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Conserved domains on  [gi|212642107|ref|NP_001129775|]
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Globin domain-containing protein [Caenorhabditis elegans]

Protein Classification

globin( domain architecture ID 10099307)

M-family globin similar to a variety of single-domain globins such as myoglobin and hemoglobin

CATH:  1.10.490.10
Gene Ontology:  GO:0019825|GO:0020037|GO:0005344|GO:0005506|GO:0015671
PubMed:  32863222|16061809|19281958|23209182
SCOP:  4000551

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Mb-like cd01040
myoglobin-like; M family globin domain; This family includes chimeric (FHbs/flavohemoglobins) ...
 82-224 2.29e-22

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: 89.05  E-value: 2.29e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  82 LRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFISKYQgDEWKESKEFRSQALKFVQTLAQVVKNIYHMERTESFLY 161
Cdd:cd01040    1 VKSSWARVKKDKEEFGVAIFLRLFEANPELKKLFPKFAGVD-LDLKGSPEFKAHAKRVVGALDSLIDNLDDPEALDALLR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212642107 162 MVGQKHVKfadRGFKHEYWDIFQDAMEFALEHRLSimtdldDNQKRDAVTVWRTLALYTTVHM 224
Cdd:cd01040   80 KLGKRHKR---RGVTPEHFEVFGEALLETLEEVLG------EAFTPEVEAAWRKLLDYIANAI 133
 
Name Accession Description Interval E-value
Mb-like cd01040
myoglobin-like; M family globin domain; This family includes chimeric (FHbs/flavohemoglobins) ...
 82-224 2.29e-22

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: 89.05  E-value: 2.29e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  82 LRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFISKYQgDEWKESKEFRSQALKFVQTLAQVVKNIYHMERTESFLY 161
Cdd:cd01040    1 VKSSWARVKKDKEEFGVAIFLRLFEANPELKKLFPKFAGVD-LDLKGSPEFKAHAKRVVGALDSLIDNLDDPEALDALLR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212642107 162 MVGQKHVKfadRGFKHEYWDIFQDAMEFALEHRLSimtdldDNQKRDAVTVWRTLALYTTVHM 224
Cdd:cd01040   80 KLGKRHKR---RGVTPEHFEVFGEALLETLEEVLG------EAFTPEVEAAWRKLLDYIANAI 133
Globin pfam00042
Globin;
98-200 6.13e-21

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 84.65  E-value: 6.13e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107   98 SAIYCYIFDHNPNCKQLFPFiSKYQGDEWKESKEFRSQALKFVQTLAQVVKNIYHMERTESFLYMVGQKHVKfaDRGFKH 177
Cdd:pfam00042   1 AEILARLFTAYPDTKAYFPR-FEKSADDLKGSPKFKAHGKKVLAALGEAVKHLDDLAALNAALKKLGARHKE--KRGVDP 77

                          90       100
                  ....*....|....*....|...
gi 212642107  178 EYWDIFQDAMEFALEHRLSIMTD 200
Cdd:pfam00042  78 ANFKLFGEALLVVLAEHLGEFTP 100
 
Name Accession Description Interval E-value
Mb-like cd01040
myoglobin-like; M family globin domain; This family includes chimeric (FHbs/flavohemoglobins) ...
 82-224 2.29e-22

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: 89.05  E-value: 2.29e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  82 LRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFISKYQgDEWKESKEFRSQALKFVQTLAQVVKNIYHMERTESFLY 161
Cdd:cd01040    1 VKSSWARVKKDKEEFGVAIFLRLFEANPELKKLFPKFAGVD-LDLKGSPEFKAHAKRVVGALDSLIDNLDDPEALDALLR 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 212642107 162 MVGQKHVKfadRGFKHEYWDIFQDAMEFALEHRLSimtdldDNQKRDAVTVWRTLALYTTVHM 224
Cdd:cd01040   80 KLGKRHKR---RGVTPEHFEVFGEALLETLEEVLG------EAFTPEVEAAWRKLLDYIANAI 133
Globin pfam00042
Globin;
98-200 6.13e-21

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 84.65  E-value: 6.13e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107   98 SAIYCYIFDHNPNCKQLFPFiSKYQGDEWKESKEFRSQALKFVQTLAQVVKNIYHMERTESFLYMVGQKHVKfaDRGFKH 177
Cdd:pfam00042   1 AEILARLFTAYPDTKAYFPR-FEKSADDLKGSPKFKAHGKKVLAALGEAVKHLDDLAALNAALKKLGARHKE--KRGVDP 77

                          90       100
                  ....*....|....*....|...
gi 212642107  178 EYWDIFQDAMEFALEHRLSIMTD 200
Cdd:pfam00042  78 ANFKLFGEALLVVLAEHLGEFTP 100
GbX cd12137
Globin_X (GbX); Zebrafish globin X (GbX) is expressed at low levels in neurons of the central ...
 78-227 9.48e-11

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: 58.08  E-value: 9.48e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  78 EKELLRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFISKYQGDEWKESKEFRSQALKFVQTLAQVVKNIYHMERTE 157
Cdd:cd12137    5 QKQLIESSWSILQEDIAKVGVIMFVRLFETHPDCKDAFFPFRDVDLEDLRHSKELRAHGLRVLSFVEKSLARLHQPDKLE 84

