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Conserved domains on  [gi|1650054243|gb|QCQ45712|]
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DNA-binding protein [Bacteroides fragilis]

Protein Classification

HU_rel family protein( domain architecture ID 10018753)

HU_rel family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HU_rel TIGR01201
DNA-binding protein, histone-like, putative; This model describes a set of proteins related to ...
 3-143 2.12e-58

DNA-binding protein, histone-like, putative; This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe. [DNA metabolism, Chromosome-associated proteins]


:

Pssm-ID: 273496  Cd Length: 145  Bit Score: 178.32  E-value: 2.12e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650054243   3 LFYRARQSQLKTKE-GKKQWHLTLVKVGKMvTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTF 81
Cdd:TIGR01201   2 IKYKVKERKAKIGKtGKTMWYPQTVKSGVM-DFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1650054243  82 TMKACTQGNGVDQEEEVNPNQVKALRCLFTAEYTRPAAIGTTRALLQGVEFQKASAIGGAIN 143
Cdd:TIGR01201  81 RLSATAKGSGVEEAEEVSAEQVNKARVLFTPEKTLKTATREIRLALINRYLKKPDDAGGAPN 142
 
Name Accession Description Interval E-value
HU_rel TIGR01201
DNA-binding protein, histone-like, putative; This model describes a set of proteins related to ...
 3-143 2.12e-58

DNA-binding protein, histone-like, putative; This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe. [DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 273496  Cd Length: 145  Bit Score: 178.32  E-value: 2.12e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650054243   3 LFYRARQSQLKTKE-GKKQWHLTLVKVGKMvTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTF 81
Cdd:TIGR01201   2 IKYKVKERKAKIGKtGKTMWYPQTVKSGVM-DFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1650054243  82 TMKACTQGNGVDQEEEVNPNQVKALRCLFTAEYTRPAAIGTTRALLQGVEFQKASAIGGAIN 143
Cdd:TIGR01201  81 RLSATAKGSGVEEAEEVSAEQVNKARVLFTPEKTLKTATREIRLALINRYLKKPDDAGGAPN 142
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-134 5.62e-12

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: 59.13  E-value: 5.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650054243   1 MPLFYRARQS-QLKTKEGKKQWHLTLVkVGKMVTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLG 79
Cdd:pfam18291   1 MAIKYDLYKRpNPKGEGEPQKLYARVV-PKGTVTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1650054243  80 TFTMkaCTQGNGVDQEEEVNPNQVKALRCLFTAEYtrpaaigTTRALLQGVEFQK 134
Cdd:pfam18291  80 YFSL--SLSSKGVDDKKEVRANSIKFRNINFRPGK-------KLKRELKGLSFER 125
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
32-84 6.47e-08

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 47.82  E-value: 6.47e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1650054243  32 VTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMK 84
Cdd:COG0776     1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVR 53
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 36-84 8.66e-04

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: 36.32  E-value: 8.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1650054243  36 QLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMK 84
Cdd:cd13832     3 DLIEEIAEKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVK 51
BHL smart00411
bacterial (prokaryotic) histone like domain;
32-85 4.77e-03

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 34.46  E-value: 4.77e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1650054243   32 VTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMKA 85
Cdd:smart00411   1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRE 54
 
Name Accession Description Interval E-value
HU_rel TIGR01201
DNA-binding protein, histone-like, putative; This model describes a set of proteins related to ...
 3-143 2.12e-58

DNA-binding protein, histone-like, putative; This model describes a set of proteins related to but longer than DNA-binding protein HU. Its distinctive domain architecture compared to HU and related histone-like DNA-binding proteins justifies the designation as superfamily. Members include, so far, one from Bacteroides fragilis, a gut bacterium, and ten from Porphyromonas gingivalis, an oral anaerobe. [DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 273496  Cd Length: 145  Bit Score: 178.32  E-value: 2.12e-58
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650054243   3 LFYRARQSQLKTKE-GKKQWHLTLVKVGKMvTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTF 81
Cdd:TIGR01201   2 IKYKVKERKAKIGKtGKTMWYPQTVKSGVM-DFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTF 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1650054243  82 TMKACTQGNGVDQEEEVNPNQVKALRCLFTAEYTRPAAIGTTRALLQGVEFQKASAIGGAIN 143
Cdd:TIGR01201  81 RLSATAKGSGVEEAEEVSAEQVNKARVLFTPEKTLKTATREIRLALINRYLKKPDDAGGAPN 142
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-134 5.62e-12

