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Conserved domains on  [gi|239786031|gb|ACS16233|]
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beta-globin subunit [Peromyscus maniculatus]

Protein Classification

hemoglobin beta-like protein( domain architecture ID 10172378)

hemoglobin beta-like protein is either one of gamma, delta, epsilon, or 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.

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Hb-beta-like cd08925
Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport ...
 8-146 1.82e-81

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: 236.00  E-value: 1.82e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   8 EKALVTGLWGKVKPEEIGGEALGRLLAVYPWTQRFFDSFGDLSSASAIMGNAKVKAHGKKVIDSFSEGLKHLDNLKGTFA 87
Cdd:cd08925    1 EKAAITAVWGKVDVDEVGAEALARLLIVYPWTQRYFSSFGDLSSAAAIAGNPKVAAHGKKVLGALGEAIKHLDDIKATFA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 239786031  88 SLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATALAHKY 146
Cdd:cd08925   81 DLSEKHSEKLHVDPENFKLLGDCLVVVLAAHFGKEFTPEVQAAWEKFFAVVVDALSKGY 139
 
Name Accession Description Interval E-value
Hb-beta-like cd08925
Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport ...
 8-146 1.82e-81

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: 236.00  E-value: 1.82e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   8 EKALVTGLWGKVKPEEIGGEALGRLLAVYPWTQRFFDSFGDLSSASAIMGNAKVKAHGKKVIDSFSEGLKHLDNLKGTFA 87
Cdd:cd08925    1 EKAAITAVWGKVDVDEVGAEALARLLIVYPWTQRYFSSFGDLSSAAAIAGNPKVAAHGKKVLGALGEAIKHLDDIKATFA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 239786031  88 SLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATALAHKY 146
Cdd:cd08925   81 DLSEKHSEKLHVDPENFKLLGDCLVVVLAAHFGKEFTPEVQAAWEKFFAVVVDALSKGY 139
Globin pfam00042
Globin;
27-142 1.35e-33

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 113.92  E-value: 1.35e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   27 EALGRLLAVYPWTQRFFDSFGDlsSASAIMGNAKVKAHGKKVIDSFSEGLKHLDNLK---GTFASLSELHCDKLHVDPEN 103
Cdd:pfam00042   2 EILARLFTAYPDTKAYFPRFEK--SADDLKGSPKFKAHGKKVLAALGEAVKHLDDLAalnAALKKLGARHKEKRGVDPAN 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 239786031  104 FKLLGNMIVIVMAHHLGKdFTPAAQSAYQKVVSGVATAL 142
Cdd:pfam00042  80 FKLFGEALLVVLAEHLGE-FTPETKAAWDKALDVIAAAL 117
 
Name Accession Description Interval E-value
Hb-beta-like cd08925
Hemoglobin beta, gamma, delta, epsilon, and related Hb subunits; Hb is the oxygen transport ...
 8-146 1.82e-81

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: 236.00  E-value: 1.82e-81
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   8 EKALVTGLWGKVKPEEIGGEALGRLLAVYPWTQRFFDSFGDLSSASAIMGNAKVKAHGKKVIDSFSEGLKHLDNLKGTFA 87
Cdd:cd08925    1 EKAAITAVWGKVDVDEVGAEALARLLIVYPWTQRYFSSFGDLSSAAAIAGNPKVAAHGKKVLGALGEAIKHLDDIKATFA 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 239786031  88 SLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATALAHKY 146
Cdd:cd08925   81 DLSEKHSEKLHVDPENFKLLGDCLVVVLAAHFGKEFTPEVQAAWEKFFAVVVDALSKGY 139
Hb cd14765
Hemoglobins; Hb is the oxygen transport protein of erythrocytes. It is an allosterically ...
 8-143 2.03e-67

