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Conserved domains on  [gi|1372199305|gb|AVR67133|]
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integration host factor subunit beta [Pseudomonas paraeruginosa]

Protein Classification

integration host factor subunit beta( domain architecture ID 10791831)

integration host factor is involved in condensation of the bacterial nucleoid and in regulation of a variety of cellular functions such as DNA replication and transcription

Gene Ontology:  GO:0006355|GO:0006417|GO:0003677|GO:0006310
PubMed:  17097674|9032076|12842466|20484776|15102446
SCOP:  3000426

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
ihfB PRK00199
integration host factor subunit beta; Reviewed
 1-91 7.80e-64

integration host factor subunit beta; Reviewed


:

Pssm-ID: 178925  Cd Length: 94  Bit Score: 187.39  E-value: 7.80e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:PRK00199   1 MTKSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEKYVPHF 80

                         90
                 ....*....|.
gi 1372199305 81 KPGKELRDRVN 91
Cdd:PRK00199  81 KPGKELRERVN 91
 
Name Accession Description Interval E-value
ihfB PRK00199
integration host factor subunit beta; Reviewed
 1-91 7.80e-64

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 187.39  E-value: 7.80e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:PRK00199   1 MTKSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEKYVPHF 80

                         90
                 ....*....|.
gi 1372199305 81 KPGKELRDRVN 91
Cdd:PRK00199  81 KPGKELRERVN 91
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 1-94 2.10e-60

integration host factor, beta subunit; This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130061  Cd Length: 94  Bit Score: 178.95  E-value: 2.10e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:TIGR00988  1 MTKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80

                         90
                 ....*....|....
gi 1372199305 81 KPGKELRDRVNEPE 94
Cdd:TIGR00988 81 KPGKELRDRANIYE 94
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 1-89 2.45e-46

Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259858  Cd Length: 89  Bit Score: 142.98  E-value: 2.45e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:cd13836    1 MTKSELIKRIAEKTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


                 ....*....
gi 1372199305 81 KPGKELRDR 89
Cdd:cd13836   81 KPGKELKER 89
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-93 3.52e-44

Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];


Pssm-ID: 440539  Cd Length: 92  Bit Score: 137.96  E-value: 3.52e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:COG0776    1 MTKSELIEAIAEKTG-LSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKF 79

                         90
                 ....*....|...
gi 1372199305 81 KPGKELRDRVNEP 93
Cdd:COG0776   80 KPGKELKDAVNGS 92
BHL smart00411
bacterial (prokaryotic) histone like domain;
1-91 4.22e-39

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 124.99  E-value: 4.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305   1 MTKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:smart00411  1 MTKSELIDAIAEKTG-LSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKF 79

                          90
                  ....*....|.
gi 1372199305  81 KPGKELRDRVN 91
Cdd:smart00411 80 KPGKALKDAVN 90
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
2-90 7.19e-32

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 106.45  E-value: 7.19e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  2 TKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFK 81
Cdd:pfam00216  1 TKKELIKAIAEKTG-LSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFK 79


                 ....*....
gi 1372199305 82 PGKELRDRV 90
Cdd:pfam00216 80 PGKALKEAV 88
 
Name Accession Description Interval E-value
ihfB PRK00199
integration host factor subunit beta; Reviewed
 1-91 7.80e-64

integration host factor subunit beta; Reviewed


Pssm-ID: 178925  Cd Length: 94  Bit Score: 187.39  E-value: 7.80e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:PRK00199   1 MTKSELIERLAARNPHLSAKDVENAVKEILEEMSDALARGDRIEIRGFGSFSLHYRPPRVGRNPKTGEKVELEEKYVPHF 80

                         90
                 ....*....|.
gi 1372199305 81 KPGKELRDRVN 91
Cdd:PRK00199  81 KPGKELRERVN 91
hip TIGR00988
integration host factor, beta subunit; This protein forms a site-specific DNA-binding ...
 1-94 2.10e-60

integration host factor, beta subunit; This protein forms a site-specific DNA-binding heterodimer with the homologous integration host factor alpha subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130061  Cd Length: 94  Bit Score: 178.95  E-value: 2.10e-60
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:TIGR00988  1 MTKSELIERIATQQSHLPAKDVEDAVKTMLEHMASALAQGDRIEIRGFGSFSLHYRAPRTGRNPKTGDSVELDGKYVPHF 80

