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Conserved domains on  [gi|1691013096|ref|WP_139685870|]
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capsule biosynthesis GfcC family protein [Vibrio tasmaniensis]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Caps_syn_GfcC_C super family cl28741
Capsule biosynthesis GfcC C-terminal; Many bacteria are covered in a layer of ...
 202-285 3.64e-26

Capsule biosynthesis GfcC C-terminal; Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This is the C-terminal domain which covers D3 and D4 domains.


The actual alignment was detected with superfamily member pfam06251:

Pssm-ID: 461862  Cd Length: 90  Bit Score: 98.69  E-value: 3.64e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1691013096 202 LIEHGTLNDYLDAFPngfIGESADKSVVYVVQPDGVVQTIQFAYWNEQPVYLAPGAIVFMAFYS--LPSEYSTLNQDIVD 279
Cdd:pfam06251   7 FLPGRSVADYLDDQP---LLSGADRSYVYVIYPDGRTQKAPVALWNKRHVEPMPGSTIFVGFSPsvLPEDYSSLNEQIVQ 83


                  ....*.
gi 1691013096 280 LLRHKV 285
Cdd:pfam06251  84 LLTNRI 89
Caps_syn_GfcC_N super family cl48764
Capsule biosynthesis GfcC, N-terminal; Many bacteria are covered in a layer of ...
 43-153 5.69e-05

Capsule biosynthesis GfcC, N-terminal; Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This entry represents D2 domain found at the N-terminal.


The actual alignment was detected with superfamily member pfam20616:

Pssm-ID: 466765  Cd Length: 129  Bit Score: 42.10  E-value: 5.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1691013096  43 TVELPLQGVTLEYKADVRMLQVLDDANSSFNANSgigyfpLSAQLFDKANTEAIEAKKRNVLNQL-----EAFAIEEPE- 116
Cdd:pfam20616   6 SVFLPGESEVLTLTDAERLEQLVGQPQLLANSWW------PGAVISDEAATQKALKQRQVLLAQLaslsaEWLFSADGDl 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1691013096 117 ---ANLVRQQLTSFQYLNRVFIELDRNAVISQSDKNPLLV 153
Cdd:pfam20616  80 aaaINQLRQQLQNLNVTGRIFVNLDPDVVRVDERSNPPLV 119
 
Name Accession Description Interval E-value
Caps_syn_GfcC_C pfam06251
Capsule biosynthesis GfcC C-terminal; Many bacteria are covered in a layer of ...
 202-285 3.64e-26

Capsule biosynthesis GfcC C-terminal; Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This is the C-terminal domain which covers D3 and D4 domains.


Pssm-ID: 461862  Cd Length: 90  Bit Score: 98.69  E-value: 3.64e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1691013096 202 LIEHGTLNDYLDAFPngfIGESADKSVVYVVQPDGVVQTIQFAYWNEQPVYLAPGAIVFMAFYS--LPSEYSTLNQDIVD 279
Cdd:pfam06251   7 FLPGRSVADYLDDQP---LLSGADRSYVYVIYPDGRTQKAPVALWNKRHVEPMPGSTIFVGFSPsvLPEDYSSLNEQIVQ 83


                  ....*.
gi 1691013096 280 LLRHKV 285
Cdd:pfam06251  84 LLTNRI 89
Caps_syn_GfcC_N pfam20616
Capsule biosynthesis GfcC, N-terminal; Many bacteria are covered in a layer of ...
 43-153 5.69e-05

Capsule biosynthesis GfcC, N-terminal; Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This entry represents D2 domain found at the N-terminal.


Pssm-ID: 466765  Cd Length: 129  Bit Score: 42.10  E-value: 5.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1691013096  43 TVELPLQGVTLEYKADVRMLQVLDDANSSFNANSgigyfpLSAQLFDKANTEAIEAKKRNVLNQL-----EAFAIEEPE- 116
Cdd:pfam20616   6 SVFLPGESEVLTLTDAERLEQLVGQPQLLANSWW------PGAVISDEAATQKALKQRQVLLAQLaslsaEWLFSADGDl 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1691013096 117 ---ANLVRQQLTSFQYLNRVFIELDRNAVISQSDKNPLLV 153
Cdd:pfam20616  80 aaaINQLRQQLQNLNVTGRIFVNLDPDVVRVDERSNPPLV 119
 
Name Accession Description Interval E-value
Caps_syn_GfcC_C pfam06251
Capsule biosynthesis GfcC C-terminal; Many bacteria are covered in a layer of ...
 202-285 3.64e-26

Capsule biosynthesis GfcC C-terminal; Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This is the C-terminal domain which covers D3 and D4 domains.


Pssm-ID: 461862  Cd Length: 90  Bit Score: 98.69  E-value: 3.64e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1691013096 202 LIEHGTLNDYLDAFPngfIGESADKSVVYVVQPDGVVQTIQFAYWNEQPVYLAPGAIVFMAFYS--LPSEYSTLNQDIVD 279
Cdd:pfam06251   7 FLPGRSVADYLDDQP---LLSGADRSYVYVIYPDGRTQKAPVALWNKRHVEPMPGSTIFVGFSPsvLPEDYSSLNEQIVQ 83


                  ....*.
gi 1691013096 280 LLRHKV 285
Cdd:pfam06251  84 LLTNRI 89
Caps_syn_GfcC_N pfam20616
Capsule biosynthesis GfcC, N-terminal; Many bacteria are covered in a layer of ...
 43-153 5.69e-05

Capsule biosynthesis GfcC, N-terminal; Many bacteria are covered in a layer of surface-associated polysaccharide called the capsule. These capsules can be divided into four groups depending upon the organization of genes responsible for capsule assembly, the assembly pathway and regulation. This family plays a role in group 4 capsule biosynthesis. These proteins have a beta-grasp fold. Two beta-grasp domains, D2 and D3, are arranged in tandem. There is a C-terminal amphipathic helix which packs against D3. A helical hairpin insert in D2 binds to D3 and constrains its position, a conserved arginine residue at the end of this hairpin is essential for structural integrity. This entry represents D2 domain found at the N-terminal.


Pssm-ID: 466765  Cd Length: 129  Bit Score: 42.10  E-value: 5.69e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1691013096  43 TVELPLQGVTLEYKADVRMLQVLDDANSSFNANSgigyfpLSAQLFDKANTEAIEAKKRNVLNQL-----EAFAIEEPE- 116
Cdd:pfam20616   6 SVFLPGESEVLTLTDAERLEQLVGQPQLLANSWW------PGAVISDEAATQKALKQRQVLLAQLaslsaEWLFSADGDl 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1691013096 117 ---ANLVRQQLTSFQYLNRVFIELDRNAVISQSDKNPLLV 153
Cdd:pfam20616  80 aaaINQLRQQLQNLNVTGRIFVNLDPDVVRVDERSNPPLV 119
 
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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