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: 200.27  E-value: 2.03e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   8 EKALVTGLWGKVKPEEIGGEALGRLLAVYPWTQRFFDSFGDLSSasaimGNAKVKAHGKKVIDSFSEGLKHLDNLKGTFA 87
Cdd:cd14765    1 EKSTIKALWGKVNVEEYGAEALARLFVVYPWTKRYFPKFDDSSS-----GNPKVKAHGKKVLGALGDAVKHLDDLKNTFS 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 239786031  88 SLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATALA 143
Cdd:cd14765   76 DLSELHADKLHVDPENFKLLSDCLIVVLAAHLGKEFTPEVHAAWDKFLAVVAAALS 131
Hb-alpha-like cd08927
Hemoglobin alpha, zeta, mu, theta, and related Hb subunits; Hb is the oxygen transport protein ...
 4-146 9.20e-47

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: 148.10  E-value: 9.20e-47
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   4 LTDAEKALVTGLWGKVKP--EEIGGEALGRLLAVYPWTQRFFDSFgDLSSasaimGNAKVKAHGKKVIDSFSEGLKHLDN 81
Cdd:cd08927    1 LSAADKALIKALWGKIAGhaEAIGAEALARMFLSFPQTKTYFPHF-DLSA-----GSAQVKAHGKKVMDALGDAVKHLDD 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 239786031  82 LKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATALAHKY 146
Cdd:cd08927   75 LPGALSKLSDLHAYKLRVDPVNFKLLSHCILVTLAAHLPEDFTPEVHAALDKFLAAVSHVLSSKY 139
Globin pfam00042
Globin;
27-142 1.35e-33

Globin;


Pssm-ID: 459646 [Multi-domain]  Cd Length: 117  Bit Score: 113.92  E-value: 1.35e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   27 EALGRLLAVYPWTQRFFDSFGDlsSASAIMGNAKVKAHGKKVIDSFSEGLKHLDNLK---GTFASLSELHCDKLHVDPEN 103
Cdd:pfam00042   2 EILARLFTAYPDTKAYFPRFEK--SADDLKGSPKFKAHGKKVLAALGEAVKHLDDLAalnAALKKLGARHKEKRGVDPAN 79

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 239786031  104 FKLLGNMIVIVMAHHLGKdFTPAAQSAYQKVVSGVATAL 142
Cdd:pfam00042  80 FKLFGEALLVVLAEHLGE-FTPETKAAWDKALDVIAAAL 117
Mb-like cd01040
myoglobin-like; M family globin domain; This family includes chimeric (FHbs/flavohemoglobins) ...
 16-142 8.02e-18

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: 74.41  E-value: 8.02e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031  16 WGKVKP--EEIGGEALGRLLAVYPWTQRFFDSFGDLSSAsaIMGNAKVKAHGKKVIDSFSEGLKHLDNLKGTFASLSEL- 92
Cdd:cd01040    5 WARVKKdkEEFGVAIFLRLFEANPELKKLFPKFAGVDLD--LKGSPEFKAHAKRVVGALDSLIDNLDDPEALDALLRKLg 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 239786031  93 --HCdKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATAL 142
Cdd:cd01040   83 krHK-RRGVTPEHFEVFGEALLETLEEVLGEAFTPEVEAAWRKLLDYIANAI 133
Mb cd08926
Animal Myoglobins; Myoglobin (Mb) is a monomeric pentacoordinate heme-bound globin protein ...
 7-146 4.08e-17

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: 72.87  E-value: 4.08e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   7 AEKALVTGLWGKVKPE--EIGGEALGRLLAVYPWTQRFFDSFGDLSSAsAIMGNAKVKAHGKKVIDSFSEGLK----HLD 80
Cdd:cd08926    1 ADWDLVLKVWAKVEADltGIGQEVLLRLFKEHPETQEHFPKFKGISQD-DLKSNEDLKKHGVTVLTALGEILKqkgsHEA 79

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 239786031  81 NLKgtfaSLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATALAHKY 146
Cdd:cd08926   80 ELK----PLAQTHATKHKIPPKYFELITEIIVKVLAEKHPSEMGAPAQAAFSKAFELICSDIEANY 141
Cygb cd08924
Cytoglobin and related globins; Cygb is a hexacoordinated heme-containing protein, able to ...
 4-136 8.40e-17

