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Conserved domains on  [gi|495919589|ref|WP_008644168|]
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MULTISPECIES: HU family DNA-binding protein [Bacteroidales]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HU-HIG super family cl38933
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-123 5.28e-23

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.


The actual alignment was detected with superfamily member pfam18291:

Pssm-ID: 436389  Cd Length: 125  Bit Score: 88.02  E-value: 5.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589    1 MAIPFKRMGRKDPRKVDGVVKYHPQLVTQGqSVDLDKLAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFG 80
Cdd:pfam18291   1 MAIKYDLYKRPNPKGEGEPQKLYARVVPKG-TVTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 495919589   81 VFSLSATTRGVDTKDECTMKNIKTVNINFRPSSSVRPNLTSTR 123
Cdd:pfam18291  80 YFSLSLSSKGVDDKKEVRANSIKFRNINFRPGKKLKRELKGLS 122
 
Name Accession Description Interval E-value
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-123 5.28e-23

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: 88.02  E-value: 5.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589    1 MAIPFKRMGRKDPRKVDGVVKYHPQLVTQGqSVDLDKLAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFG 80
Cdd:pfam18291   1 MAIKYDLYKRPNPKGEGEPQKLYARVVPKG-TVTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 495919589   81 VFSLSATTRGVDTKDECTMKNIKTVNINFRPSSSVRPNLTSTR 123
Cdd:pfam18291  80 YFSLSLSSKGVDDKKEVRANSIKFRNINFRPGKKLKRELKGLS 122
HU_rel TIGR01201
DNA-binding protein, histone-like, putative; This model describes a set of proteins related to ...
 3-124 7.93e-20

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: 80.48  E-value: 7.93e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589    3 IPFKRMGRKDPRKVDGVVKYHPQLVTQGqSVDLDKLAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFGVF 82
Cdd:TIGR01201   2 IKYKVKERKAKIGKTGKTMWYPQTVKSG-VMDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 495919589   83 SLSATTRG--VDTKDECTMKNIKTVNINFRPSSSVRPNLTSTRA 124
Cdd:TIGR01201  81 RLSATAKGsgVEEAEEVSAEQVNKARVLFTPEKTLKTATREIRL 124
HU_IHF_like cd13833
Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains; ...
 21-112 6.81e-06

Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains; This subfamily consists of uncharacterized proteins similar to integration host factor (IHF) and HU domains, including hypothetical protein Bvu_2165 from Bacteroides vulgatus. 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: 259855  Cd Length: 97  Bit Score: 42.66  E-value: 6.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589  21 KYHPQLVTQGqSVDLDKLAYTM-KEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIhdfGVFSLSATTRGV-DTKDECT 98
Cdd:cd13833    1 DYIARVVRTG-SLDLEDIIDRIvAKGSTLRAETIEHILELFDKVVSEALQEGYSVNT---GLGYLYIAISGVfEGETDSF 76

                         90
                 ....*....|....
gi 495919589  99 MKNIKTVNINFRPS 112
Cdd:cd13833   77 DPAKHSITVSFTPG 90
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
38-116 5.85e-05

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 39.74  E-value: 5.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589  38 LAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFGVFSLSAttrgvdtKDECTMKNIKT---VNIN------ 108
Cdd:COG0776    6 LIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRK-------RAARTGRNPKTgeeIKIPakkvvk 78


                 ....*...
gi 495919589 109 FRPSSSVR 116
Cdd:COG0776   79 FKPGKELK 86
 
Name Accession Description Interval E-value
HU-HIG pfam18291
HU domain fused to wHTH, Ig, or Glycine-rich motif; Rapidly-diverging family of HU domains ...
 1-123 5.28e-23

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: 88.02  E-value: 5.28e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589    1 MAIPFKRMGRKDPRKVDGVVKYHPQLVTQGqSVDLDKLAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFG 80
Cdd:pfam18291   1 MAIKYDLYKRPNPKGEGEPQKLYARVVPKG-TVTLKELEDRISKATTLTRADVKGVLEALIDELVDYLADGYRVHLGELG 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 495919589   81 VFSLSATTRGVDTKDECTMKNIKTVNINFRPSSSVRPNLTSTR 123
Cdd:pfam18291  80 YFSLSLSSKGVDDKKEVRANSIKFRNINFRPGKKLKRELKGLS 122
HU_rel TIGR01201
DNA-binding protein, histone-like, putative; This model describes a set of proteins related to ...
 3-124 7.93e-20

