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Conserved domains on  [gi|668768006|gb|AIH14561|]
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allophycocyanin subunit beta, partial [Fischerella thermalis WC114]

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
ApcB super family cl47388
Allophycocyanin beta chain [Energy production and conversion];
1-57 2.49e-30

Allophycocyanin beta chain [Energy production and conversion];


The actual alignment was detected with superfamily member COG5685:

Pssm-ID: 444399 [Multi-domain]  Cd Length: 162  Bit Score: 103.48  E-value: 2.49e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGasfVDEPFDYMTRELS 57
Cdd:COG5685  109 VLNGLRETYNSLGVPIGPTVRGIQIMKEVVKSMVADAGGAE---VDEYFDHLIRGLS 162
 
Name Accession Description Interval E-value
ApcB COG5685
Allophycocyanin beta chain [Energy production and conversion];
1-57 2.49e-30

Allophycocyanin beta chain [Energy production and conversion];


Pssm-ID: 444399 [Multi-domain]  Cd Length: 162  Bit Score: 103.48  E-value: 2.49e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGasfVDEPFDYMTRELS 57
Cdd:COG5685  109 VLNGLRETYNSLGVPIGPTVRGIQIMKEVVKSMVADAGGAE---VDEYFDHLIRGLS 162
APC_beta cd12126
Allophycocyanin beta subunit of the phycobilisome core; Phycobilisomes (PBSs) are the main ...
 1-56 8.24e-27

Allophycocyanin beta subunit of the phycobilisome core; Phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC).


Pssm-ID: 271281 [Multi-domain]  Cd Length: 163  Bit Score: 94.71  E-value: 8.24e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGaSFVDEPFDYMTREL 56
Cdd:cd12126  109 VLNGLKDTYNSLGVPIGPTVRAIQLMKEVVKELVGTAIDAG-KFVDEPFDYMIRGL 163
apcF CHL00089
allophycocyanin beta 18 subunit
 1-61 8.46e-23

allophycocyanin beta 18 subunit


Pssm-ID: 100206  Cd Length: 169  Bit Score: 84.46  E-value: 8.46e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGASFVDEPFDYMTRELSEKDI 61
Cdd:CHL00089 109 VLDGLKDTYNSLGVPIAPTVRSIELLKEIIKEEIKSQNIDAHDYIDEPFQYMIKNLSEQDL 169
Phycobilisome pfam00502
Phycobilisome protein;
1-56 3.47e-20

Phycobilisome protein;


Pssm-ID: 425723 [Multi-domain]  Cd Length: 155  Bit Score: 77.53  E-value: 3.47e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 668768006    1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAgvsGASFVDEPFDYMTREL 56
Cdd:pfam00502 103 GLNGLRETYNSLGVPIGAMVEAIQCMKEAALQLLSPE---AAAEAAPYFDYLINAL 155
 
Name Accession Description Interval E-value
ApcB COG5685
Allophycocyanin beta chain [Energy production and conversion];
1-57 2.49e-30

Allophycocyanin beta chain [Energy production and conversion];


Pssm-ID: 444399 [Multi-domain]  Cd Length: 162  Bit Score: 103.48  E-value: 2.49e-30
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGasfVDEPFDYMTRELS 57
Cdd:COG5685  109 VLNGLRETYNSLGVPIGPTVRGIQIMKEVVKSMVADAGGAE---VDEYFDHLIRGLS 162
APC_beta cd12126
Allophycocyanin beta subunit of the phycobilisome core; Phycobilisomes (PBSs) are the main ...
 1-56 8.24e-27

Allophycocyanin beta subunit of the phycobilisome core; Phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC).


Pssm-ID: 271281 [Multi-domain]  Cd Length: 163  Bit Score: 94.71  E-value: 8.24e-27
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGaSFVDEPFDYMTREL 56
Cdd:cd12126  109 VLNGLKDTYNSLGVPIGPTVRAIQLMKEVVKELVGTAIDAG-KFVDEPFDYMIRGL 163
apcF CHL00089
allophycocyanin beta 18 subunit
 1-61 8.46e-23

allophycocyanin beta 18 subunit


Pssm-ID: 100206  Cd Length: 169  Bit Score: 84.46  E-value: 8.46e-23
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGASFVDEPFDYMTRELSEKDI 61
Cdd:CHL00089 109 VLDGLKDTYNSLGVPIAPTVRSIELLKEIIKEEIKSQNIDAHDYIDEPFQYMIKNLSEQDL 169
Phycobilisome pfam00502
Phycobilisome protein;
1-56 3.47e-20

Phycobilisome protein;


