NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|502609901|ref|WP_012846921|]
View 

MULTISPECIES: IS21 family transposase [Enterobacterales]

Protein Classification

IS21 family transposase( domain architecture ID 1750055)

IS21 family transposase binds to the end of a transposon and catalyzes the movement of the transposon to another part of the genome by a cut and paste mechanism or a replicative transposition mechanism

Gene Ontology:  GO:0003677|GO:0032196|GO:0015074
PubMed:  11315188

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
transpos_IS21 NF033546
IS21 family transposase;
10-304 1.18e-111

IS21 family transposase;


:

Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 326.47  E-value: 1.18e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  10 IKILHKQGMSSRAIARELGISRNTVKRYLRAQ--SEPPKYTPRPATASLLDEYRDYIRQRIADAHPYK-IPATVIAREIT 86
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRRAglDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  87 EQGYRGGMTILREFIRSL-AIPQEQEPVVRFETEPGRQMQVDWGTM----RNGKSP-LHVFVAVLGFSRMLYIEFTDNMR 160
Cdd:NF033546  81 AEGYPGSYSTVRRYVRRWrAEQGPAKVFVRLEHAPGEQAQVDFGEAtvvvTGGTGKiLHVFVAVLGYSRYTYVEATPSES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 161 YDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRDAYraGQHRFNPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYT 240
Cdd:NF033546 161 QEDLLDGHQRAFEFFGGVPREIVYDNLKTAVDKRDRY--EEPRLNPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVGYV 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502609901 241 RNSFYIPLMTRLRplgitvDVETANRYGLRWLHDVANQRRHETIQTRPCDRWIEEQQSMLALPT 304
Cdd:NF033546 239 RRWFLRLRGRRFE------SLAELNAALAEWLAELANQRPHGTTGGSPAERFEEERPALQPLPA 296
 
Name Accession Description Interval E-value
transpos_IS21 NF033546
IS21 family transposase;
10-304 1.18e-111

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 326.47  E-value: 1.18e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  10 IKILHKQGMSSRAIARELGISRNTVKRYLRAQ--SEPPKYTPRPATASLLDEYRDYIRQRIADAHPYK-IPATVIAREIT 86
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRRAglDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  87 EQGYRGGMTILREFIRSL-AIPQEQEPVVRFETEPGRQMQVDWGTM----RNGKSP-LHVFVAVLGFSRMLYIEFTDNMR 160
Cdd:NF033546  81 AEGYPGSYSTVRRYVRRWrAEQGPAKVFVRLEHAPGEQAQVDFGEAtvvvTGGTGKiLHVFVAVLGYSRYTYVEATPSES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 161 YDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRDAYraGQHRFNPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYT 240
Cdd:NF033546 161 QEDLLDGHQRAFEFFGGVPREIVYDNLKTAVDKRDRY--EEPRLNPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVGYV 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502609901 241 RNSFYIPLMTRLRplgitvDVETANRYGLRWLHDVANQRRHETIQTRPCDRWIEEQQSMLALPT 304
Cdd:NF033546 239 RRWFLRLRGRRFE------SLAELNAALAEWLAELANQRPHGTTGGSPAERFEEERPALQPLPA 296
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-303 4.48e-105

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 316.39  E-value: 4.48e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLRAQSEPP-KYTPRPATASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  80 VIAREITEQ-GYRGGMTILREFIRSLAIPQEQEPVVRFETEPGRQMQVDWGTMR----NGKS-PLHVFVAVLGFSRMLYI 153
Cdd:COG4584   79 RIWEELKEEhGYTGSYSTVRRYVRRLRPEYPKEAFVRLEHPPGEQAQVDWGEATvppiTGERrKVYVFVAVLGYSRYKYV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 154 EFTDNMRYDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRDAYragQHRFNPSLWQFGKEMGFSPRLCRPFRAQTKGKV 233
Cdd:COG4584  159 EAYPSQTQEDLLEAHVRAFEFFGGVPREIVYDNLKTAVTKADRG---EPVLNERFLAFAAHYGFEPRPCRPRRPKEKGKV 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 234 ERMVQYTRNSFYIPLMTrlrplgiTVDVETANRYGLRWLHDVANQRRHETIQTRPCDRWIEEQQSMLALP 303
Cdd:COG4584  236 ENAVGYVRRNFLAPRPR-------FTSLEELNAALLEWLERVANRRIHGTTGESPAERFAEEEEALLPLP 298
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 120-226 8.61e-18