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: 80.48  E-value: 7.93e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589    3 IPFKRMGRKDPRKVDGVVKYHPQLVTQGqSVDLDKLAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFGVF 82
Cdd:TIGR01201   2 IKYKVKERKAKIGKTGKTMWYPQTVKSG-VMDFEEIAELIAEESSLSPGDVKGIIDRLAYVLRRELANGKTVRLGEIGTF 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 495919589   83 SLSATTRG--VDTKDECTMKNIKTVNINFRPSSSVRPNLTSTRA 124
Cdd:TIGR01201  81 RLSATAKGsgVEEAEEVSAEQVNKARVLFTPEKTLKTATREIRL 124
HU_IHF_like cd13833
Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains; ...
 21-112 6.81e-06

Uncharacterized proteins similar to DNA sequence specific (IHF) and non-specific (HU) domains; This subfamily consists of uncharacterized proteins similar to integration host factor (IHF) and HU domains, including hypothetical protein Bvu_2165 from Bacteroides vulgatus. 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: 259855  Cd Length: 97  Bit Score: 42.66  E-value: 6.81e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589  21 KYHPQLVTQGqSVDLDKLAYTM-KEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIhdfGVFSLSATTRGV-DTKDECT 98
Cdd:cd13833    1 DYIARVVRTG-SLDLEDIIDRIvAKGSTLRAETIEHILELFDKVVSEALQEGYSVNT---GLGYLYIAISGVfEGETDSF 76

                         90
                 ....*....|....
gi 495919589  99 MKNIKTVNINFRPS 112
Cdd:cd13833   77 DPAKHSITVSFTPG 90
HU-DNA_bdg pfam14848
DNA-binding domain;
22-124 1.33e-05

DNA-binding domain;


Pssm-ID: 434264  Cd Length: 123  Bit Score: 42.33  E-value: 1.33e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589   22 YHPQLVTQGQSVDLDKLAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNihdFGVFSLSATTRGV-DTKDECTMK 100
Cdd:pfam14848  19 YIAQVEDARSLTIDDIIDEMVKKGTEVRKETILHILNLFNREVSEAVLNGYSVN---TGLGRTSPTIKGVfDGKTSAFDP 95

                          90       100
                  ....*....|....*....|....
gi 495919589  101 NIKTVNINFRPSSSVRPNLTSTRA 124
Cdd:pfam14848  96 NRHSIYVNLTQGAALREALANTKV 119
HimA COG0776
Bacterial nucleoid DNA-binding protein IHF-alpha [Replication, recombination and repair];
38-116 5.85e-05

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


Pssm-ID: 440539  Cd Length: 92  Bit Score: 39.74  E-value: 5.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589  38 LAYTMKEKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFGVFSLSAttrgvdtKDECTMKNIKT---VNIN------ 108
Cdd:COG0776    6 LIEAIAEKTGLSKKDAEAAVDAFLDEITEALAKGERVELRGFGTFSVRK-------RAARTGRNPKTgeeIKIPakkvvk 78


                 ....*...
gi 495919589 109 FRPSSSVR 116
Cdd:COG0776   79 FKPGKELK 86
IHF cd13832
Integration host factor (IHF) and similar proteins; This subfamily includes integration host ...
 44-116 4.31e-03

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: 34.77  E-value: 4.31e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 495919589  44 EKSSLSLGDIQSVLTNLVEAMRTALFDGKSVNIHDFGVFSlsattrgVDTKDECTMKNIKT---VNIN------FRPSSS 114
Cdd:cd13832   10 EKTGLSKKDVKKVVDAFFDEIKEALKEGERVELRGFGTFE-------VKKRKARIGRNPKTgekIVIParkvvkFKPSKE 82


                 ..
gi 495919589 115 VR 116
Cdd:cd13832   83 LK 84
 
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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