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Conserved domains on  [gi|18959234|ref|NP_579832|]
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transmembrane glycoprotein NMB precursor [Rattus norvegicus]

Protein Classification

PKD domain-containing protein( domain architecture ID 10065681)

PKD domain-containing protein similar to melanocyte protein PMEL and transmembrane glycoprotein NMB

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 417-467 5.77e-27

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://doi.org/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://doi.org/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: 103.13  E-value: 5.77e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18959234   417 TCKGATPTEACTIISDPTCQIAQNRVCSPVAVDELCLLSVRRAFNGSGTYC 467
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPECQLVLRRAFNGSGTYC 51
PKD cd00146
polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an ...
 263-316 9.01e-10

polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.


:

Pssm-ID: 238084 [Multi-domain]  Cd Length: 81  Bit Score: 55.20  E-value: 9.01e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 18959234 263 FDVLIHDPSHflnYSAISYKWNFGDNTGlFVSNNHTLNHTYVLNGTFNFNLTVQ 316
Cdd:cd00146  17 VTFSASDSSG---GSIVSYKWDFGDGEV-SSSGEPTVTHTYTKPGTYTVTLTVT 66
 
Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 417-467 5.77e-27

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://doi.org/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://doi.org/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: 103.13  E-value: 5.77e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18959234   417 TCKGATPTEACTIISDPTCQIAQNRVCSPVAVDELCLLSVRRAFNGSGTYC 467
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPECQLVLRRAFNGSGTYC 51
PKD cd00146
polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an ...
 263-316 9.01e-10

polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.


Pssm-ID: 238084 [Multi-domain]  Cd Length: 81  Bit Score: 55.20  E-value: 9.01e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 18959234 263 FDVLIHDPSHflnYSAISYKWNFGDNTGlFVSNNHTLNHTYVLNGTFNFNLTVQ 316
Cdd:cd00146  17 VTFSASDSSG---GSIVSYKWDFGDGEV-SSSGEPTVTHTYTKPGTYTVTLTVT 66
PKD smart00089
Repeats in polycystic kidney disease 1 (PKD1) and other proteins; Polycystic kidney disease 1 ...
 263-319 2.99e-09

Repeats in polycystic kidney disease 1 (PKD1) and other proteins; Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.


Pssm-ID: 214510 [Multi-domain]  Cd Length: 79  Bit Score: 53.61  E-value: 2.99e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 18959234    263 FDVLIHDPSHfLNYSAISYKWNFGDNTglfVSNNHTLNHTYVLNGTFNFNLTVQTAV 319
Cdd:smart00089  15 ESVTFTATSS-DDGSIVSYTWDFGDGT---SSTGPTVTHTYTKPGTYTVTLTVTNAV 67
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 259-319 1.20e-04

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: 40.45  E-value: 1.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18959234   259 LPIFFDVLIHDPShflnysAISYKWNFGDNTGLfVSNNHTLNHTYVLNGTFNFNLTVQTAV 319
Cdd:pfam00801  12 QPVTFTATLADGS------NVTYTWDFGDSPGT-SGSGPTVTHTYLSPGTYTVTLTASNAV 65
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 232-319 6.69e-04

polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a huge protein of 4303aas. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative TMSs in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na+, K+ and Ca2+) channel that is activated by Ca2+. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects. Note: this model is restricted to the amino half.


Pssm-ID: 188093 [Multi-domain]  Cd Length: 2740  Bit Score: 42.76  E-value: 6.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959234    232 ITDQIPIFV-TMYQKNDRNSSDETFLRDLPIFFDvlihdPSHFLNYSAISYKWNFGDNTGLFVSNNHTLNHTYVLNGTFN 310
Cdd:TIGR00864 1075 ISQQINMSVrAILPRVAIGTEDGLLLAGKPADFE-----AHPLPSPGGIHYEWDFGDGSALLQGRQPAAAHTFAKRGPFH 1149


                   ....*....
gi 18959234    311 FNLTVQTAV 319
Cdd:TIGR00864 1150 VCLEVNNTI 1158
 
Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 417-467 5.77e-27

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://doi.org/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://doi.org/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: 103.13  E-value: 5.77e-27
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 18959234   417 TCKGATPTEACTIISDPTCQIAQNRVCSPVAVDELCLLSVRRAFNGSGTYC 467
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPECQLVLRRAFNGSGTYC 51
PKD cd00146
polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an ...
 263-316 9.01e-10

polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an IG-like fold; domain probably functions as a ligand binding site in protein-protein or protein-carbohydrate interactions; a single instance of the repeat is presented here. The domain is also found in microbial collagenases and chitinases.