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 77.35  E-value: 8.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  120 PGRQMQVDWGTMR--NGKSPLHVFVAVLGFSRMLYIEF-TDNMRYDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRda 196
Cdd:pfam00665   1 PNQLWQGDFTYIRipGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA-- 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 502609901  197 yragqhrfnpsLWQFGKEMGFSPRLCRPFR 226
Cdd:pfam00665  79 -----------FREFLKDLGIKPSFSRPGN 97
transpos_IS481 NF033577
IS481 family transposase; null
 15-292 3.49e-17

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 80.33  E-value: 3.49e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  15 KQGMSSRAIARELGISRNTV----KRYLRAQSEP-------PKYTPRPATASLLDEYRDYIRQRiadahpyKIPATVIAR 83
Cdd:NF033577  11 EDGWSVREAARRFGISRKTVykwlKRYRAGGEEGlidrsrrPHRSPRRTSPETEARILALRREL-------RLGPRRIAY 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  84 EITEQG--------YRggmtILRE--FIRSLAIPQEQEPVVRFETE-PGRQMQVD---WGTMRnGKSPLHVFVAVLGFSR 149
Cdd:NF033577  84 ELERQGpgvsrstvHR----ILRRhgLSRLRALDRKTGKVKRYERAhPGELWHIDikkLGRIP-DVGRLYLHTAIDDHSR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 150 MLYIEFTDNMRYDTLEECHRNAFSFFGGVPREVLYDNMKtvvlqrdAYRAGQHRFNpslwQFGKEMGFSPRLCRPFRAQT 229
Cdd:NF033577 159 FAYAELYPDETAETAADFLRRAFAEHGIPIRRVLTDNGS-------EFRSRAHGFE----LALAELGIEHRRTRPYHPQT 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 502609901 230 KGKVERMVQYTRNSF-YIPLMTRLRPLGITVDvetanryglRWLHDVANQRRHETI--QTrPCDRW 292
Cdd:NF033577 228 NGKVERFHRTLKDEFaYARPYESLAELQAALD---------EWLHHYNHHRPHSALggKT-PAERF 283
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 6-39 1.19e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 42.13  E-value: 1.19e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 502609901     6 TVMEIKILHK--QGMSSRAIARELGISRNTVKRYLR 39
Cdd:smart00421   5 TPREREVLRLlaEGLTNKEIAERLGISEKTVKTHLS 40
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 3-38 1.45e-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: 41.54  E-value: 1.45e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 502609901   3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd00569    7 TPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
transpos_IS630 NF033545
IS630 family transposase;
8-73 4.68e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 41.47  E-value: 4.68e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 502609901   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLR---------AQSEPPKYTPRpataSLLDEYRDYIRQRIADAHP 73
Cdd:NF033545   3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKrfnegglegLLDKPRPGRPR----KLLSEQQAELLALLLEEPP 73
transpos_IS1 NF033558
IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family ...
 17-51 3.68e-03

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: 38.02  E-value: 3.68e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 502609901  17 GMSSRAIARELGISRNTVKRYLRaQSEPPKYTPRP 51
Cdd:NF033558  55 GMGFRAIARVLGVSHNTVLRWLK-KLGPRQVTPEP 88
 
Name Accession Description Interval E-value
transpos_IS21 NF033546
IS21 family transposase;
10-304 1.18e-111

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 326.47  E-value: 1.18e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  10 IKILHKQGMSSRAIARELGISRNTVKRYLRAQ--SEPPKYTPRPATASLLDEYRDYIRQRIADAHPYK-IPATVIAREIT 86
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRRAglDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  87 EQGYRGGMTILREFIRSL-AIPQEQEPVVRFETEPGRQMQVDWGTM----RNGKSP-LHVFVAVLGFSRMLYIEFTDNMR 160
Cdd:NF033546  81 AEGYPGSYSTVRRYVRRWrAEQGPAKVFVRLEHAPGEQAQVDFGEAtvvvTGGTGKiLHVFVAVLGYSRYTYVEATPSES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 161 YDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRDAYraGQHRFNPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYT 240
Cdd:NF033546 161 QEDLLDGHQRAFEFFGGVPREIVYDNLKTAVDKRDRY--EEPRLNPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVGYV 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 502609901 241 RNSFYIPLMTRLRplgitvDVETANRYGLRWLHDVANQRRHETIQTRPCDRWIEEQQSMLALPT 304
Cdd:NF033546 239 RRWFLRLRGRRFE------SLAELNAALAEWLAELANQRPHGTTGGSPAERFEEERPALQPLPA 296
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-303 4.48e-105

