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Conserved domains on  [gi|2116773515|ref|XP_044201904|]
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myoglobin [Thunnus albacares]

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 ...
 2-147 1.65e-80

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 cd08926:

Pssm-ID: 473869  Cd Length: 148  Bit Score: 233.89  E-value: 1.65e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515   2 ADFDAVLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAHGATVLKKLGELLKAKGSHAAI 81
Cdd:cd08926     1 ADWDLVLKVWAKVEADLTGIGQEVLLRLFKEHPETQEHFPKFKGISQDDLKSNEDLKKHGVTVLTALGEILKQKGSHEAE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2116773515  82 LKPLANSHATKHKIPINNFKLISEVLVKVMHEKAG--LDAGGQTALRNVMGIIIADLEANYKELGFSG 147
Cdd:cd08926    81 LKPLAQTHATKHKIPPKYFELITEIIVKVLAEKHPseMGAPAQAAFSKAFELICSDIEANYKELGFQG 148
 
Name Accession Description Interval E-value
Mb cd08926
Animal Myoglobins; Myoglobin (Mb) is a monomeric pentacoordinate heme-bound globin protein ...
 2-147 1.65e-80

Animal Myoglobins; Myoglobin (Mb) is a monomeric pentacoordinate heme-bound globin protein whose expression has long been considered limited to cardiomyocytes and striated skeletal muscle cell, however it has recently been found localized in a wide variety of tissues including smooth muscle cells. As a physiological catalyst, it can modulate reactive oxygen species levels, facilitate oxygen diffusion within the cell, and scavenge or generate NO depending on oxygen tensions within the cell. Through its NO dioxygenase and nitrite reductase activities, Mb regulates mitochondrial function in energy-demanding tissues.


Pssm-ID: 271277  Cd Length: 148  Bit Score: 233.89  E-value: 1.65e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515   2 ADFDAVLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAHGATVLKKLGELLKAKGSHAAI 81
Cdd:cd08926     1 ADWDLVLKVWAKVEADLTGIGQEVLLRLFKEHPETQEHFPKFKGISQDDLKSNEDLKKHGVTVLTALGEILKQKGSHEAE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2116773515  82 LKPLANSHATKHKIPINNFKLISEVLVKVMHEKAG--LDAGGQTALRNVMGIIIADLEANYKELGFSG 147
Cdd:cd08926    81 LKPLAQTHATKHKIPPKYFELITEIIVKVLAEKHPseMGAPAQAAFSKAFELICSDIEANYKELGFQG 148
Globin pfam00042
Globin;
25-136 3.40e-22

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 85.03  E-value: 3.40e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515  25 VLTRLFKEHPETQKLFPKFAGIAqADIAGNAAISAHGATVLKKLGELLKAKGSHA---AILKPLANSHATKHKIPINNFK 101
Cdd:pfam00042   3 ILARLFTAYPDTKAYFPRFEKSA-DDLKGSPKFKAHGKKVLAALGEAVKHLDDLAalnAALKKLGARHKEKRGVDPANFK 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2116773515 102 LISEVLVKVMHEKAG-LDAGGQTALRNVMGIIIADL 136
Cdd:pfam00042  82 LFGEALLVVLAEHLGeFTPETKAAWDKALDVIAAAL 117
 
Name Accession Description Interval E-value
Mb cd08926
Animal Myoglobins; Myoglobin (Mb) is a monomeric pentacoordinate heme-bound globin protein ...
 2-147 1.65e-80

Animal Myoglobins; Myoglobin (Mb) is a monomeric pentacoordinate heme-bound globin protein whose expression has long been considered limited to cardiomyocytes and striated skeletal muscle cell, however it has recently been found localized in a wide variety of tissues including smooth muscle cells. As a physiological catalyst, it can modulate reactive oxygen species levels, facilitate oxygen diffusion within the cell, and scavenge or generate NO depending on oxygen tensions within the cell. Through its NO dioxygenase and nitrite reductase activities, Mb regulates mitochondrial function in energy-demanding tissues.


