NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|446178089|ref|WP_000255944|]
View 

MULTISPECIES: IS21-like element IS100 family transposase [Bacteria]

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 super family cl41315
IS21 family transposase;
10-304 1.71e-111

IS21 family transposase;


The actual alignment was detected with superfamily member NF033546:

Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 326.09  E-value: 1.71e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ--AKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYK-IPATVIAREIR 86
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRraGLDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  87 DQGYRGGMTILRAFIRSLSVPQEQEPA-VRFETEPGRQMQVDWGTM----RNGRSP-LHVFVAVLGYSRMLYIEFTDNMR 160
Cdd:NF033546  81 AEGYPGSYSTVRRYVRRWRAEQGPAKVfVRLEHAPGEQAQVDFGEAtvvvTGGTGKiLHVFVAVLGYSRYTYVEATPSES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 161 YDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYqtGQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYT 240
Cdd:NF033546 161 QEDLLDGHQRAFEFFGGVPREIVYDNLKTAVDKRDRY--EEPRLNPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVGYV 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446178089 241 RNSFYIPLMTRLRpmgitvDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPP 304
Cdd:NF033546 239 RRWFLRLRGRRFE------SLAELNAALAEWLAELANQRPHGTTGGSPAERFEEERPALQPLPA 296
 
Name Accession Description Interval E-value
transpos_IS21 NF033546
IS21 family transposase;
10-304 1.71e-111

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 326.09  E-value: 1.71e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ--AKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYK-IPATVIAREIR 86
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRraGLDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  87 DQGYRGGMTILRAFIRSLSVPQEQEPA-VRFETEPGRQMQVDWGTM----RNGRSP-LHVFVAVLGYSRMLYIEFTDNMR 160
Cdd:NF033546  81 AEGYPGSYSTVRRYVRRWRAEQGPAKVfVRLEHAPGEQAQVDFGEAtvvvTGGTGKiLHVFVAVLGYSRYTYVEATPSES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 161 YDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYqtGQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYT 240
Cdd:NF033546 161 QEDLLDGHQRAFEFFGGVPREIVYDNLKTAVDKRDRY--EEPRLNPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVGYV 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446178089 241 RNSFYIPLMTRLRpmgitvDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPP 304
Cdd:NF033546 239 RRWFLRLRGRRFE------SLAELNAALAEWLAELANQRPHGTTGGSPAERFEEERPALQPLPA 296
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-304 1.99e-105

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 317.16  E-value: 1.99e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPP-KYTPRPAVASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  80 VIAREIRDQ-GYRGGMTILRAFIRSLSVPQEQEPAVRFETEPGRQMQVDWGTMR-----NGRSPLHVFVAVLGYSRMLYI 153
Cdd:COG4584   79 RIWEELKEEhGYTGSYSTVRRYVRRLRPEYPKEAFVRLEHPPGEQAQVDWGEATvppitGERRKVYVFVAVLGYSRYKYV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 154 EFTDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYqtgQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKV 233
Cdd:COG4584  159 EAYPSQTQEDLLEAHVRAFEFFGGVPREIVYDNLKTAVTKADRG---EPVLNERFLAFAAHYGFEPRPCRPRRPKEKGKV 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446178089 234 ERMVQYTRNSFYIPLMTrlrpmgiTVDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPP 304
Cdd:COG4584  236 ENAVGYVRRNFLAPRPR-------FTSLEELNAALLEWLERVANRRIHGTTGESPAERFAEEEEALLPLPP 299
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 120-226 5.68e-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: 77.74  E-value: 5.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  120 PGRQMQVDWGTMR--NGRSPLHVFVAVLGYSRMLYIEF-TDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRda 196
Cdd:pfam00665   1 PNQLWQGDFTYIRipGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA-- 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 446178089  197 yqtgqhrfhpsLWQFGKEMGFSPRLCRPFR 226
Cdd:pfam00665  79 -----------FREFLKDLGIKPSFSRPGN 97
transpos_IS481 NF033577
IS481 family transposase; null
 15-292 4.36e-16