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 316.39  E-value: 4.48e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLRAQSEPP-KYTPRPATASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  80 VIAREITEQ-GYRGGMTILREFIRSLAIPQEQEPVVRFETEPGRQMQVDWGTMR----NGKS-PLHVFVAVLGFSRMLYI 153
Cdd:COG4584   79 RIWEELKEEhGYTGSYSTVRRYVRRLRPEYPKEAFVRLEHPPGEQAQVDWGEATvppiTGERrKVYVFVAVLGYSRYKYV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 154 EFTDNMRYDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRDAYragQHRFNPSLWQFGKEMGFSPRLCRPFRAQTKGKV 233
Cdd:COG4584  159 EAYPSQTQEDLLEAHVRAFEFFGGVPREIVYDNLKTAVTKADRG---EPVLNERFLAFAAHYGFEPRPCRPRRPKEKGKV 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 234 ERMVQYTRNSFYIPLMTrlrplgiTVDVETANRYGLRWLHDVANQRRHETIQTRPCDRWIEEQQSMLALP 303
Cdd:COG4584  236 ENAVGYVRRNFLAPRPR-------FTSLEELNAALLEWLERVANRRIHGTTGESPAERFAEEEEALLPLP 298
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 120-226 8.61e-18

Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain pfam02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain pfam00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyzes the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site.


Pssm-ID: 459897 [Multi-domain]  Cd Length: 98  Bit Score: 77.35  E-value: 8.61e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  120 PGRQMQVDWGTMR--NGKSPLHVFVAVLGFSRMLYIEF-TDNMRYDTLEECHRNAFSFFGGVPREVLYDNMKTVVLQRda 196
Cdd:pfam00665   1 PNQLWQGDFTYIRipGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA-- 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 502609901  197 yragqhrfnpsLWQFGKEMGFSPRLCRPFR 226
Cdd:pfam00665  79 -----------FREFLKDLGIKPSFSRPGN 97
transpos_IS481 NF033577
IS481 family transposase; null
 15-292 3.49e-17

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 80.33  E-value: 3.49e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  15 KQGMSSRAIARELGISRNTV----KRYLRAQSEP-------PKYTPRPATASLLDEYRDYIRQRiadahpyKIPATVIAR 83
Cdd:NF033577  11 EDGWSVREAARRFGISRKTVykwlKRYRAGGEEGlidrsrrPHRSPRRTSPETEARILALRREL-------RLGPRRIAY 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  84 EITEQG--------YRggmtILRE--FIRSLAIPQEQEPVVRFETE-PGRQMQVD---WGTMRnGKSPLHVFVAVLGFSR 149
Cdd:NF033577  84 ELERQGpgvsrstvHR----ILRRhgLSRLRALDRKTGKVKRYERAhPGELWHIDikkLGRIP-DVGRLYLHTAIDDHSR 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901 150 MLYIEFTDNMRYDTLEECHRNAFSFFGGVPREVLYDNMKtvvlqrdAYRAGQHRFNpslwQFGKEMGFSPRLCRPFRAQT 229
Cdd:NF033577 159 FAYAELYPDETAETAADFLRRAFAEHGIPIRRVLTDNGS-------EFRSRAHGFE----LALAELGIEHRRTRPYHPQT 227

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 502609901 230 KGKVERMVQYTRNSF-YIPLMTRLRPLGITVDvetanryglRWLHDVANQRRHETI--QTrPCDRW 292
Cdd:NF033577 228 NGKVERFHRTLKDEFaYARPYESLAELQAALD---------EWLHHYNHHRPHSALggKT-PAERF 283
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
9-41 1.07e-06