Pssm-ID: 238084 [Multi-domain]  Cd Length: 81  Bit Score: 55.20  E-value: 9.01e-10
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....
gi 18959234 263 FDVLIHDPSHflnYSAISYKWNFGDNTGlFVSNNHTLNHTYVLNGTFNFNLTVQ 316
Cdd:cd00146  17 VTFSASDSSG---GSIVSYKWDFGDGEV-SSSGEPTVTHTYTKPGTYTVTLTVT 66
PKD smart00089
Repeats in polycystic kidney disease 1 (PKD1) and other proteins; Polycystic kidney disease 1 ...
 263-319 2.99e-09

Repeats in polycystic kidney disease 1 (PKD1) and other proteins; Polycystic kidney disease 1 protein contains 14 repeats, present elsewhere such as in microbial collagenases.


Pssm-ID: 214510 [Multi-domain]  Cd Length: 79  Bit Score: 53.61  E-value: 2.99e-09
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*..
gi 18959234    263 FDVLIHDPSHfLNYSAISYKWNFGDNTglfVSNNHTLNHTYVLNGTFNFNLTVQTAV 319
Cdd:smart00089  15 ESVTFTATSS-DDGSIVSYTWDFGDGT---SSTGPTVTHTYTKPGTYTVTLTVTNAV 67
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 259-319 1.20e-04

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: 40.45  E-value: 1.20e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 18959234   259 LPIFFDVLIHDPShflnysAISYKWNFGDNTGLfVSNNHTLNHTYVLNGTFNFNLTVQTAV 319
Cdd:pfam00801  12 QPVTFTATLADGS------NVTYTWDFGDSPGT-SGSGPTVTHTYLSPGTYTVTLTASNAV 65
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 232-319 6.69e-04

polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a huge protein of 4303aas. Its repeated leucine-rich (LRR) segment is found in many proteins. It contains 16 polycystic kidney disease (PKD) domains, one LDL-receptor class A domain, one C-type lectin family domain, and 16-18 putative TMSs in positions between residues 2200 and 4100. Polycystin-L has been shown to be a cation (Na+, K+ and Ca2+) channel that is activated by Ca2+. Two members of the PCC family (polycystin 1 and 2) are mutated in autosomal dominant polycystic kidney disease, and polycystin-L is deleted in mice with renal and retinal defects. Note: this model is restricted to the amino half.


Pssm-ID: 188093 [Multi-domain]  Cd Length: 2740  Bit Score: 42.76  E-value: 6.69e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 18959234    232 ITDQIPIFV-TMYQKNDRNSSDETFLRDLPIFFDvlihdPSHFLNYSAISYKWNFGDNTGLFVSNNHTLNHTYVLNGTFN 310
Cdd:TIGR00864 1075 ISQQINMSVrAILPRVAIGTEDGLLLAGKPADFE-----AHPLPSPGGIHYEWDFGDGSALLQGRQPAAAHTFAKRGPFH 1149


                   ....*....
gi 18959234    311 FNLTVQTAV 319
Cdd:TIGR00864 1150 VCLEVNNTI 1158
PKD_4 pfam18911
PKD domain; This entry is composed of PKD domains found in bacterial surface proteins.
 259-315 1.06e-03

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


Pssm-ID: 436824 [Multi-domain]  Cd Length: 85  Bit Score: 38.41  E-value: 1.06e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 18959234   259 LPIFFDVLIHDPShflNYSAISYKWNFGDNTGLFVSNnhtLNHTYVLNGTFNFNLTV 315
Cdd:pfam18911  18 ETVTFDASASDDP---DGDILSYRWDFGDGTTATGAN---VSHTYAAPGTYTVTLTV 68
 
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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