGR03830
putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of ...
 9-73 4.40e-03

putative zinc finger/helix-turn-helix protein, YgiT family; This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.


Pssm-ID: 274805 [Multi-domain]  Cd Length: 127  Bit Score: 33.37  E-value: 4.40e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 485765987    9 EIKILHKQ-GMSSRAIARELGISRNTVKRYLQAKSEPPKytprpAVASLLdeyrdyirqRIADAHP 73
Cdd:TIGR03830  69 EIRRIRKKlGLSQREAAELLGGGVNAFSRYERGEVRPSK-----ALDKLL---------RLLDKHP 120
HTH_35 pfam13693
Winged helix-turn-helix DNA-binding;
13-38 5.00e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 433408  Cd Length: 70  Bit Score: 32.59  E-value: 5.00e-03
                         10        20
                 ....*....|....*....|....*.
gi 485765987  13 LHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:pfam13693 11 LRKRGTTLAALSRSAGLSSSTLSNAL 36
HTH_IclR pfam09339
IclR helix-turn-helix domain;
14-40 5.32e-03

IclR helix-turn-helix domain;


Pssm-ID: 430539 [Multi-domain]  Cd Length: 52  Bit Score: 31.99  E-value: 5.32e-03
                         10        20
                 ....*....|....*....|....*..
gi 485765987  14 HKQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:pfam09339 15 APGPLTLTEIARRTGLPKSTAHRLLQT 41
YozG COG3655
DNA-binding transcriptional regulator, XRE family [Transcription];
11-47 5.99e-03

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


Pssm-ID: 442872 [Multi-domain]  Cd Length: 69  Bit Score: 32.04  E-value: 5.99e-03
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 485765987 11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEPPKY 47
Cdd:COG3655   8 ELLAERGMTKKELAEATGISRATLSRLKNGKAKAVRL 44
HolA COG1466
DNA polymerase III, delta subunit [Replication, recombination and repair];
4-40 6.75e-03

DNA polymerase III, delta subunit [Replication, recombination and repair];


Pssm-ID: 441075 [Multi-domain]  Cd Length: 305  Bit Score: 33.69  E-value: 6.75e-03
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 485765987   4 FETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:COG1466  239 FRLLLQVKALLAQGKSLAEIAKELGVPPFRVKLALRA 275
GerE pfam00196
Bacterial regulatory proteins, luxR family;
16-38 7.40e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 31.79  E-value: 7.40e-03
                         10        20
                 ....*....|....*....|...
gi 485765987  16 QGMSSRAIARELGISRNTVKRYL 38
Cdd:pfam00196 16 AGKSNKEIADELGISEKTVKVHR 38
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 15-44 7.91e-03

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: 31.36  E-value: 7.91e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 485765987  15 KQGMSSRAIARELGISRNTVKRYLQAKSEP 44
Cdd:pfam01381  7 ELGLSQEELAEKLGVSRSTISKIENGKREP 36
FixJ COG4566
DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal ...
 16-42 8.78e-03

DNA-binding response regulator, FixJ family, consists of REC and HTH domains [Signal transduction mechanisms, Transcription];


Pssm-ID: 443623 [Multi-domain]  Cd Length: 196  Bit Score: 33.15  E-value: 8.78e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 485765987  16 QGMSSRAIARELGISRNTVKRY-------LQAKS 42
Cdd:COG4566  151 AGLSNKQIARELGISPRTVEVHranvmekLGARS 184
 
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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