Pssm-ID: 271277  Cd Length: 148  Bit Score: 233.89  E-value: 1.65e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515   2 ADFDAVLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAHGATVLKKLGELLKAKGSHAAI 81
Cdd:cd08926     1 ADWDLVLKVWAKVEADLTGIGQEVLLRLFKEHPETQEHFPKFKGISQDDLKSNEDLKKHGVTVLTALGEILKQKGSHEAE 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2116773515  82 LKPLANSHATKHKIPINNFKLISEVLVKVMHEKAG--LDAGGQTALRNVMGIIIADLEANYKELGFSG 147
Cdd:cd08926    81 LKPLAQTHATKHKIPPKYFELITEIIVKVLAEKHPseMGAPAQAAFSKAFELICSDIEANYKELGFQG 148
Globin pfam00042
Globin;
25-136 3.40e-22

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 85.03  E-value: 3.40e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515  25 VLTRLFKEHPETQKLFPKFAGIAqADIAGNAAISAHGATVLKKLGELLKAKGSHA---AILKPLANSHATKHKIPINNFK 101
Cdd:pfam00042   3 ILARLFTAYPDTKAYFPRFEKSA-DDLKGSPKFKAHGKKVLAALGEAVKHLDDLAalnAALKKLGARHKEKRGVDPANFK 81

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2116773515 102 LISEVLVKVMHEKAG-LDAGGQTALRNVMGIIIADL 136
Cdd:pfam00042  82 LFGEALLVVLAEHLGeFTPETKAAWDKALDVIAAAL 117
Mb-like cd01040
myoglobin-like; M family globin domain; This family includes chimeric (FHbs/flavohemoglobins) ...
 7-134 4.37e-17

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: 72.49  E-value: 4.37e-17
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515   7 VLKCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIaQADIAGNAAISAHGATVLKKLGELLKAKGSHA---AILK 83
Cdd:cd01040     1 VKSSWARVKKDKEEFGVAIFLRLFEANPELKKLFPKFAGV-DLDLKGSPEFKAHAKRVVGALDSLIDNLDDPEaldALLR 79

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2116773515  84 PLANSHAtKHKIPINNFKLISEVLVKVMHEKAGLDAGGQT--ALRNVMGIIIA 134
Cdd:cd01040    80 KLGKRHK-RRGVTPEHFEVFGEALLETLEEVLGEAFTPEVeaAWRKLLDYIAN 131
Hb-beta-like cd08925
Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport ...
 11-140 2.04e-14

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: 65.74  E-value: 2.04e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515  11 WGPVEADytTMGGLVLTRLFKEHPETQKLFPKFAGIAQAD-IAGNAAISAHGATVLKKLGELLKAKGSHAAILKPLANSH 89
Cdd:cd08925     9 WGKVDVD--EVGAEALARLLIVYPWTQRYFSSFGDLSSAAaIAGNPKVAAHGKKVLGALGEAIKHLDDIKATFADLSEKH 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|...
gi 2116773515  90 ATKHKIPINNFKLISEVLVKVM--HEKAGLDAGGQTALRNVMGIIIADLEANY 140
Cdd:cd08925    87 SEKLHVDPENFKLLGDCLVVVLaaHFGKEFTPEVQAAWEKFFAVVVDALSKGY 139
Hb cd14765
Hemoglobins; Hb is the oxygen transport protein of erythrocytes. It is an allosterically ...
 5-111 2.98e-13

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: 62.37  E-value: 2.98e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515   5 DAVLKCWGPVEADytTMGGLVLTRLFKEHPETQKLFPKFAGIAqadiAGNAAISAHGATVLKKLGELLKAKGSHAAILKP 84
Cdd:cd14765     3 STIKALWGKVNVE--EYGAEALARLFVVYPWTKRYFPKFDDSS----SGNPKVKAHGKKVLGALGDAVKHLDDLKNTFSD 76

