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Conserved domains on  [gi|1958675563|ref|XP_038947696|]
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protein FAM161A isoform X7 [Rattus norvegicus]

Protein Classification

globin family protein( domain architecture ID 229384)

globin family protein is an all-helical protein that may bind porphyrins, phycobilins, and other non-heme cofactors, and may play various roles including as a sensor or transporter of oxygen

CATH:  1.10.490.10
Gene Ontology:  GO:0019825|GO:0020037
PubMed:  32863222|16061809|19281958
SCOP:  3000554

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Globin-like super family cl21461
Globin-like protein superfamily; This globin-like domain superfamily contains a wide variety ...
 37-109 8.08e-04

Globin-like protein superfamily; This globin-like domain superfamily contains a wide variety of all-helical proteins that bind porphyrins, phycobilins, and other non-heme cofactors, and play various roles in all three kingdoms of life, including sensors or transporters of oxygen. It includes the M/myoglobin-like, S/sensor globin, and T/truncated globin (TrHb) families, and the phycobiliproteins (PBPs). The M family includes chimeric (FHbs/flavohemoglobins) and single-domain globins: FHbs, Ngbs/neuroglobins, Cygb/cytoglobins, GbE/avian eye specific globin E, GbX/globin X, amphibian GbY/globin Y, Mb/myoglobin, HbA/hemoglobin-alpha, HbB/hemoglobin-beta, SDgbs/single-domain globins related to FHbs, and Adgb/androglobin. The S family includes GCS/globin-coupled sensors, Pgbs/protoglobins, and SSDgbs/sensor single domain globins. The T family is classified into three main groups: TrHb1s (N), TrHb2s (O) and TrHb3s (P). The M- and S families exhibit the canonical secondary structure of hemoglobins, a 3-over-3 alpha-helical sandwich structure (3/3 Mb-fold), built by eight alpha-helical segments (named A through H). For M family Adgbs, this globin domain is permuted, such that C-H are followed by A-B. The T family globins adopt a 2-on-2 alpha-helical sandwich structure, resulting from extensive and complex modifications of the canonical 3-on-3 alpha-helical sandwich that are distributed throughout the whole protein molecule. PBPs bind the linear tetrapyrrole chromophore, phycobilin, a prosthetic group chemically and metabolically related to iron protoporphyrin IX/protoheme. Examples of other globin-like domains which bind non-heme cofactors include those of the Bacillus anthracis sporulation inhibitors pXO1-118 and pXO2-61 which bind fatty acid and halide in vitro, and the globin-like domain of Bacillus subtilis RsbRA which is presumed to channel sensory input to the C-terminal sulfate transporter/ anti-sigma factor antagonist (STAT) domain. RsbRA is a component of the sigma B-activating stressosome, and a regulator of the RNA polymerase sigma factor subunit sigma (B).


The actual alignment was detected with superfamily member pfam11563:

Pssm-ID: 473869 [Multi-domain]  Cd Length: 149  Bit Score: 38.34  E-value: 8.08e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958675563  37 LENTMNFSDIYHSDEEYFRKLKDLRAAHAEAMVKL--EKMYQDKLTMKDIQaalvgDDSSRRSEKARMKEYWQEL 109
Cdd:pfam11563   4 LAYRLRFLGFTEEDLAALRALRPLIEPHIPAIVDAfyDKLLSFPETARIFT-----TSSQIERLKDTLKAYLLRL 73
 
Name Accession Description Interval E-value
Protoglobin pfam11563
Protoglobin; This family includes protoglobin from Methanosarcina acetivorans C2A. It is also ...
 37-109 8.08e-04

Protoglobin; This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis. It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site. In HemAT it acts as an oxygen sensor domain. It can also recognize cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 431935 [Multi-domain]  Cd Length: 149  Bit Score: 38.34  E-value: 8.08e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958675563  37 LENTMNFSDIYHSDEEYFRKLKDLRAAHAEAMVKL--EKMYQDKLTMKDIQaalvgDDSSRRSEKARMKEYWQEL 109
Cdd:pfam11563   4 LAYRLRFLGFTEEDLAALRALRPLIEPHIPAIVDAfyDKLLSFPETARIFT-----TSSQIERLKDTLKAYLLRL 73
M3B_PepF cd09609
Peptidase family M3B, oligopeptidase F (PepF); Peptidase family M3B oligopeptidase F (PepF; ...
 33-88 7.02e-03

Peptidase family M3B, oligopeptidase F (PepF); Peptidase family M3B oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and is similar to oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid.


Pssm-ID: 341072 [Multi-domain]  Cd Length: 586  Bit Score: 37.18  E-value: 7.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958675563  33 KEVTLENTMNFSDIYHSDEEYFRKLKDLRaahaEAMVKLEKMYQDKL-TMKDIQAAL 88
Cdd:cd09609     2 SEVPEEETWDLTDLFKDEEAFEAALEELE----QLVDEFKKKYKGKLtDAEDILNAL 54
 
Name Accession Description Interval E-value
Protoglobin pfam11563
Protoglobin; This family includes protoglobin from Methanosarcina acetivorans C2A. It is also ...
 37-109 8.08e-04

Protoglobin; This family includes protoglobin from Methanosarcina acetivorans C2A. It is also found near the N-terminus of the Haem-based aerotactic transducer HemAT in Bacillus subtilis. It is part of the haemoglobin superfamily. Protoglobin has specific loops and an amino-terminal extension which leads to the burying of the haem within the matrix of the protein. Protoglobin-specific apolar tunnels allow the access of O2, CO and NO to the haem distal site. In HemAT it acts as an oxygen sensor domain. It can also recognize cyanide (Matilla et. al., FEMS Microbiology Reviews, fuab043, 45, 2021, 1. https://doi.org/10.1093/femsre/fuab043).


Pssm-ID: 431935 [Multi-domain]  Cd Length: 149  Bit Score: 38.34  E-value: 8.08e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958675563  37 LENTMNFSDIYHSDEEYFRKLKDLRAAHAEAMVKL--EKMYQDKLTMKDIQaalvgDDSSRRSEKARMKEYWQEL 109
Cdd:pfam11563   4 LAYRLRFLGFTEEDLAALRALRPLIEPHIPAIVDAfyDKLLSFPETARIFT-----TSSQIERLKDTLKAYLLRL 73
M3B_PepF cd09609
Peptidase family M3B, oligopeptidase F (PepF); Peptidase family M3B oligopeptidase F (PepF; ...
 33-88 7.02e-03

Peptidase family M3B, oligopeptidase F (PepF); Peptidase family M3B oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and is similar to oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the Bacillus amyloliquefaciens PepF oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over-expressed from a multicopy plasmid.


Pssm-ID: 341072 [Multi-domain]  Cd Length: 586  Bit Score: 37.18  E-value: 7.02e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958675563  33 KEVTLENTMNFSDIYHSDEEYFRKLKDLRaahaEAMVKLEKMYQDKL-TMKDIQAAL 88
Cdd:cd09609     2 SEVPEEETWDLTDLFKDEEAFEAALEELE----QLVDEFKKKYKGKLtDAEDILNAL 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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