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 77.25  E-value: 4.36e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  15 KQGMSSRAIARELGISRNTV----KRYLQAKSEP-------PKYTPR---PAVASLLDEYRdyiRQRiadahpyKIPATV 80
Cdd:NF033577  11 EDGWSVREAARRFGISRKTVykwlKRYRAGGEEGlidrsrrPHRSPRrtsPETEARILALR---REL-------RLGPRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  81 IAREIRDQG--------YRggmtILR--AFIRSLSVPQEQEPAVRFETE-PGRQMQVD---WGTMRNGRSpLHVFVAVLG 146
Cdd:NF033577  81 IAYELERQGpgvsrstvHR----ILRrhGLSRLRALDRKTGKVKRYERAhPGELWHIDikkLGRIPDVGR-LYLHTAIDD 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 147 YSRMLYIEFTDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKtvvlqrdAYQTGQHRFHpslwQFGKEMGFSPRLCRPFR 226
Cdd:NF033577 156 HSRFAYAELYPDETAETAADFLRRAFAEHGIPIRRVLTDNGS-------EFRSRAHGFE----LALAELGIEHRRTRPYH 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446178089 227 AQTKGKVERMVQYTRNSFyipLMTRLRPmgitvDVETANRHGLRWLHDVANQRKHETI-QARPCDRW 292
Cdd:NF033577 225 PQTNGKVERFHRTLKDEF---AYARPYE-----SLAELQAALDEWLHHYNHHRPHSALgGKTPAERF 283
HTH_Hin_like cd00569
Helix-turn-helix domain of Hin and related proteins; This domain model summarizes a family of ...
 3-38 1.04e-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: 41.93  E-value: 1.04e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446178089   3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd00569    7 TPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 6-38 2.77e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 41.36  E-value: 2.77e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 446178089     6 TVMEIKILHK--QGMSSRAIARELGISRNTVKRYL 38
Cdd:smart00421   5 TPREREVLRLlaEGLTNKEIAERLGISEKTVKTHL 39
transpos_IS630 NF033545
IS630 family transposase;
8-73 2.78e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 42.24  E-value: 2.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446178089   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLQ---------AKSEPPKYTPRpavaSLLDEYRDYIRQRIADAHP 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 3.17e-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: 38.41  E-value: 3.17e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446178089  17 GMSSRAIARELGISRNTVKRYLQaKSEPPKYTPRP 51
Cdd:NF033558  55 GMGFRAIARVLGVSHNTVLRWLK-KLGPRQVTPEP 88
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
9-39 5.75e-03

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 37.39  E-value: 5.75e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 446178089   9 EIKILHKQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:PRK13413 164 KIKKLLDKGTSKSEIARKLGVSRTTLARFLK 194
 
Name Accession Description Interval E-value
transpos_IS21 NF033546
IS21 family transposase;
10-304 1.71e-111

IS21 family transposase;


Pssm-ID: 468077 [Multi-domain]  Cd Length: 296  Bit Score: 326.09  E-value: 1.71e-111
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ--AKSEPPKYTPRPAVASLLDEYRDYIRQRIADAHPYK-IPATVIAREIR 86
Cdd:NF033546   1 IRLLFRQGLSIREIARELGISRNTVRKYLRraGLDEPPKYERRPPRPSKLDPFEPYIPDWLEAHLRKPgVTATLLWEELR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  87 DQGYRGGMTILRAFIRSLSVPQEQEPA-VRFETEPGRQMQVDWGTM----RNGRSP-LHVFVAVLGYSRMLYIEFTDNMR 160
Cdd:NF033546  81 AEGYPGSYSTVRRYVRRWRAEQGPAKVfVRLEHAPGEQAQVDFGEAtvvvTGGTGKiLHVFVAVLGYSRYTYVEATPSES 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 161 YDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYqtGQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKVERMVQYT 240
Cdd:NF033546 161 QEDLLDGHQRAFEFFGGVPREIVYDNLKTAVDKRDRY--EEPRLNPRFAAFAAHYGFEPRPCRPYRPQEKGKVERAVGYV 238

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 446178089 241 RNSFYIPLMTRLRpmgitvDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPP 304
Cdd:NF033546 239 RRWFLRLRGRRFE------SLAELNAALAEWLAELANQRPHGTTGGSPAERFEEERPALQPLPA 296
COG4584 COG4584
Transposase [Mobilome: prophages, transposons];
1-304 1.99e-105

Transposase [Mobilome: prophages, transposons];


Pssm-ID: 443641 [Multi-domain]  Cd Length: 484  Bit Score: 317.16  E-value: 1.99e-105
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089   1 MVTFETVMEIKILHKQGMSSRAIARELGISRNTVKRYLQAKSEPP-KYTPRPAVASLLDEYRDYIRQRIADAHpyKIPAT 79
Cdd:COG4584    1 MLTMEQIREIRRLLREGLSIREIARELGISRNTVRKYLRRAEEWPeLYPRRRPRPSKLDPYKEYIDEWLEEGP--RVTAK 78

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  80 VIAREIRDQ-GYRGGMTILRAFIRSLSVPQEQEPAVRFETEPGRQMQVDWGTMR-----NGRSPLHVFVAVLGYSRMLYI 153
Cdd:COG4584   79 RIWEELKEEhGYTGSYSTVRRYVRRLRPEYPKEAFVRLEHPPGEQAQVDWGEATvppitGERRKVYVFVAVLGYSRYKYV 158

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 154 EFTDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRDAYqtgQHRFHPSLWQFGKEMGFSPRLCRPFRAQTKGKV 233
Cdd:COG4584  159 EAYPSQTQEDLLEAHVRAFEFFGGVPREIVYDNLKTAVTKADRG---EPVLNERFLAFAAHYGFEPRPCRPRRPKEKGKV 235

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 446178089 234 ERMVQYTRNSFYIPLMTrlrpmgiTVDVETANRHGLRWLHDVANQRKHETIQARPCDRWLEEQQSMLALPP 304
Cdd:COG4584  236 ENAVGYVRRNFLAPRPR-------FTSLEELNAALLEWLERVANRRIHGTTGESPAERFAEEEEALLPLPP 299
rve pfam00665
Integrase core domain; Integrase mediates integration of a DNA copy of the viral genome into ...
 120-226 5.68e-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: 77.74  E-value: 5.68e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  120 PGRQMQVDWGTMR--NGRSPLHVFVAVLGYSRMLYIEF-TDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKTVVLQRda 196
Cdd:pfam00665   1 PNQLWQGDFTYIRipGGGGKLYLLVIVDDFSREILAWAlSSEMDAELVLDALERAIAFRGGVPLIIHSDNGSEYTSKA-- 78

                          90       100       110
                  ....*....|....*....|....*....|
gi 446178089  197 yqtgqhrfhpsLWQFGKEMGFSPRLCRPFR 226
Cdd:pfam00665  79 -----------FREFLKDLGIKPSFSRPGN 97
transpos_IS481 NF033577
IS481 family transposase; null
 15-292 4.36e-16

IS481 family transposase; null


Pssm-ID: 468094 [Multi-domain]  Cd Length: 283  Bit Score: 77.25  E-value: 4.36e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  15 KQGMSSRAIARELGISRNTV----KRYLQAKSEP-------PKYTPR---PAVASLLDEYRdyiRQRiadahpyKIPATV 80
Cdd:NF033577  11 EDGWSVREAARRFGISRKTVykwlKRYRAGGEEGlidrsrrPHRSPRrtsPETEARILALR---REL-------RLGPRR 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  81 IAREIRDQG--------YRggmtILR--AFIRSLSVPQEQEPAVRFETE-PGRQMQVD---WGTMRNGRSpLHVFVAVLG 146
Cdd:NF033577  81 IAYELERQGpgvsrstvHR----ILRrhGLSRLRALDRKTGKVKRYERAhPGELWHIDikkLGRIPDVGR-LYLHTAIDD 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089 147 YSRMLYIEFTDNMRYDTLETCHRNAFRFFGGVPREVLYDNMKtvvlqrdAYQTGQHRFHpslwQFGKEMGFSPRLCRPFR 226
Cdd:NF033577 156 HSRFAYAELYPDETAETAADFLRRAFAEHGIPIRRVLTDNGS-------EFRSRAHGFE----LALAELGIEHRRTRPYH 224

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 446178089 227 AQTKGKVERMVQYTRNSFyipLMTRLRPmgitvDVETANRHGLRWLHDVANQRKHETI-QARPCDRW 292
Cdd:NF033577 225 PQTNGKVERFHRTLKDEF---AYARPYE-----SLAELQAALDEWLHHYNHHRPHSALgGKTPAERF 283
HTH_7 pfam02796
Helix-turn-helix domain of resolvase;
9-41 2.76e-06

Helix-turn-helix domain of resolvase;


Pssm-ID: 397088 [Multi-domain]  Cd Length: 45  Bit Score: 43.88  E-value: 2.76e-06
                          10        20        30
                  ....*....|....*....|....*....|...
gi 446178089    9 EIKILHKQGMSSRAIARELGISRNTVKRYLQAK 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 6.78e-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: 47.41  E-value: 6.78e-06
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089    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 1.04e-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: 41.93  E-value: 1.04e-05
                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 446178089   3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd00569    7 TPEQIAEARRLLAAGESVAEIARELGVSRSTLYRYL 42
HTH_38 pfam13936
Helix-turn-helix domain; This helix-turn-helix domain is often found in transferases and is ...
 3-36 1.84e-05

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: 41.34  E-value: 1.84e-05
                          10        20        30
                  ....*....|....*....|....*....|....
gi 446178089    3 TFETVMEIKILHKQGMSSRAIARELGISRNTVKR 36
Cdd:pfam13936   6 SLEEREEIARLLAEGLSLREIARRLGRSPSTISR 39
HTH_LUXR smart00421
helix_turn_helix, Lux Regulon; lux regulon (activates the bioluminescence operon
 6-38 2.77e-05

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


Pssm-ID: 197715 [Multi-domain]  Cd Length: 58  Bit Score: 41.36  E-value: 2.77e-05
                           10        20        30
                   ....*....|....*....|....*....|....*
gi 446178089     6 TVMEIKILHK--QGMSSRAIARELGISRNTVKRYL 38
Cdd:smart00421   5 TPREREVLRLlaEGLTNKEIAERLGISEKTVKTHL 39
SfsB COG3423
Predicted transcriptional regulator, lambda repressor-like DNA-binding domain [Transcription];
13-58 4.99e-05

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


Pssm-ID: 442649 [Multi-domain]  Cd Length: 69  Bit Score: 40.97  E-value: 4.99e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 446178089  13 LHKQGMSSRAIARELGISRNTVKRYLQAKSepPKYtpRPAVASLLD 58
Cdd:COG3423   16 LRKRGTSLAALAREAGLSSSTLSNALTRPW--PKG--ERAIAEALG 57
CitB COG2197
DNA-binding response regulator, NarL/FixJ family, contains REC and HTH domains [Signal ...
 9-40 9.67e-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: 41.80  E-value: 9.67e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446178089   9 EIKILH--KQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:COG2197   74 EREVLRllAEGLSNKEIAERLGISERTVKTHVSN 107
AF0184 COG2522
Predicted transcriptional regulator, contains XRE-type HTH domain [Transcription];
8-89 1.40e-04

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


Pssm-ID: 442012 [Multi-domain]  Cd Length: 99  Bit Score: 40.19  E-value: 1.40e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLQAK-SEPPKYTPRPAVASLLDEyrdyIRQRIADAHPYKIPA--TVIARE 84
Cdd:COG2522   19 LLAKELVERGLSQSEIAKLLGITQAAVSQYLSGKrGASERIEFDEEIKELIEE----LAEGLASGKPEDALAeiCRLCRE 94


                 ....*
gi 446178089  85 IRDQG 89
Cdd:COG2522   95 LLKRG 99
LuxR_C_like cd06170
C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix ...
 9-38 2.00e-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: 38.67  E-value: 2.00e-04
                         10        20        30
                 ....*....|....*....|....*....|..
gi 446178089   9 EIKILH--KQGMSSRAIARELGISRNTVKRYL 38
Cdd:cd06170    5 EREVLRllAEGKTNKEIADILGISEKTVKTHL 36
CsgD COG2771
DNA-binding transcriptional regulator, CsgD family [Transcription];
6-40 2.57e-04

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


Pssm-ID: 442052 [Multi-domain]  Cd Length: 188  Bit Score: 41.28  E-value: 2.57e-04
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 446178089   6 TVMEIKILH--KQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:COG2771  129 TPREREVLRllAEGLTLKEIARILGISERTVRTHLKR 165
transpos_IS630 NF033545
IS630 family transposase;
8-73 2.78e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 42.24  E-value: 2.78e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 446178089   8 MEIKILHKQGMSSRAIARELGISRNTVKRYLQ---------AKSEPPKYTPRpavaSLLDEYRDYIRQRIADAHP 73
Cdd:NF033545   3 ARILLLAAEGLSITEIAERLGVSRSTVYRWLKrfnegglegLLDKPRPGRPR----KLLSEQQAELLALLLEEPP 73
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 13-88 3.70e-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: 41.76  E-value: 3.70e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 446178089  13 LHKQGMSSRAIARELGISRNTVKRYLQAKSE-------PPKYTPRPavASLLDEYRDYIRQRIADAHPYKIP---ATVIA 82
Cdd:COG3415   34 LLAEGLSVREIAERLGVSRSTVYRWLKRYREgglaglkDRPRGGRP--SKLSDEQRERLLELLREKSPDQGSrwtLAELA 111


                 ....*.
gi 446178089  83 REIRDQ 88
Cdd:COG3415  112 ELLEEE 117
MalT COG2909
ATP-, maltotriose- and DNA-dependent transcriptional regulator MalT [Transcription];
16-39 6.72e-04

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


Pssm-ID: 442153 [Multi-domain]  Cd Length: 184  Bit Score: 40.07  E-value: 6.72e-04
                         10        20
                 ....*....|....*....|....
gi 446178089  16 QGMSSRAIARELGISRNTVKRYLQ 39
Cdd:COG2909  136 EGLSNKEIAERLFISVNTVKTHLR 159
GerE COG5905
Spore transcriptional regulator GerE (stand-alone HTH domain) [Cell cycle control, cell ...
 9-38 1.12e-03

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: 37.25  E-value: 1.12e-03
                         10        20        30
                 ....*....|....*....|....*....|..
gi 446178089   9 EIKILHK--QGMSSRAIARELGISRNTVKRYL 38
Cdd:COG5905   17 EREVLELlaEGLTNKEIARQLFISEKTVKNHV 48
HTH_XRE cd00093
Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the ...
 11-44 1.37e-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: 36.38  E-value: 1.37e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 446178089  11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEP 44
Cdd:cd00093    6 ELRKEKGLTQEELAEKLGVSRSTISRIENGKRNP 39
HTH_XRE smart00530
Helix-turn-helix XRE-family like proteins;
11-44 2.74e-03

Helix-turn-helix XRE-family like proteins;


Pssm-ID: 197775 [Multi-domain]  Cd Length: 56  Bit Score: 35.57  E-value: 2.74e-03
                           10        20        30
                   ....*....|....*....|....*....|....
gi 446178089    11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEP 44
Cdd:smart00530   4 ELREEKGLTQEELAEKLGVSRSTLSRIENGKRKP 37
HTH_26 pfam13443
Cro/C1-type HTH DNA-binding domain; This is a helix-turn-helix domain that probably binds to ...
 11-58 2.83e-03

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: 35.59  E-value: 2.83e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 446178089   11 KILHKQGMSSRAIARELGISRNTVKRYLQAKSEPPKYTPRPAVASLLD 58
Cdd:pfam13443   4 KLMADRGISKSDLARATGISRATLSRLRKGKPKRVSLDTLDKICDALG 51
HTH_23 pfam13384
Homeodomain-like domain;
13-40 2.85e-03

Homeodomain-like domain;


Pssm-ID: 433164 [Multi-domain]  Cd Length: 50  Bit Score: 35.32  E-value: 2.85e-03
                          10        20
                  ....*....|....*....|....*...
gi 446178089   13 LHKQGMSSRAIARELGISRNTVKRYLQA 40
Cdd:pfam13384  13 LLAEGLSVKEIAELLGVSRRTVYRWLKR 40
transpos_IS1 NF033558
IS1 family transposase; Proteins of this family are DDE transposases encoded by the IS1 family ...
 17-51 3.17e-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: 38.41  E-value: 3.17e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 446178089  17 GMSSRAIARELGISRNTVKRYLQaKSEPPKYTPRP 51
Cdd:NF033558  55 GMGFRAIARVLGVSHNTVLRWLK-KLGPRQVTPEP 88
YiaG COG2944
DNA-binding transcriptional regulator YiaG, XRE-type HTH domain [Transcription];
6-73 3.29e-03

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


Pssm-ID: 442187 [Multi-domain]  Cd Length: 64  Bit Score: 35.68  E-value: 3.29e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 446178089   6 TVMEIKILHKQ-GMSSRAIARELGISRNTVKRYLQAKSEPPkytprPAVASLLdeyrdyirqRIADAHP 73
Cdd:COG2944    7 TPEEIRALRERlGLSQAEFAALLGVSVSTVRRWEQGRRKPS-----GAALKLL---------RLLEKHP 61
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 4.21e-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: 35.12  E-value: 4.21e-03
                          10        20
                  ....*....|....*....|....
gi 446178089   16 QGMSSRAIARELGISRNTVKRYLQ 39
Cdd:pfam08281  25 EGLSYAEIAELLGISEGTVKSRLS 48
HTH_3 pfam01381
Helix-turn-helix; This large family of DNA binding helix-turn helix proteins includes Cro and ...
 15-44 5.00e-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: 34.82  E-value: 5.00e-03
                          10        20        30
                  ....*....|....*....|....*....|
gi 446178089   15 KQGMSSRAIARELGISRNTVKRYLQAKSEP 44
Cdd:pfam01381   7 ELGLSQEELAEKLGVSRSTISKIENGKREP 36
mpi PRK13413
master DNA invertase Mpi family serine-type recombinase;
9-39 5.75e-03

master DNA invertase Mpi family serine-type recombinase;


Pssm-ID: 184041 [Multi-domain]  Cd Length: 200  Bit Score: 37.39  E-value: 5.75e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 446178089   9 EIKILHKQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:PRK13413 164 KIKKLLDKGTSKSEIARKLGVSRTTLARFLK 194
HTH_24 pfam13412
Winged helix-turn-helix DNA-binding;
9-39 6.53e-03

Winged helix-turn-helix DNA-binding;


Pssm-ID: 404317 [Multi-domain]  Cd Length: 45  Bit Score: 34.33  E-value: 6.53e-03
                          10        20        30
                  ....*....|....*....|....*....|....*
gi 446178089    9 EIKILH----KQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:pfam13412   3 DRKILNllqeNPRISQRELAERLGLSPSTVNRRLK 37
InsA COG3677
Transposase InsA [Mobilome: prophages, transposons];
10-39 7.43e-03

Transposase InsA [Mobilome: prophages, transposons];


Pssm-ID: 442893 [Multi-domain]  Cd Length: 241  Bit Score: 37.54  E-value: 7.43e-03
                         10        20        30
                 ....*....|....*....|....*....|
gi 446178089  10 IKILHKQGMSSRAIARELGISRNTVKRYLQ 39
Cdd:COG3677   68 AIRLLLNGISLRQIARVLGVSYKTVWRWLH 97
DeoR COG2390
DNA-binding transcriptional regulator LsrR, DeoR family [Transcription];
14-43 9.08e-03

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


Pssm-ID: 441955 [Multi-domain]  Cd Length: 301  Bit Score: 37.42  E-value: 9.08e-03
                         10        20        30
                 ....*....|....*....|....*....|.
gi 446178089  14 HKQGMSSRAIARELGISRNTVKRYLQ-AKSE 43
Cdd:COG2390    7 YVEGLTQREIAERLGISRRTVSRLLAeAREE 37
 
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