                          90       100
                  ....*....|....*....|....*..
gi 2116773515  85 LANSHATKHKIPINNFKLISEVLVKVM 111
Cdd:cd14765    77 LSELHADKLHVDPENFKLLSDCLIVVL 103
Cygb cd08924
Cytoglobin and related globins; Cygb is a hexacoordinated heme-containing protein, able to ...
 11-145 9.30e-12

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: 59.09  E-value: 9.30e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515  11 WGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQ-ADIAGNAAISAHGATVLKKLGELLKAKGSH---AAILKPLA 86
Cdd:cd08924    13 WARVYANCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDpLEMERSSQLRKHARRVMGALNTVVENLHDPdkvSSVLALVG 92

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2116773515  87 NSHATKHKIPINNFKLISEVLVKVMHEKAGLD--AGGQTALRNVMGIIIADLEANYKELGF 145
Cdd:cd08924    93 KAHALKHKVEPVYFKILSGVILEVLAEEFAQDftPEVQSAWSKLRGLIYSHVTAAYKEVGW 153
Hb-alpha-like cd08927
Hemoglobin alpha, zeta, mu, theta, and related Hb subunits; Hb is the oxygen transport protein ...
 11-111 1.59e-08

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: 50.26  E-value: 1.59e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515  11 WGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFagiaqaDI-AGNAAISAHGATVLKKLGELLKAKGSHAAILKPLANSH 89
Cdd:cd08927    13 WGKIAGHAEAIGAEALARMFLSFPQTKTYFPHF------DLsAGSAQVKAHGKKVMDALGDAVKHLDDLPGALSKLSDLH 86

                          90       100
                  ....*....|....*....|..
gi 2116773515  90 ATKHKIPINNFKLISEVLVKVM 111
Cdd:cd08927    87 AYKLRVDPVNFKLLSHCILVTL 108
GbX cd12137
Globin_X (GbX); Zebrafish globin X (GbX) is expressed at low levels in neurons of the central ...
 11-65 3.36e-06

Globin_X (GbX); Zebrafish globin X (GbX) is expressed at low levels in neurons of the central nervous system, and appears to be associated with the sensory system. GbX is likely to be attached to the cell membrane via S-palmitoylation and N-myristoylation. It's unlikely to have a true respiratory function as it is membrane-associated. It has been suggested that it may protect the lipids in the cell membrane from oxidation or act as a redox-sensing or signaling protein. Zebrafish GbX is hexacoordinate, and displays cooperative O2 binding.


Pssm-ID: 271287  Cd Length: 145  Bit Score: 43.83  E-value: 3.36e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2116773515  11 WGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQADIAGNAAISAHGATVL 65
Cdd:cd12137    13 WSILQEDIAKVGVIMFVRLFETHPDCKDAFFPFRDVDLEDLRHSKELRAHGLRVL 67
CeGLB25-like cd14766
Caenorhabditis elegans globin GLB-25, and related globins; The C. elegans genome contains 33 ...
 9-108 7.80e-06

Caenorhabditis elegans globin GLB-25, and related globins; The C. elegans genome contains 33 genes encoding globins that are all transcribed. These are very diverse in gene and protein structure and are localized in a variety of cells. The C. elegans globin GLB-25 (locus tag T06A1.3), like the majority of them, was expressed in neuronal cells in the head and tail portions of the body and in the nerve cord.


Pssm-ID: 381279  Cd Length: 137  Bit Score: 42.69  E-value: 7.80e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2116773515   9 KCWGPVEADYTTMGGLVLTRLFKEHPETQKLFPKFAGIAQ--ADIAGNAAISAHGATVLKKLGELLKAKG-SHAAI--LK 83
Cdd:cd14766     3 KSWKGIARKIDETGKTMFLRMLTENPELKELFPKLKNLEDeeDELRSSEILENHAARVMDTLDEAISNIEnVDYVIdlLH 82

                          90       100
                  ....*....|....*....|....*
gi 2116773515  84 PLANSHATKHKIPINNFKLISEVLV 108
Cdd:cd14766    83 KVGKMHAKKPGFRPEMFWKIEEPFL 107
 
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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