                         90
                 ....*....|....
gi 1372199305 81 KPGKELRDRVNEPE 94
Cdd:TIGR00988 81 KPGKELRDRANIYE 94
IHF_B cd13836
Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of ...
 1-89 2.45e-46

Beta subunit of integration host factor (IHFB); This subfamily consists of the beta subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259858  Cd Length: 89  Bit Score: 142.98  E-value: 2.45e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:cd13836    1 MTKSELIKRIAEKTPGLSKKDVEAVVDAILDEIKEALARGERIEIRGFGSFSVKKRKARIGRNPKTGEKVVVPAKYVPHF 80


                 ....*....
gi 1372199305 81 KPGKELRDR 89
Cdd:cd13836   81 KPGKELKER 89
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
1-93 3.52e-44

Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];


Pssm-ID: 440539  Cd Length: 92  Bit Score: 137.96  E-value: 3.52e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:COG0776    1 MTKSELIEAIAEKTG-LSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRKRAARTGRNPKTGEEIKIPAKKVVKF 79

                         90
                 ....*....|...
gi 1372199305 81 KPGKELRDRVNEP 93
Cdd:COG0776   80 KPGKELKDAVNGS 92
BHL smart00411
bacterial (prokaryotic) histone like domain;
1-91 4.22e-39

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 124.99  E-value: 4.22e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305   1 MTKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:smart00411  1 MTKSELIDAIAEKTG-LSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRERKAREGRNPKTGEEIEIPAKKVPKF 79

                          90
                  ....*....|.
gi 1372199305  81 KPGKELRDRVN 91
Cdd:smart00411 80 KPGKALKDAVN 90
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
2-90 7.19e-32

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 106.45  E-value: 7.19e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  2 TKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFK 81
Cdd:pfam00216  1 TKKELIKAIAEKTG-LSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRNPKTGETITIPAKKVVKFK 79


                 ....*....
gi 1372199305 82 PGKELRDRV 90
Cdd:pfam00216 80 PGKALKEAV 88
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 3-88 5.81e-31

Integration host factor (IHF) and similar proteins; This subfamily includes integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms. This subfamily also includes the protein Hbb from tick-borne spirochete Borrelia burgdorferi, responsible for causing Lyme disease in humans. Hbb, a homodimer, shows DNA sequence preferences that are related, yet distinct from those of IHF.


Pssm-ID: 259854  Cd Length: 85  Bit Score: 104.11  E-value: 5.81e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  3 KSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFKP 82
Cdd:cd13832    1 KADLIEEIAEKTG-LSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVKKRKARIGRNPKTGEKIVIPARKVVKFKP 79


                 ....*.
gi 1372199305 83 GKELRD 88
Cdd:cd13832   80 SKELKE 85
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 2-88 8.13e-29

histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta). In E. coli, HU binds uniformly to the chromosome, with a preference for damaged or distorted DNA structures and can introduce negative supercoils into closed circular DNA in the presence of topoisomerase I. Anabaena HU (AHU) shows preference for A/T-rich region in the center of its DNA binding site.


Pssm-ID: 259853  Cd Length: 86  Bit Score: 98.62  E-value: 8.13e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  2 TKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFK 81
Cdd:cd13831    1 NKAELIDAVAEKAG-LSKKDAEKALDAVLETITEALKKGEKVTLVGFGTFEVRERAARTGRNPQTGEKIKIPASKVPKFK 79


                 ....*..
gi 1372199305 82 PGKELRD 88
Cdd:cd13831   80 PGKALKD 86
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 3-88 2.86e-27

DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). Bacillus phage SPO1-encoded transcription factor 1 (TF1) is another related type II DNA-binding protein. Like IHF, TF1 binds DNA specifically and bends DNA sharply.