Pssm-ID: 425723 [Multi-domain]  Cd Length: 155  Bit Score: 77.53  E-value: 3.47e-20
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 668768006    1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAgvsGASFVDEPFDYMTREL 56
Cdd:pfam00502 103 GLNGLRETYNSLGVPIGAMVEAIQCMKEAALQLLSPE---AAAEAAPYFDYLINAL 155
apcB CHL00088
allophycocyanin beta subunit
 1-57 1.43e-10

allophycocyanin beta subunit


Pssm-ID: 164493 [Multi-domain]  Cd Length: 161  Bit Score: 52.68  E-value: 1.43e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQL-AEAGVSGASFvdepFDYMTRELS 57
Cdd:CHL00088 108 VLNGLKETYNSLGVPIGATIQAIQAMKEVTASLVgPDAGKEMGVY----FDYICSGLS 161
CpcB COG5688
Phycocyanin/phycoerythrin beta chain, CpcB/CpeB [Energy production and conversion];
2-29 5.46e-09

Phycocyanin/phycoerythrin beta chain, CpcB/CpeB [Energy production and conversion];


Pssm-ID: 444402  Cd Length: 172  Bit Score: 48.87  E-value: 5.46e-09
                         10        20
                 ....*....|....*....|....*...
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKDI 29
Cdd:COG5688  110 LNGLRETYQALGVPGASVARGVQKMKAA 137
PBP-like cd08919
Phycobiliproteins (PBPs) and related proteins; phycobilisomes (PBSs) are the main ...
 1-37 6.54e-07

Phycobiliproteins (PBPs) and related proteins; phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This family also contains allophycocyanin-like (Apl) proteins, which conserve the residues critical for chromophore interactions, but may not maintain the proper alpha-beta subunit interactions and tertiary structure of PBPs. The genes encoding the Apl proteins cluster with light-responsive regulatory components, so these may have photoresponsive regulatory role(s). Included in this family is the PBP-like domain of the core-membrane linker polypeptide (LCM). The LCM serves both as a terminal energy acceptor and as a linker polypeptide. Its single phycocyanobilin (PCB) chromophore is one of two terminal energy transmitters, and transfers excitations from the hundreds of chromophores of the PBS to the RCs. This family also includes some proteins which have glutathione-S-transferases (GST) domains N-terminal to this PBP-like domain.


Pssm-ID: 381259  Cd Length: 153  Bit Score: 43.05  E-value: 6.54e-07
                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEA 37
Cdd:cd08919  101 LLNWLREIYKALGVPLDAYAAAYKDMKEAASQLLTPE 137
apcA CHL00086
allophycocyanin alpha subunit
 2-51 1.42e-06

allophycocyanin alpha subunit


Pssm-ID: 164492 [Multi-domain]  Cd Length: 161  Bit Score: 42.28  E-value: 1.42e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGASFVdepFDY 51
Cdd:CHL00086 109 LVGVKEMYNSLGTPISGVAEGVRSMKSVACSLLAGEDSAEAGFY---FDY 155
PE-PC-PEC_beta cd12127
Beta subunits of phycocyanin, phycoerythrin and phycoerythrocyanin; phycobilisome rod ...
 2-28 2.72e-06

Beta subunits of phycocyanin, phycoerythrin and phycoerythrocyanin; phycobilisome rod components; phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This family also includes the beta subunits of Cryptophyte phycobiliproteins which represent another type of biliprotein antenna with different structure and organization. The beta subunits of cryptophyte PBPs share a high degree of sequence identity with both the alpha and beta subunits of the cyanobacterial and red algal PBPs, however the alpha cryptophyte subunits are shorter, and unrelated. There is only one type of PBP present in a single species, either phycocyanin or phycoerythrin, but not allophycocyanin. Structurally, phycoerythrin in cryptophytes is an alpha1alpha2betabeta dimer and not a trimer as in the PBS.


Pssm-ID: 381266  Cd Length: 174  Bit Score: 41.70  E-value: 2.72e-06
                         10        20
                 ....*....|....*....|....*..
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKD 28
Cdd:cd12127  110 LNGLKETYQALGVPGSSVARAIEKMKE 136
PE_beta-like cd14767
Phycoerythrin beta subunit, a component of the phycobilisome rod; and related proteins; ...
 2-27 7.98e-06

Phycoerythrin beta subunit, a component of the phycobilisome rod; and related proteins; phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC). This subfamily also includes the beta subunits of Cryptophyte phycobiliproteins which represent another type of biliprotein antenna with different structure and organization. The beta subunits of cryptophyte PBPs share a high degree of sequence identity with both the alpha and beta subunits of the cyanobacterial and red algal PBPs, however the alpha cryptophyte subunits are shorter, and unrelated. There is only one type of PBP present in a single species, either phycocyanin or phycoerythrin, but not allophycocyanin. Structurally, phycoerythrin in cryptophytes is an alpha1alpha2betabeta dimer and not a trimer as in the PBS.