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: 59.13  E-value: 5.62e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1650054243   1 MPLFYRARQS-QLKTKEGKKQWHLTLVkVGKMVTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLG 79
Cdd:pfam18291   1 MAIKYDLYKRpNPKGEGEPQKLYARVV-PKGTVTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELG 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1650054243  80 TFTMkaCTQGNGVDQEEEVNPNQVKALRCLFTAEYtrpaaigTTRALLQGVEFQK 134
Cdd:pfam18291  80 YFSL--SLSSKGVDDKKEVRANSIKFRNINFRPGK-------KLKRELKGLSFER 125
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
32-84 6.47e-08

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 47.82  E-value: 6.47e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1650054243  32 VTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMK 84
Cdd:COG0776     1 MTKSELIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVR 53
Bac_DNA_binding pfam00216
Bacterial DNA-binding protein;
33-93 1.03e-06

Bacterial DNA-binding protein;


Pssm-ID: 425532  Cd Length: 88  Bit Score: 44.43  E-value: 1.03e-06
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1650054243  33 TSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMKACTQGNGVD 93
Cdd:pfam00216   1 TKKELIKAIAEKTGLSKKEAERVVDAFLEVIKEALKKGEKVELRGFGTFEVRERAARTGRN 61
HU-CCDC81_euk_1 pfam14908
CCDC81 eukaryotic HU domain 1; This is the first of two HU domains found in the CCDC81-like ...
 42-86 3.50e-04

CCDC81 eukaryotic HU domain 1; This is the first of two HU domains found in the CCDC81-like proteins. CCDC81 has been experimentally linked to the centrosome; eukaryotic CCDC81 HU domains are predicted to function in protein-protein interactions in centrosome organization and potentially contribute to cargo-binding in conjunction with Dynein-VII. A striking lineage-specific expansion of the domain is observed in birds, where the HU domains could function in recognition of non-self molecules.


Pssm-ID: 464364  Cd Length: 89  Bit Score: 37.62  E-value: 3.50e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1650054243  42 AEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMKAC 86
Cdd:pfam14908  14 TLKPLLTEEQLLSIWDALGEYIEEQLSQGKGVHIPGFGTFTFERQ 58
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 36-84 8.66e-04

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: 36.32  E-value: 8.66e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1650054243  36 QLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMK 84
Cdd:cd13832     3 DLIEEIAEKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFEVK 51
HU_IHF cd00591
DNA sequence specific (IHF) and non-specific (HU) domains; This family includes integration ...
 35-85 1.26e-03

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: 36.01  E-value: 1.26e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1650054243  35 QQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMKA 85
Cdd:cd00591     2 KELIDAIAAKTGLTKKQAEAVLDAFEEVITEALAAGEEVTLPGFGKFKVKK 52
HU cd13831
histone-like DNA-binding protein HU; This subfamily includes HU and HU-like domains. HU is a ...
 35-81 4.38e-03

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: 34.67  E-value: 4.38e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1650054243  35 QQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTF 81
Cdd:cd13831     3 AELIDAVAEKAGLSKKDAEKALDAVLETITEALKKGEKVTLVGFGTF 49
BHL smart00411
bacterial (prokaryotic) histone like domain;
32-85 4.77e-03

bacterial (prokaryotic) histone like domain;


Pssm-ID: 197709  Cd Length: 90  Bit Score: 34.46  E-value: 4.77e-03
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1650054243   32 VTSQQLAEVIAEKSSLTPGDVHNVIRNLMTAMRKELLNSRSVRLEGLGTFTMKA 85
Cdd:smart00411   1 MTKSELIDAIAEKTGLSKKDAKAAVDAFLEEITEALKKGEKVELRGFGTFEVRE 54
 
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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