Pssm-ID: 259852  Cd Length: 85  Bit Score: 94.94  E-value: 2.86e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  3 KSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFKP 82
Cdd:cd00591    1 KKELIDAIAAKTG-LTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKKRAARTGRNPATGETIEIPAKKVVKFTP 79


                 ....*.
gi 1372199305 83 GKELRD 88
Cdd:cd00591   80 SKALKD 85
IHF_A cd13835
Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit ...
 2-90 2.25e-23

Alpha subunit of integration host factor (IHFA); This subfamily consists of the alpha subunit of integration host factor (IHF) and IHF-like domains. IHF is a nucleoid-associated protein (NAP) that binds and sharply bends many DNA targets in a sequence specific manner. It is a heterodimeric protein composed of two highly homologous subunits IHFA (IHF-alpha) and IHFB (IHF-beta). It is known to act as a transcription factor at many gene regulatory regions in E. coli. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups). IHF is also involved in formation as well as maintenance of bacterial biofilms since it is found in complex with extracellular DNA (eDNA) within the extracellular polymeric substances (EPS) matrix of many biofilms.


Pssm-ID: 259857  Cd Length: 88  Bit Score: 85.19  E-value: 2.25e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  2 TKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFK 81
Cdd:cd13835    1 TKADLAEAIYEKLG-LSRKEAAELVESVFEEIKEALERGEDVKISGFGTFEVRDKKARPGRNPKTGEEVTISARRVVTFK 79


                 ....*....
gi 1372199305 82 PGKELRDRV 90
Cdd:cd13835   80 PSPKLKKRI 88
ihfA PRK00285
integration host factor subunit alpha; Reviewed
 1-92 1.04e-18

integration host factor subunit alpha; Reviewed


Pssm-ID: 178961  Cd Length: 99  Bit Score: 73.72  E-value: 1.04e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:PRK00285   3 LTKADLAEALFEKVG-LSKREAKELVELFFEEIRDALENGEQVKLSGFGNFQLRDKNQRPGRNPKTGEEIPISARRVVTF 81

                         90
                 ....*....|..
gi 1372199305 81 KPGKELRDRVNE 92
Cdd:PRK00285  82 RPSQKLKSRVEN 93
himA TIGR00987
integration host factor, alpha subunit; This protein forms a site-specific DNA-binding ...
 1-92 1.69e-18

integration host factor, alpha subunit; This protein forms a site-specific DNA-binding heterodimer with the integration host factor beta subunit. It is closely related to the DNA-binding protein HU. [DNA metabolism, DNA replication, recombination, and repair]


Pssm-ID: 130060  Cd Length: 96  Bit Score: 73.00  E-value: 1.69e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:TIGR00987  2 LTKAEMSEYLFDELG-LSKREAKELVELFFEEIRRALENGEQVKLSGFGNFDLRDKNQRPGRNPKTGEEIPITARRVVTF 80

                         90
                 ....*....|..
gi 1372199305 81 KPGKELRDRVNE 92
Cdd:TIGR00987 81 RPGQKLKSRVEN 92
PRK10664 PRK10664
DNA-binding protein HU-beta;
1-91 2.47e-18

DNA-binding protein HU-beta;


Pssm-ID: 170612  Cd Length: 90  Bit Score: 72.39  E-value: 2.47e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIERIVThQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:PRK10664   1 MNKSQLIDKIAA-GADISKAAAGRALDAIIASVTESLKEGDDVALVGFGTFAVKERAARTGRNPQTGKEITIAAAKVPSF 79

                         90
                 ....*....|.
gi 1372199305 81 KPGKELRDRVN 91
Cdd:PRK10664  80 RAGKALKDAVN 90
SPO1_TF1_like cd14435
Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to ...
 2-88 1.48e-17