Pssm-ID: 271300  Cd Length: 176  Bit Score: 40.26  E-value: 7.98e-06
                         10        20
                 ....*....|....*....|....*.
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMK 27
Cdd:cd14767  110 LNGLKETYIALGVPTNSNIRAVSIMK 135
cpeB CHL00172
phycoerythrin beta subunit; Provisional
 2-27 8.72e-06

phycoerythrin beta subunit; Provisional


Pssm-ID: 133617  Cd Length: 177  Bit Score: 40.44  E-value: 8.72e-06
                         10        20
                 ....*....|....*....|....*.
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMK 27
Cdd:CHL00172 110 LNGLKETYIALGVPANSSARAVSIMK 135
ApcA COG5684
Allophycocyanin alpha chain [Energy production and conversion];
2-57 3.02e-05

Allophycocyanin alpha chain [Energy production and conversion];


Pssm-ID: 444398 [Multi-domain]  Cd Length: 161  Bit Score: 38.69  E-value: 3.02e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVSGASFVdepFDYMTRELS 57
Cdd:COG5684  109 LIGVREMYQSLGVPLPAMVEGIRCLKEASLSLLSGEDAAEAAPY---FDYLIQAMS 161
PC_PEC_beta cd14768
Beta subunits of phycoerythrin and phycoerythrocyanin; phycobilisome rod components; ...
 2-28 3.11e-05

Beta subunits of phycoerythrin and phycoerythrocyanin; phycobilisome rod components; phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC).


Pssm-ID: 271301  Cd Length: 171  Bit Score: 38.66  E-value: 3.11e-05
                         10        20
                 ....*....|....*....|....*..
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKD 28
Cdd:cd14768  110 LNGLRETYQALGTPGSSVAVGVQKMKE 136
APC_alpha cd12125
Allophycocyanin alpha subunit of the phycobilisome core; Phycobilisomes (PBSs) are the main ...
 2-56 2.11e-04

Allophycocyanin alpha subunit of the phycobilisome core; Phycobilisomes (PBSs) are the main light-harvesting complex in cyanobacteria and red algae. In general, they consist of a central core and surrounding rods and function to harvest and channel light energy toward the photosynthetic reaction centers within the membrane. They are comprised of phycobiliproteins/chromophorylated proteins (PBPs) maintained together by linker polypeptides. PBPs have different numbers of chromophores, and the basic monomer component (alpha/beta heterodimers) can further oligomerize to ring-shaped trimers (heterohexamers) and hexamers (heterododecamers). Stacked PBP hexamers form both the core and the rods of the PBS; the core is mainly made up by allophycocyanin (APC) while the rods can be composed of the PBPs phycoerythrin (PE), phycocyanin (PC) and phycoerythrocyanin (PEC).


Pssm-ID: 381265 [Multi-domain]  Cd Length: 159  Bit Score: 36.49  E-value: 2.11e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKDIVkqqLAEAGVSGASFVDEPFDYMTREL 56
Cdd:cd12125  108 LIGVREMYNSLGVPLPNMVEAMRCLKEAA---LALLSPEDAAEAAPYFDYIIQAM 159
apcD CHL00090
allophycocyanin gamma subunit
 2-57 5.37e-04

allophycocyanin gamma subunit


Pssm-ID: 164494  Cd Length: 161  Bit Score: 35.53  E-value: 5.37e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKDIVKQQLAEAGVsgaSFVDEPFDYMTRELS 57
Cdd:CHL00090 109 IIGVREMYNSLGVPIIGMVDSIQCLKEAALEVLSPEDV---KIIEPYFDYIIQGMS 161
cpcB CHL00171
phycocyanin beta subunit; Reviewed
 2-28 5.79e-04

phycocyanin beta subunit; Reviewed


Pssm-ID: 100271  Cd Length: 172  Bit Score: 35.36  E-value: 5.79e-04
                         10        20
                 ....*....|....*....|....*..
gi 668768006   2 LQGLRETYNSLGVPIGPTVRGIQIMKD 28
Cdd:CHL00171 110 LNGLRETYQALGVPGSSVAVAVQKMKE 136
Globin-like cd01067
Globin-like protein superfamily; This globin-like domain superfamily contains a wide variety ...
 1-28 7.56e-03

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: 32.04  E-value: 7.56e-03
                         10        20
                 ....*....|....*....|....*...
gi 668768006   1 VLQGLRETYNSLGVPIGPTVRGIQIMKD 28
Cdd:cd01067   63 GLAGLGEAHKSLGVPISYFIAALNVMKD 90
 
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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