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Conserved domains on  [gi|189532310|ref|XP_691804|]
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transmembrane glycoprotein NMB isoform X2 [Danio rerio]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PKAT_KLD super family cl48588
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 463-514 5.42e-10

PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, Transmembrane glycoprotein NMB (GPNMB) and TMEM130, which is downstream the PKD domain. It contains six highly conserved cysteine residues that form the disulphide bonds of mature PMEL dimers. (Chrystal et. al., Molecules 2021, 26(12), 3529; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123529). This domain is perfectly conserved in PMEL and GPNMB which suggests that GPNMB also forms dimers. PMEL and GPNMB, together with TMEM130 (its most ancient paralogue), have a conserved domain architecture and have been recently described as the PKAT (PKD- and KLD-Associated Transmembrane) protein family (Chrystal et. al., Molecules 2021, 26(12), 3529; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123529). PMEL and GPNMB share overlapping phenotypes and disease associations, such as melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma.


The actual alignment was detected with superfamily member pfam20433:

Pssm-ID: 466582  Cd Length: 51  Bit Score: 54.98  E-value: 5.42e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 189532310  463 TCSGSVPSVACTIVANSACREVKNIVCEDVTPYDEgCKISLTRIFQTPGTYC 514
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPE-CQLVLRRAFNGSGTYC 51
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 244-311 5.13e-05

PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold.


:

Pssm-ID: 395646 [Multi-domain]  Cd Length: 70  Bit Score: 41.60  E-value: 5.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 189532310  244 RADRNIFVRGSDVIFNVQLHDPSNylktadaVDFIWDFRDGNQLVTHSSVATHAYDMLGNVTVKLLVE 311
Cdd:pfam00801   2 SASGTVVAAGQPVTFTATLADGSN-------VTYTWDFGDSPGTSGSGPTVTHTYLSPGTYTVTLTAS 62
 
Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 463-514 5.42e-10

PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, Transmembrane glycoprotein NMB (GPNMB) and TMEM130, which is downstream the PKD domain. It contains six highly conserved cysteine residues that form the disulphide bonds of mature PMEL dimers. (Chrystal et. al., Molecules 2021, 26(12), 3529; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123529). This domain is perfectly conserved in PMEL and GPNMB which suggests that GPNMB also forms dimers. PMEL and GPNMB, together with TMEM130 (its most ancient paralogue), have a conserved domain architecture and have been recently described as the PKAT (PKD- and KLD-Associated Transmembrane) protein family (Chrystal et. al., Molecules 2021, 26(12), 3529; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123529). PMEL and GPNMB share overlapping phenotypes and disease associations, such as melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma.


Pssm-ID: 466582  Cd Length: 51  Bit Score: 54.98  E-value: 5.42e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 189532310  463 TCSGSVPSVACTIVANSACREVKNIVCEDVTPYDEgCKISLTRIFQTPGTYC 514
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPE-CQLVLRRAFNGSGTYC 51
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 244-311 5.13e-05

PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold.


Pssm-ID: 395646 [Multi-domain]  Cd Length: 70  Bit Score: 41.60  E-value: 5.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 189532310  244 RADRNIFVRGSDVIFNVQLHDPSNylktadaVDFIWDFRDGNQLVTHSSVATHAYDMLGNVTVKLLVE 311
Cdd:pfam00801   2 SASGTVVAAGQPVTFTATLADGSN-------VTYTWDFGDSPGTSGSGPTVTHTYLSPGTYTVTLTAS 62
 
Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 463-514 5.42e-10

PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, Transmembrane glycoprotein NMB (GPNMB) and TMEM130, which is downstream the PKD domain. It contains six highly conserved cysteine residues that form the disulphide bonds of mature PMEL dimers. (Chrystal et. al., Molecules 2021, 26(12), 3529; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123529). This domain is perfectly conserved in PMEL and GPNMB which suggests that GPNMB also forms dimers. PMEL and GPNMB, together with TMEM130 (its most ancient paralogue), have a conserved domain architecture and have been recently described as the PKAT (PKD- and KLD-Associated Transmembrane) protein family (Chrystal et. al., Molecules 2021, 26(12), 3529; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26123529). PMEL and GPNMB share overlapping phenotypes and disease associations, such as melanin-based pigmentation, cancer, neurodegenerative disease and glaucoma.


Pssm-ID: 466582  Cd Length: 51  Bit Score: 54.98  E-value: 5.42e-10
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 189532310  463 TCSGSVPSVACTIVANSACREVKNIVCEDVTPYDEgCKISLTRIFQTPGTYC 514
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPE-CQLVLRRAFNGSGTYC 51
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 244-311 5.13e-05

PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. This domain has been predicted to contain an Ig-like fold.


Pssm-ID: 395646 [Multi-domain]  Cd Length: 70  Bit Score: 41.60  E-value: 5.13e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 189532310  244 RADRNIFVRGSDVIFNVQLHDPSNylktadaVDFIWDFRDGNQLVTHSSVATHAYDMLGNVTVKLLVE 311
Cdd:pfam00801   2 SASGTVVAAGQPVTFTATLADGSN-------VTYTWDFGDSPGTSGSGPTVTHTYLSPGTYTVTLTAS 62
PKD_4 pfam18911
PKD domain; This entry is composed of PKD domains found in bacterial surface proteins.
 245-311 2.44e-04

PKD domain; This entry is composed of PKD domains found in bacterial surface proteins.


Pssm-ID: 436824 [Multi-domain]  Cd Length: 85  Bit Score: 40.33  E-value: 2.44e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 189532310  245 ADRNIFVrGSDVIFNVQLHDPSnylkTADAVDFIWDFRDGNQLVThsSVATHAYDMLGNVTVKLLVE 311
Cdd:pfam18911  10 GDRIVAE-GETVTFDASASDDP----DGDILSYRWDFGDGTTATG--ANVSHTYAAPGTYTVTLTVT 69
 
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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