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 45.04  E-value: 1.07e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 502609901    9 EIKILHKQGMSSRAIARELGISRNTVKRYLRAQ 41
Cdd:pfam02796  13 EVITLLEEGISIKQIAKIFGISRSTVYRYLAAS 45
TnsD pfam15978
Tn7-like transposition protein D; TnsD is a family of putative Tn7-like transposition proteins ...
 9-73 1.27e-06

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: 49.72  E-value: 1.27e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901    9 EIKILHKQ-GMSSRAIARELGISRNTVKRYLRAQSEPPKYTPRPATASLLDE-YRDYIRQR---IADAHP 73
Cdd:pfam15978 190 RLKILVEDeGLSLREIAKELGVDIKTVKRYARKLGLLHPWTKVKKRDRELSSsDREKHRKEwleLIRNYP 259
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 3-39 5.60e-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: 42.88  E-value: 5.60e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 502609901    3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLR 39
Cdd:pfam13936   6 SLEEREEIARLLAEGLSLREIARRLGRSPSTISRELR 42
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 6-39 1.19e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 42.13  E-value: 1.19e-05
                           10        20        30
                   ....*....|....*....|....*....|....*.
gi 502609901     6 TVMEIKILHK--QGMSSRAIARELGISRNTVKRYLR 39
Cdd:smart00421   5 TPREREVLRLlaEGLTNKEIAERLGISEKTVKTHLS 40
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 3-38 1.45e-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: 41.54  E-value: 1.45e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 502609901   3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd00569    7 TPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 9-40 5.02e-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: 42.57  E-value: 5.02e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 502609901   9 EIKILH--KQGMSSRAIARELGISRNTVKRYLRA 40
Cdd:COG2197   74 EREVLRllAEGLSNKEIAERLGISERTVKTHVSN 107
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 9-39 7.79e-05

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: 39.83  E-value: 7.79e-05
                         10        20        30
                 ....*....|....*....|....*....|...
gi 502609901   9 EIKILH--KQGMSSRAIARELGISRNTVKRYLR 39
Cdd:cd06170    5 EREVLRllAEGKTNKEIADILGISEKTVKTHLR 37
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
6-40 1.15e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 42.44  E-value: 1.15e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 502609901   6 TVMEIKILH--KQGMSSRAIARELGISRNTVKRYLRA 40
Cdd:COG2771  129 TPREREVLRllAEGLTLKEIARILGISERTVRTHLKR 165
SfsB COG3423
Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription];
13-54 1.59e-04

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


Pssm-ID: 442649 [Multi-domain]  Cd Length: 69  Bit Score: 39.43  E-value: 1.59e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 502609901  13 LHKQGMSSRAIARELGISRNTVKRYLRAQSepPKYTPRPATA 54
Cdd:COG3423   16 LRKRGTSLAALAREAGLSSSTLSNALTRPW--PKGERAIAEA 55
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 13-75 2.18e-04

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: 42.53  E-value: 2.18e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 502609901  13 LHKQGMSSRAIARELGISRNTVKRYLRAQSE-------PPKYTPRPATasLLDEYRDYIRQRIADAHPYK 75
Cdd:COG3415   34 LLAEGLSVREIAERLGVSRSTVYRWLKRYREgglaglkDRPRGGRPSK--LSDEQRERLLELLREKSPDQ 101
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
16-39 2.82e-04

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 41.23  E-value: 2.82e-04
                         10        20
                 ....*....|....*....|....
gi 502609901  16 QGMSSRAIARELGISRNTVKRYLR 39
Cdd:COG2909  136 EGLSNKEIAERLFISVNTVKTHLR 159
transpos_IS630 NF033545
IS630 family transposase;
8-73 4.68e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 41.47  E-value: 4.68e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 502609901   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLR---------AQSEPPKYTPRpataSLLDEYRDYIRQRIADAHP 73
Cdd:NF033545   3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKrfnegglegLLDKPRPGRPR----KLLSEQQAELLALLLEEPP 73
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 9-39 6.53e-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: 38.02  E-value: 6.53e-04
                         10        20        30
                 ....*....|....*....|....*....|...
gi 502609901   9 EIKILHK--QGMSSRAIARELGISRNTVKRYLR 39
Cdd:COG5905   17 EREVLELlaEGLTNKEIARQLFISEKTVKNHVS 49
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
8-70 1.21e-03

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


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 37.88  E-value: 1.21e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 502609901   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLRAQseppkytpRPATASLL--DEYRDYIRqRIAD 70
Cdd:COG2522   19 LLAKELVERGLSQSEIAKLLGITQAAVSQYLSGK--------RGASERIEfdEEIKELIE-ELAE 74
HTH_22 pfam13309
HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding ...
 10-39 1.90e-03

HTH domain; This domain is a helix-turn-helix domain that is likely to act as a DNA-binding domain.