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 212642107 158 SFLYMVGQKHVKFadrGFKHEYWDI----FQDAMEFALEHRLSimTDLDDnqkrdavtVWRTLALYTTVHMRNG 227
Cdd:cd12137   85 ELLHELGRKHYRY---NAKVKYVDLvgqqFIFAIEPVLKEQWT--PELEE--------AWKTLFRYLTYVMKEG 145
HGbI-like cd12131
Hell's gate globin I (HGbI) from Methylacidophilum infernorum and related proteins; HGbI is a ...
 78-195 2.64e-07

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: 48.32  E-value: 2.64e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  78 EKELLRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPfiskyqgdewkeSKEFRSQALKFVQTLAQVVKNIYHMERTE 157
Cdd:cd12131    1 QIELVQQSFAKVEPIADEAAALFYERLFELDPELKPLFK------------GTDMEEQGRKLMAMLVLVVKGLDDLEALL 68

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 212642107 158 SFLYMVGQKHVKFadrGFKHEYWDIFQDAMEFALEHRL 195
Cdd:cd12131   69 PALQDLGRRHVKY---GVKPEHYPLVGEALLWTLEEGL 103
Cygb cd08924
Cytoglobin and related globins; Cygb is a hexacoordinated heme-containing protein, able to ...
 78-167 1.32e-03

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: 38.28  E-value: 1.32e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  78 EKELLRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFP-FISKYQGDEWKESKEFRSQALKFVQTLAQVVKNIYHMERT 156
Cdd:cd08924    5 ERKVIQDTWARVYANCEDVGVAILVRFFVNFPSAKQYFSqFKHMEDPLEMERSSQLRKHARRVMGALNTVVENLHDPDKV 84

                         90
                 ....*....|.
gi 212642107 157 ESFLYMVGQKH 167
Cdd:cd08924   85 SSVLALVGKAH 95
Adgb_C_mid-like cd22307
C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted ...
 79-126 1.78e-03

C-terminal middle region of Androglobins (Adgbs) and related proteins; including permuted globin domain and IQ motif; Androglobin (Adgb, also known as Calpain-7-like protein, CAPN7L) is a large multidomain protein consisting of an N-terminal peptidase C2 family calpain-like domain, an IQ calmodulin-binding motif, and an internal, circularly permuted globin domain. The canonical secondary structure of hemoglobins is an 3-over-3 alpha-helical sandwich structure, where the eight alpha-helical segments are conventionally labeled, A-H, according to their sequential order; Adgbs differ from this in having helices C-H followed by A-B. Adgbs and other phylogenetically ancient globins, such as neuroglobins and globin X, form hexacoordinated heme iron complexes. Globins contain various highly conserved residues of the heme pocket: including a Phe in the interhelical position CD1 (Phe CD1, first position in the loop between the helices C and D) that is packed against the heme, a His at the 7th position of the E-helix (His E7) that binds the heme iron distally, and a His at the 8th position of the F-helix (His F8) that binds the heme iron proximally. Unlike other hexacoordinated globins, Adgbs have an E7 Gln; their hexacoordination scheme is [Gln]-Fe-[His]. In mammals, Adgb is mainly expressed in the testes and may play an important role in spermatogenesis. Arthropod Adgbs have degenerate globin domains (DOI:10.3389/fgene.2020.00858). This model spans the permuted globin domain, the IQ motif, and a conserved region of about 200 amino acid residues located C-terminal to the globin domain; it does not include the N-terminal protease domain or the large uncharacterized C-terminal domain of approximately 500 residues.


Pssm-ID: 412094  Cd Length: 416  Bit Score: 39.07  E-value: 1.78e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 212642107  79 KELLRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFISkyqgDEW 126
Cdd:cd22307  180 AETLKKIWEKIESNLESLAASLLRYMFKNNPKLKELYPCYE----DEW 223
Mb-like_oxidoreductase cd19753
Globin domain of uncharacterized oxidoreductases containing a FAD/NADH binding domain; This ...
 82-193 6.33e-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: 35.68  E-value: 6.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  82 LRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPfiskyqgdewkESKEfrSQALKFVQTLAQVVKNIYHMERTESFLY 161
Cdd:cd19753    1 LRASLAAVEDGPDELARRFYARLFAEAPELRDLFP-----------ADMD--AQRDRLARALTHVVENLDDPDGLVPFLA 67

                         90       100       110
                 ....*....|....*....|....*....|..
gi 212642107 162 MVGQKHVKFadrGFKHEYWDIFQDAMEFALEH 193
Cdd:cd19753   68 QLGRDHRKY---GVAPEHYPAVGAALLAALRH 96
Ngb cd08920
Neuroglobins; The Ngb described in this subfamily is a hexacoordinated heme globin chiefly ...
 78-195 7.23e-03

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: 35.97  E-value: 7.23e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 212642107  78 EKELLRRTWSDEFDNLYELGSAIYCYIFDHNPNCKQLFPFISKYQGD--EWKESKEFRSQALKFVQTLAQVVKNIYHMER 155
Cdd:cd08920    5 QKELIRESWRSVSRSPLEHGTVLFSRLFELEPDLLPLFQYNGRQFSSpqDCLSSPEFLDHIRKVMLVIDAAVSHLEDLSS 84

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 212642107 156 TESFLYMVGQKHVKFadrGFKHEYWDIFQDAMEFALEHRL 195
Cdd:cd08920   85 LEEYLTSLGRKHRAV---GVKLESFSTVGESLLYMLESSL 121
 
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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