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Conserved domains on  [gi|359500101|gb|AEV52618|]
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omega globin, partial [Dendrolagus goodfellowi]

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 ...
 1-57 2.51e-25

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 cd08925:

Pssm-ID: 473869  Cd Length: 139  Bit Score: 90.01  E-value: 2.51e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101   1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd08925   77 ATFADLSEKHSEKLHVDPENFKLLGDCLVVVLAAHFGKEFTPEVQAAWEKFFAVVVD 133
 
Name Accession Description Interval E-value
Hb-beta-like cd08925
Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport ...
 1-57 2.51e-25

Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary hemoglobin throughout most of gestation. These Hbs types have differences in O2 affinity and in their interactions with allosteric effectors.


Pssm-ID: 381262  Cd Length: 139  Bit Score: 90.01  E-value: 2.51e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101   1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd08925   77 ATFADLSEKHSEKLHVDPENFKLLGDCLVVVLAAHFGKEFTPEVQAAWEKFFAVVVD 133
Globin pfam00042
Globin;
1-57 2.08e-11

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 53.83  E-value: 2.08e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101    1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKdFTIEAQAAWQKLVGVVAA 57
Cdd:pfam00042  60 AALKKLGARHKEKRGVDPANFKLFGEALLVVLAEHLGE-FTPETKAAWDKALDVIAA 115
 
Name Accession Description Interval E-value
Hb-beta-like cd08925
Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport ...
 1-57 2.51e-25

Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary hemoglobin throughout most of gestation. These Hbs types have differences in O2 affinity and in their interactions with allosteric effectors.


Pssm-ID: 381262  Cd Length: 139  Bit Score: 90.01  E-value: 2.51e-25
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101   1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd08925   77 ATFADLSEKHSEKLHVDPENFKLLGDCLVVVLAAHFGKEFTPEVQAAWEKFFAVVVD 133
Hb cd14765
Hemoglobins; Hb is the oxygen transport protein of erythrocytes. It is an allosterically ...
 1-57 1.18e-20

Hemoglobins; Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which, in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary Hb throughout most of gestation. These Hb types have differences in O2 affinity and in their interactions with allosteric effectors.


Pssm-ID: 381278  Cd Length: 131  Bit Score: 77.78  E-value: 1.18e-20
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101   1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd14765   72 NTFSDLSELHADKLHVDPENFKLLSDCLIVVLAAHLGKEFTPEVHAAWDKFLAVVAA 128
Hb-alpha-like cd08927
Hemoglobin alpha, zeta, mu, theta, and related Hb subunits; Hb is the oxygen transport protein ...
 1-57 1.41e-13

Hemoglobin alpha, zeta, mu, theta, and related Hb subunits; Hb is the oxygen transport protein of erythrocytes. It is an allosterically modulated heterotetramer. Hemoglobin A (HbA) is the most common Hb in adult humans, and is formed from two alpha-chains and two beta-chains (alpha2beta2). An equilibrium exists between deoxygenated/unliganded/T(tense state) Hb having low oxygen affinity, and oxygenated /liganded/R(relaxed state) Hb having a high oxygen affinity. Various endogenous heterotropic effectors bind Hb to modulate its oxygen affinity and cooperative behavior, e.g. hydrogen ions, chloride ions, carbon dioxide and 2,3-bisphosphoglycerate. Hb is also an allosterically regulated nitrite reductase; the plasma nitrite anion may be activated by hemoglobin in areas of hypoxia to bring about vasodilation. Other Hb types are: HbA2 (alpha2delta2) which in normal individuals, is naturally expressed at a low level; Hb Portland-1 (zeta2gamma2), Hb Gower-1 (zeta2epsilon2), and Hb Gower-2 (alpha2epsilon2), which are Hbs present during the embryonic period; and fetal hemoglobin (HbF, alpha2gamma2), the primary hemoglobin throughout most of gestation. These Hbs types have differences in O2 affinity and in their interactions with allosteric effectors.


Pssm-ID: 381263  Cd Length: 140  Bit Score: 59.89  E-value: 1.41e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101   1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd08927   77 GALSKLSDLHAYKLRVDPVNFKLLSHCILVTLAAHLPEDFTPEVHAALDKFLAAVSH 133
Globin pfam00042
Globin;
1-57 2.08e-11

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 53.83  E-value: 2.08e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101    1 ATFDKLSQLHSDKLHVDPQNFRLLGDNLIIALAAALGKdFTIEAQAAWQKLVGVVAA 57
Cdd:pfam00042  60 AALKKLGARHKEKRGVDPANFKLFGEALLVVLAEHLGE-FTPETKAAWDKALDVIAA 115
Mb-like cd01040
myoglobin-like; M family globin domain; This family includes chimeric (FHbs/flavohemoglobins) ...
 1-57 1.16e-06

myoglobin-like; M family globin domain; This 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 M family exhibits 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). In Adgbs, the globin domain is split into two: helices C-H are followed by helices A-B and the two parts are separated by the IQ motif. Although rearranged, the globin domain of most Adgbs contains a number of conserved residues which play critical roles in heme-coordination and gas ligand binding. Adgbs have been omitted from this A-H helix cd.