Bacteriophage SPO1-encoded TF1 binds and bends DNA; This group contains proteins related to bacillus phage SPO1-encoded transcription factor 1 (TF1), a type II DNA-binding protein related to the DNA sequence specific (IHF) and non-specific (HU) domains. Type II DNA-binding proteins bind and bend DNA as dimers. Like IHF, TF1 binds DNA specifically and bends DNA sharply. Bacteriophage SPO1-encoded TF1 recognizes SPO1 phage DNA containing 5-(hydroxymethyl)-2'-deoxyuridine as opposed to thymine, Related family members includes integration host factor (IHF) and HU, also called type II DNA-binding proteins (DNABII), which are small dimeric proteins that specifically bind the DNA minor groove, inducing large bends in the DNA and serving as architectural factors in a variety of cellular processes such as recombination, initiation of replication/transcription and gene regulation. IHF binds DNA in a sequence specific manner while HU displays little or no sequence preference. IHF homologs are usually heterodimers, while HU homologs are typically homodimers (except HU heterodimers from E. coli and other enterobacteria). HU is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. IHF is an essential cofactor in phage lambda site-specific recombination, having an architectural role during assembly of specialized nucleoprotein structures (snups).


Pssm-ID: 259859  Cd Length: 87  Bit Score: 70.41  E-value: 1.48e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  2 TKSELIERIVTHQGqLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHFK 81
Cdd:cd14435    1 NKTELVAAIAQKAG-LTQAQVSKVLDAFEDVLTEAVAKGEKVTLPGLLTFERVERAARTGRNPQTGEAIQIPAGYGVKFS 79


                 ....*..
gi 1372199305 82 PGKELRD 88
Cdd:cd14435   80 AGSKLKK 86
PRK10753 PRK10753
DNA-binding protein HU-alpha;
1-90 1.88e-17

DNA-binding protein HU-alpha;


Pssm-ID: 138142  Cd Length: 90  Bit Score: 70.19  E-value: 1.88e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  1 MTKSELIErIVTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPKTGESVRLDGKFVPHF 80
Cdd:PRK10753   1 MNKTQLID-VIADKAELSKTQAKAALESTLAAITESLKEGDAVQLVGFGTFKVNHRAERTGRNPQTGKEIKIAAANVPAF 79

                         90
                 ....*....|
gi 1372199305 81 KPGKELRDRV 90
Cdd:PRK10753  80 VSGKALKDAV 89
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-91 3.39e-05

HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains predominantly observed in the bacteroidetes lineage with a predicted role in recognition and possible interception of the DNA of parasitic elements, a counter-conflict strategy preventing incorporation of these elements into the host genome.


Pssm-ID: 436389  Cd Length: 125  Bit Score: 39.49  E-value: 3.39e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305   1 MTKSELIERIvTHQGQLSAKDVELAIKTMLEQMSQALATGDRIEIRGFGSFSLHYRAPRVGRNPK-TGESVRLDGKfvpH 79
Cdd:pfam18291  32 VTLKELEDRI-SKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELGYFSLSLSSKGVDDKKEvRANSIKFRNI---N 107

                          90
                  ....*....|..
gi 1372199305  80 FKPGKELRDRVN 91
Cdd:pfam18291 108 FRPGKKLKRELK 119
HU_like cd13834
DNA-binding proteins similar to HU domains; This subfamily consists of DNA-binding proteins ...
 2-75 3.79e-03

DNA-binding proteins similar to HU domains; This subfamily consists of DNA-binding proteins similar to HU domains. HU is a conserved nucleoid-associated protein (NAP) which binds non-specifically to duplex DNA with a particular preference for targeting nicked and bent DNA. It is highly basic and contributes to chromosomal compaction and maintenance of negative supercoiling, thus often referred to as histone-like protein. HU can induce DNA bends, condense DNA in a fiber and also interact with single stranded DNA. It contains two homologous subunits, alpha and beta, typically forming homodimers (alpha-alpha and beta-beta), except in E. coli and other enterobacteria, which form heterodimers (alpha-beta).


Pssm-ID: 259856  Cd Length: 94  Bit Score: 33.35  E-value: 3.79e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1372199305  2 TKSELIERIVThQGQLSAKDVELAIKTMLEQMSQALATgdrieiRGFGSFSL-----------HYRAPRVGRNPKTGESV 70
Cdd:cd13834    1 TKSQLINALAE-ATGLSKKDVKAVLDSLEELITKELKK------KGPGEFTLpgllkikvvkkPATKARKGRNPFTGEEM 73


                 ....*
gi 1372199305 71 RLDGK 75
Cdd:cd13834   74 TFKAK 78
 
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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