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Conserved domains on  [gi|52694752|ref|NP_001005340|]
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transmembrane glycoprotein NMB isoform a precursor [Homo sapiens]

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, ...
 415-465 1.85e-29

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: 110.06  E-value: 1.85e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 52694752   415 TCQGSIPTEVCTIISDPTCEITQNTVCSPVDVDEMCLLTVRRTFNGSGTYC 465
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPECQLVLRRAFNGSGTYC 51
PKD cd00146
polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an ...
 256-319 2.82e-09

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: 54.04  E-value: 2.82e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 52694752 256 LKDLPIMFDVLIHDPSHflnYSTINYKWSFGDNTGlFVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:cd00146  10 VAELGASVTFSASDSSG---GSIVSYKWDFGDGEV-SSSGEPTVTHTYTKPGTYTVTLTVTNAV 69
 
Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 415-465 1.85e-29

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: 110.06  E-value: 1.85e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 52694752   415 TCQGSIPTEVCTIISDPTCEITQNTVCSPVDVDEMCLLTVRRTFNGSGTYC 465
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPECQLVLRRAFNGSGTYC 51
PKD cd00146
polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an ...
 256-319 2.82e-09

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: 54.04  E-value: 2.82e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 52694752 256 LKDLPIMFDVLIHDPSHflnYSTINYKWSFGDNTGlFVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:cd00146  10 VAELGASVTFSASDSSG---GSIVSYKWDFGDGEV-SSSGEPTVTHTYTKPGTYTVTLTVTNAV 69
PKD smart00089
Repeats in polycystic kidney disease 1 (PKD1) and other proteins; Polycystic kidney disease 1 ...
 262-319 3.95e-08

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: 50.53  E-value: 3.95e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 52694752    262 MFDVLIHDPSHfLNYSTINYKWSFGDNTglfVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:smart00089  14 GESVTFTATSS-DDGSIVSYTWDFGDGT---SSTGPTVTHTYTKPGTYTVTLTVTNAV 67
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 279-319 3.03e-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: 41.99  E-value: 3.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 52694752   279 INYKWSFGDNTGLfVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:pfam00801  26 VTYTWDFGDSPGT-SGSGPTVTHTYLSPGTYTVTLTASNAV 65
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 204-317 1.71e-03

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: 41.61  E-value: 1.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52694752    204 GPQLMEVTVYRRHGRAYVPIAQVKDVYVVTDQIPVFVTMFQKNDRNSSDETFLKDLPIMFDVLIHDPSHFLnystinYKW 283
Cdd:TIGR00864 1216 GPEATVEHKYAKAGNCTVNIGAANAAGHGARIIHVEVFVFEVAGIEPAACIGEHADANFRARVSGNAAHYL------FDW 1289

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 52694752    284 SFGD-NTGLFVSTNHTVNHTYVLNGTFSLNLTVKA 317
Cdd:TIGR00864 1290 SFGDgSPNETHHGCPGISHNFRGNGTFPLALTISS 1324
 
Name Accession Description Interval E-value
PKAT_KLD pfam20433
PKAT, KLD domain; This is the Kringle-like domain (KLD) found in Melanocyte protein PMEL, ...
 415-465 1.85e-29

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: 110.06  E-value: 1.85e-29
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 52694752   415 TCQGSIPTEVCTIISDPTCEITQNTVCSPVDVDEMCLLTVRRTFNGSGTYC 465
Cdd:pfam20433   1 TCQGSLPTEVCTVVSDPTCQTPQNTVCNPVSPSPECQLVLRRAFNGSGTYC 51
PKD cd00146
polycystic kidney disease I (PKD) domain; similar to other cell-surface modules, with an ...
 256-319 2.82e-09

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: 54.04  E-value: 2.82e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 52694752 256 LKDLPIMFDVLIHDPSHflnYSTINYKWSFGDNTGlFVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:cd00146  10 VAELGASVTFSASDSSG---GSIVSYKWDFGDGEV-SSSGEPTVTHTYTKPGTYTVTLTVTNAV 69
PKD smart00089
Repeats in polycystic kidney disease 1 (PKD1) and other proteins; Polycystic kidney disease 1 ...
 262-319 3.95e-08

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: 50.53  E-value: 3.95e-08
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 52694752    262 MFDVLIHDPSHfLNYSTINYKWSFGDNTglfVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:smart00089  14 GESVTFTATSS-DDGSIVSYTWDFGDGT---SSTGPTVTHTYTKPGTYTVTLTVTNAV 67
PKD pfam00801
PKD domain; This domain was first identified in the Polycystic kidney disease protein PKD1. ...
 279-319 3.03e-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: 41.99  E-value: 3.03e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 52694752   279 INYKWSFGDNTGLfVSTNHTVNHTYVLNGTFSLNLTVKAAA 319
Cdd:pfam00801  26 VTYTWDFGDSPGT-SGSGPTVTHTYLSPGTYTVTLTASNAV 65
PKD_4 pfam18911
PKD domain; This entry is composed of PKD domains found in bacterial surface proteins.
 259-315 9.81e-05

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


Pssm-ID: 436824 [Multi-domain]  Cd Length: 85  Bit Score: 41.10  E-value: 9.81e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 52694752   259 LPIMFDVLIHDPShflNYSTINYKWSFGDNTglfVSTNHTVNHTYVLNGTFSLNLTV 315
Cdd:pfam18911  18 ETVTFDASASDDP---DGDILSYRWDFGDGT---TATGANVSHTYAAPGTYTVTLTV 68
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 204-317 1.71e-03

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: 41.61  E-value: 1.71e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52694752    204 GPQLMEVTVYRRHGRAYVPIAQVKDVYVVTDQIPVFVTMFQKNDRNSSDETFLKDLPIMFDVLIHDPSHFLnystinYKW 283
Cdd:TIGR00864 1216 GPEATVEHKYAKAGNCTVNIGAANAAGHGARIIHVEVFVFEVAGIEPAACIGEHADANFRARVSGNAAHYL------FDW 1289

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 52694752    284 SFGD-NTGLFVSTNHTVNHTYVLNGTFSLNLTVKA 317
Cdd:TIGR00864 1290 SFGDgSPNETHHGCPGISHNFRGNGTFPLALTISS 1324
PCC TIGR00864
polycystin cation channel protein; The Polycystin Cation Channel (PCC) Family (TC 1.A.5) ...
 232-319 1.89e-03

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: 41.61  E-value: 1.89e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 52694752    232 VTDQIPVFV-TMFQKNDRNSSDETFLKDLPIMFDvlihdPSHFLNYSTINYKWSFGDNTGLFVSTNHTVNHTYVLNGTF- 309
Cdd:TIGR00864 1075 ISQQINMSVrAILPRVAIGTEDGLLLAGKPADFE-----AHPLPSPGGIHYEWDFGDGSALLQGRQPAAAHTFAKRGPFh 1149

                           90
                   ....*....|...
gi 52694752    310 ---SLNLTVKAAA 319
Cdd:TIGR00864 1150 vclEVNNTISGAA 1162
 
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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