Pssm-ID: 463841 [Multi-domain]  Cd Length: 63  Bit Score: 36.29  E-value: 1.90e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 502609901   10 IKILHKQGM-----SSRAIARELGISRNTVKRYLR 39
Cdd:pfam13309  29 VRALDEKGAfllkgAVEKVAKRLGVSRATVYNYLR 63
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-60 1.90e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.96  E-value: 1.90e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|
gi 502609901    11 KILHKQGMSSRAIARELGISRNTVKRYLRAqseppKYTPRPATASLLDEY 60
Cdd:smart00530   4 ELREEKGLTQEELAEKLGVSRSTLSRIENG-----KRKPSLETLKKLAKA 48
HTH_23 pfam13384
Homeodomain-like domain;
13-40 2.23e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.71  E-value: 2.23e-03
                          10        20
                  ....*....|....*....|....*...
gi 502609901   13 LHKQGMSSRAIARELGISRNTVKRYLRA 40
Cdd:pfam13384  13 LLAEGLSVKEIAELLGVSRRTVYRWLKR 40
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 15-44 2.41e-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: 35.59  E-value: 2.41e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 502609901   15 KQGMSSRAIARELGISRNTVKRYLRAQSEP 44
Cdd:pfam01381   7 ELGLSQEELAEKLGVSRSTISKIENGKREP 36
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-60 2.64e-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: 35.61  E-value: 2.64e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 502609901  11 KILHKQGMSSRAIARELGISRNTVKRYLRAqseppKYTPRPATASLLDEY 60
Cdd:cd00093    6 ELRKEKGLTQEELAEKLGVSRSTISRIENG-----KRNPSLETLEKLAKA 50
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
10-39 2.67e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 38.70  E-value: 2.67e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 502609901  10 IKILHKQGMSSRAIARELGISRNTVKRYLR 39
Cdd:COG3677   68 AIRLLLNGISLRQIARVLGVSYKTVWRWLH 97
transpos_IS1 NF033558
IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family ...
 17-51 3.68e-03

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: 38.02  E-value: 3.68e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 502609901  17 GMSSRAIARELGISRNTVKRYLRaQSEPPKYTPRP 51
Cdd:NF033558  55 GMGFRAIARVLGVSHNTVLRWLK-KLGPRQVTPEP 88
GerE pfam00196
Bacterial regulatory proteins, luxR family;
9-39 4.05e-03

Bacterial regulatory proteins, luxR family;


Pssm-ID: 425517 [Multi-domain]  Cd Length: 57  Bit Score: 35.25  E-value: 4.05e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 502609901    9 EIKILHK--QGMSSRAIARELGISRNTVKRYLR 39
Cdd:pfam00196   7 EREVLRWlaAGKSNKEIADELGISEKTVKVHRS 39
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
9-39 4.76e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 34.72  E-value: 4.76e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 502609901    9 EIKILH----KQGMSSRAIARELGISRNTVKRYLR 39
Cdd:pfam13412   3 DRKILNllqeNPRISQRELAERLGLSPSTVNRRLK 37
HTH_ARSR cd00090
Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric ...
 5-39 7.27e-03

Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.


Pssm-ID: 238042 [Multi-domain]  Cd Length: 78  Bit Score: 34.97  E-value: 7.27e-03
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 502609901   5 ETVMEI-KILHKQGMSSRAIARELGISRNTVKRYLR 39
Cdd:cd00090    7 PTRLRIlRLLLEGPLTVSELAERLGLSQSTVSRHLK 42
Sigma70_r4_2 pfam08281
Sigma-70, region 4; Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 ...
 16-40 7.76e-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: 34.35  E-value: 7.76e-03
                          10        20
                  ....*....|....*....|....*.
gi 502609901   16 QGMSSRAIARELGISRNTVKRYL-RA 40
Cdd:pfam08281  25 EGLSYAEIAELLGISEGTVKSRLsRA 50
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH