NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|17539952|ref|NP_501504|]
View 

HTH CENPB-type domain-containing protein [Caenorhabditis elegans]

Protein Classification

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
84-143 2.69e-13

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


:

Pssm-ID: 197828  Cd Length: 66  Bit Score: 63.08  E-value: 2.69e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17539952     84 PLKNVELDEKVEDWIA---SKNGKISGKDIKEYAKKIN---GNADFKASNGWLQRFMIRHGLIKAR 143
Cdd:smart00674   1 RRLYPLLEKALYEWILrqeALGIPISGEDIREKALEILqrlGLENFKASKGWLTRFKKRHNIVKTK 66
BrkDBD super family cl09825
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 21-65 1.38e-05

Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.


The actual alignment was detected with superfamily member pfam09607:

Pssm-ID: 462838 [Multi-domain]  Cd Length: 58  Bit Score: 41.65  E-value: 1.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 17539952    21 RANFTLEFKNEVIRFAEQTNNCQ-----AQKKYGVARACIQRWRHLKHEL 65
Cdd:pfam09607   3 RHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNL 52
 
Name Accession Description Interval E-value
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
84-143 2.69e-13

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


Pssm-ID: 197828  Cd Length: 66  Bit Score: 63.08  E-value: 2.69e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17539952     84 PLKNVELDEKVEDWIA---SKNGKISGKDIKEYAKKIN---GNADFKASNGWLQRFMIRHGLIKAR 143
Cdd:smart00674   1 RRLYPLLEKALYEWILrqeALGIPISGEDIREKALEILqrlGLENFKASKGWLTRFKKRHNIVKTK 66
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-140 1.19e-09

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 53.02  E-value: 1.19e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17539952    87 NVELDEKVEDWI---ASKNGKISGKDIKEYAKKI------NGNADFKASNGWLQRFMIRHGLI 140
Cdd:pfam03221   1 YPDLEKALYEWIlqlRARGIPITGPMIREKALELaqlaadLGEPDFKASKGWLDRFKKRHGIK 63
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 21-65 1.38e-05

Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.


Pssm-ID: 462838 [Multi-domain]  Cd Length: 58  Bit Score: 41.65  E-value: 1.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 17539952    21 RANFTLEFKNEVIRFAEQTNNCQ-----AQKKYGVARACIQRWRHLKHEL 65
Cdd:pfam09607   3 RHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNL 52
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 31-139 4.06e-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: 44.07  E-value: 4.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539952  31 EVIRFAEQTNNC-QAQKKYGVARACIQRWRHlkhelAFESEGKQGAKRLGGAGRPLK-NVELDEKVEDWIASKNGKISGK 108
Cdd:COG3415  30 RAVLLLAEGLSVrEIAERLGVSRSTVYRWLK-----RYREGGLAGLKDRPRGGRPSKlSDEQRERLLELLREKSPDQGSR 104

                        90       100       110
                ....*....|....*....|....*....|..
gi 17539952 109 -DIKEYAKKINGNADFKASNGWLQRFMIRHGL 139
Cdd:COG3415 105 wTLAELAELLEEEFGVEVSPSTVRRLLKRLGL 136
transpos_IS630 NF033545
IS630 family transposase;
43-143 4.96e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 40.70  E-value: 4.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539952   43 QAQKKYGVARACIQRWRHlkhelAFESEGKQGAKRLGGAGRP--LKNVELDEKVEDWIASKNGKISGKDIKEYAKKINGN 120
Cdd:NF033545  17 EIAERLGVSRSTVYRWLK-----RFNEGGLEGLLDKPRPGRPrkLLSEQQAELLALLLEEPPEGAGHWTLRELAALLEEE 91

                         90       100
                 ....*....|....*....|....*
gi 17539952  121 ADFKASNGWLQRFMIRHGL--IKAR 143
Cdd:NF033545  92 FGVEYSRSTVRRLLKRLGLspKKPR 116
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
18-60 2.02e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.44  E-value: 2.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 17539952  18 KKKRANFTLEFKNEVIRFAEQTNNCQAQ--KKYGVARACIQRWRH 60
Cdd:COG2963   2 SKKRRRYSPEFKAEAVRLVLEGGASVAEvaRELGISPSTLYRWVR 46
 
Name Accession Description Interval E-value
CENPB smart00674
Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;
84-143 2.69e-13

Putative DNA-binding domain in centromere protein B, mouse jerky and transposases;


Pssm-ID: 197828  Cd Length: 66  Bit Score: 63.08  E-value: 2.69e-13
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 17539952     84 PLKNVELDEKVEDWIA---SKNGKISGKDIKEYAKKIN---GNADFKASNGWLQRFMIRHGLIKAR 143
Cdd:smart00674   1 RRLYPLLEKALYEWILrqeALGIPISGEDIREKALEILqrlGLENFKASKGWLTRFKKRHNIVKTK 66
HTH_Tnp_Tc5 pfam03221
Tc5 transposase DNA-binding domain;
87-140 1.19e-09

Tc5 transposase DNA-binding domain;


Pssm-ID: 460850  Cd Length: 63  Bit Score: 53.02  E-value: 1.19e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 17539952    87 NVELDEKVEDWI---ASKNGKISGKDIKEYAKKI------NGNADFKASNGWLQRFMIRHGLI 140
Cdd:pfam03221   1 YPDLEKALYEWIlqlRARGIPITGPMIREKALELaqlaadLGEPDFKASKGWLDRFKKRHGIK 63
BrkDBD pfam09607
Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the ...
 21-65 1.38e-05

Brinker DNA-binding domain; This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway.


Pssm-ID: 462838 [Multi-domain]  Cd Length: 58  Bit Score: 41.65  E-value: 1.38e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 17539952    21 RANFTLEFKNEVIRFAEQTNNCQ-----AQKKYGVARACIQRWRHLKHEL 65
Cdd:pfam09607   3 RHIFDAGFKLMVLESAENDNDCKgnqraAAKKFGIHEKNIQDWLKCEPNL 52
Csa3 COG3415
CRISPR-associated protein Csa3, CARF domain [Defense mechanisms]; CRISPR-associated protein ...
 31-139 4.06e-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: 44.07  E-value: 4.06e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539952  31 EVIRFAEQTNNC-QAQKKYGVARACIQRWRHlkhelAFESEGKQGAKRLGGAGRPLK-NVELDEKVEDWIASKNGKISGK 108
Cdd:COG3415  30 RAVLLLAEGLSVrEIAERLGVSRSTVYRWLK-----RYREGGLAGLKDRPRGGRPSKlSDEQRERLLELLREKSPDQGSR 104

                        90       100       110
                ....*....|....*....|....*....|..
gi 17539952 109 -DIKEYAKKINGNADFKASNGWLQRFMIRHGL 139
Cdd:COG3415 105 wTLAELAELLEEEFGVEVSPSTVRRLLKRLGL 136
transpos_IS630 NF033545
IS630 family transposase;
43-143 4.96e-04

IS630 family transposase;


Pssm-ID: 468076 [Multi-domain]  Cd Length: 298  Bit Score: 40.70  E-value: 4.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17539952   43 QAQKKYGVARACIQRWRHlkhelAFESEGKQGAKRLGGAGRP--LKNVELDEKVEDWIASKNGKISGKDIKEYAKKINGN 120
Cdd:NF033545  17 EIAERLGVSRSTVYRWLK-----RFNEGGLEGLLDKPRPGRPrkLLSEQQAELLALLLEEPPEGAGHWTLRELAALLEEE 91

                         90       100
                 ....*....|....*....|....*
gi 17539952  121 ADFKASNGWLQRFMIRHGL--IKAR 143
Cdd:NF033545  92 FGVEYSRSTVRRLLKRLGLspKKPR 116
InsE COG2963
Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];
18-60 2.02e-03

Transposase InsE and inactivated derivatives [Mobilome: prophages, transposons];


Pssm-ID: 442203 [Multi-domain]  Cd Length: 93  Bit Score: 36.44  E-value: 2.02e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 17539952  18 KKKRANFTLEFKNEVIRFAEQTNNCQAQ--KKYGVARACIQRWRH 60
Cdd:COG2963   2 SKKRRRYSPEFKAEAVRLVLEGGASVAEvaRELGISPSTLYRWVR 46
HTH_29 pfam13551
Winged helix-turn helix; This helix-turn-helix domain is often found in transferases and is ...
 40-96 3.68e-03

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


Pssm-ID: 433301 [Multi-domain]  Cd Length: 64  Bit Score: 35.04  E-value: 3.68e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 17539952    40 NNCQAQKKYGVARACIQRWRHLkhelaFESEGKQGAKRLGGAGRPlKNVELDEKVED 96
Cdd:pfam13551  14 TVSQAARLLGLSRRTVYRWLKR-----FNEGGLAALLDRPRSGRP-RNNRLDEEQEA 64
 
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