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: 72.18  E-value: 8.40e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   4 LTDAEKALVTGLWGKV--KPEEIGGEALGRLLAVYPWTQRFFDSFGDLSSASAIMGNAKVKAHGKKV---IDSFSEGLKH 78
Cdd:cd08924    1 LTEAERKVIQDTWARVyaNCEDVGVAILVRFFVNFPSAKQYFSQFKHMEDPLEMERSSQLRKHARRVmgaLNTVVENLHD 80

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 239786031  79 LDNLKGTFASLSELHCDKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVS 136
Cdd:cd08924   81 PDKVSSVLALVGKAHALKHKVEPVYFKILSGVILEVLAEEFAQDFTPEVQSAWSKLRG 138
HGbI-like cd12131
Hell's gate globin I (HGbI) from Methylacidophilum infernorum and related proteins; HGbI is a ...
 8-134 2.42e-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: 46.77  E-value: 2.42e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   8 EKALVTGLWGKVKP--EEIGGEALGRLLAVYPWTQRFFdsfgdlssasaimGNAKVKAHGKKVIDSFS---EGLKHLDNL 82
Cdd:cd12131    1 QIELVQQSFAKVEPiaDEAAALFYERLFELDPELKPLF-------------KGTDMEEQGRKLMAMLVlvvKGLDDLEAL 67

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 239786031  83 KGTFASLSELHCdKLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKV 134
Cdd:cd12131   68 LPALQDLGRRHV-KYGVKPEHYPLVGEALLWTLEEGLGDEWTPEVKQAWTDA 118
Globin-like cd01067
Globin-like protein superfamily; This globin-like domain superfamily contains a wide variety ...
 15-134 1.86e-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).


Pssm-ID: 381255 [Multi-domain]  Cd Length: 119  Bit Score: 38.59  E-value: 1.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031  15 LWGKVK--PEEIGGEALGRLLAvYPWTQRFFDSFGDLssasaimgnAKVKAHGKKVIDSFSEGLKHLDNLKGTFASLSEL 92
Cdd:cd01067    1 AWGYLEenQEEIVDDFYDRLFA-LPSLSELFSPPGRL---------AKCIRKQMHFLRYALYGLVDGDSIEEGLAGLGEA 70

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 239786031  93 HCDkLHVDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKV 134
Cdd:cd01067   71 HKS-LGVPISYFIAALNVMKDVLTELLGDKFTPAAGEAWTKI 111
Ngb cd08920
Neuroglobins; The Ngb described in this subfamily is a hexacoordinated heme globin chiefly ...
 4-142 3.15e-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: 3.15e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031   4 LTDAEKALVTGLWGKV--KPEEIGGEALGRLLAVYPWTQRFFD-SFGDLSSASAIMGNAKVKAHGKKVIDSFSEGLKHLD 80
Cdd:cd08920    1 LSRPQKELIRESWRSVsrSPLEHGTVLFSRLFELEPDLLPLFQyNGRQFSSPQDCLSSPEFLDHIRKVMLVIDAAVSHLE 80

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 239786031  81 NLkgtfASLSELHCD--KLH----VDPENFKLLGNMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATAL 142
Cdd:cd08920   81 DL----SSLEEYLTSlgRKHravgVKLESFSTVGESLLYMLESSLGPAFTPDTREAWSTLYGAVVQAM 144
CeGLB25-like cd14766
Caenorhabditis elegans globin GLB-25, and related globins; The C. elegans genome contains 33 ...
 32-142 3.98e-03

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: 35.37  E-value: 3.98e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 239786031  32 LLAVYPWTQRFFDSFGDLSSasaimgNAKVKAHGKKVIDSFSEGLKHLDNLKGTFASLSEL---HCDKLHVDPENFKLLG 108
Cdd:cd14766   30 LKELFPKLKNLEDEEDELRS------SEILENHAARVMDTLDEAISNIENVDYVIDLLHKVgkmHAKKPGFRPEMFWKIE 103

                         90       100       110
                 ....*....|....*....|....*....|....
gi 239786031 109 NMIVIVMAHHLGKDFTPAAQSAYQKVVSGVATAL 142
Cdd:cd14766  104 EPFLEAVSETLGDRYTDNMENIYRKTIKFILQTL 137
 
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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