Pssm-ID: 381254  Cd Length: 133  Bit Score: 42.06  E-value: 1.16e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 359500101   1 ATFDKLSQLHSdKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd01040   76 ALLRKLGKRHK-RRGVTPEHFEVFGEALLETLEEVLGEAFTPEVEAAWRKLLDYIAN 131
Cygb cd08924
Cytoglobin and related globins; Cygb is a hexacoordinated heme-containing protein, able to ...
 10-55 1.02e-05

Cytoglobin and related globins; Cygb is a hexacoordinated heme-containing protein, able to bind O2, NO and carbon monoxide. It has both nitric oxide dioxygenase and lipid peroxidase activities, and potentially participates in the maintenance of normal phenotype by implementing a homeostatic effect, to counteract stress conditions imposed on a cell. Cygb is implicated in multiple human pathologies: it is up-regulated in fibrosis and neurodegenerative disorders, and down-regulated in multiple cancer types, and may have a tumor suppressor role. It is expressed ubiquitously across a broad range of vertebrate organs including liver, heart, brain, lung, retina, and gut. In the human brain, it was detected at high levels in the habenula, hypothalamus, thalamus, hippocampus and pontine tegmental nuclei, detected at a low level in the cerebral cortex, and undetected in the cerebellar cortex.


Pssm-ID: 271275  Cd Length: 153  Bit Score: 39.83  E-value: 1.02e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 359500101  10 HSDKLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVV 55
Cdd:cd08924   95 HALKHKVEPVYFKILSGVILEVLAEEFAQDFTPEVQSAWSKLRGLI 140
HGbI-like cd12131
Hell's gate globin I (HGbI) from Methylacidophilum infernorum and related proteins; HGbI is a ...
 13-56 3.12e-04

Hell's gate globin I (HGbI) from Methylacidophilum infernorum and related proteins; HGbI is a single-domain heme-containing protein isolated from Methylacidiphilum infernorum, an aerobic acidophilic and thermophilic methanotroph. M. infernorum grows optimally at pH 2.0 and 60C and its home is New Zealand's Hell's Gate geothermal park. The physiological role of HGbI has yet to be determined. It has an extremely strong resistance to auto-oxidation, and has fast oxygen-binding/slow release characteristics. Its CO on-rate is comparable to the O2 on-rate, and it is able to bind acetate with high affinity in the ferric state. The coordination of the heme iron changes in the ferrous form from pentacoordinate at low pH to predominantly hexacoordinate at high pH; in the ferric form, it is predominantly hexacoordinate at all pH.


Pssm-ID: 381269 [Multi-domain]  Cd Length: 128  Bit Score: 35.60  E-value: 3.12e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 359500101  13 KLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVA 56
Cdd:cd12131   80 KYGVKPEHYPLVGEALLWTLEEGLGDEWTPEVKQAWTDAYGILA 123
Ngb cd08920
Neuroglobins; The Ngb described in this subfamily is a hexacoordinated heme globin chiefly ...
 16-55 7.96e-04

Neuroglobins; The Ngb described in this subfamily is a hexacoordinated heme globin chiefly expressed in neurons of the brain and retina. In the human brain, it is highly expressed in the hypothalamus, amygdala, and in the pontine tegmental nuclei. It affords protection of brain neurons from ischemia and hypoxia. In rats, it plays a role in the neuroprotection of limb ischemic preconditioning (LIP). It plays roles as: a sensor of oxygen levels; a store or reservoir for oxygen; a facilitator for oxygen transport; a regulator of ROS; and a scavenger of nitric oxide. It also functions in the protection against apoptosis and in sleep regulation. This subgroup contains Ngb from mammalian and non-mammalian vertebrates, including fish, amphibians and reptiles; the functionally pentacoordinated acoelomorph Symsagittifera roscoffensis Ngb does not belong to this subgroup.


Pssm-ID: 271272  Cd Length: 148  Bit Score: 34.81  E-value: 7.96e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 359500101  16 VDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVV 55
Cdd:cd08920  101 VKLESFSTVGESLLYMLESSLGPAFTPDTREAWSTLYGAV 140
Mb-like_oxidoreductase cd19753
Globin domain of uncharacterized oxidoreductases containing a FAD/NADH binding domain; This ...
 6-57 7.45e-03

Globin domain of uncharacterized oxidoreductases containing a FAD/NADH binding domain; This subfamily is composed of uncharacterized proteins containing an N-terminal myoglobin-like (M family globin) domain and a C-terminal oxygenase reductase FAD/NADH binding domain belonging to the ferredoxin reductase (FNR) family and is usually part of multi-component bacterial oxygenases which oxidize hydrocarbons using oxygen as the oxidant. The domain architecture of this subfamily is similar to flavohemoglobins, which function primarily as nitric oxide dioxygenases (NODs, EC 1.14.12.17), converting NO and O2 to inert NO3- (nitrate). They protect from nitrosative stress (the broad range of cellular toxicities caused by NO), and modulate NO signaling pathways. NO scavenging by flavoHb attenuates the expression of the nitrosative stress response, affects the swarming behavior of Escherichia coli, and maintains squid-Vibrio fischeri and Medicago truncatula-Sinorhizobium meliloti symbioses.


Pssm-ID: 381293 [Multi-domain]  Cd Length: 121  Bit Score: 31.83  E-value: 7.45e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 359500101   6 LSQLHSD--KLHVDPQNFRLLGDNLIIALAAALGKDFTIEAQAAWQKLVGVVAA 57
Cdd:cd19753   66 LAQLGRDhrKYGVAPEHYPAVGAALLAALRHFAGEAWTPELEAAWAEAYTLIAG 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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