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Conserved domains on  [gi|1694579910|ref|XP_029468607|]
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peroxisome assembly protein 12 [Rhinatrema bivittatum]

Protein Classification

peroxin family protein( domain architecture ID 12057465)

peroxin family protein containing a C-terminal ring finger domain, such as peroxisome assembly protein 12, which is required for import of proteins into peroxisomes

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Pex2_Pex12 pfam04757
Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of ...
 26-267 1.15e-44

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.


:

Pssm-ID: 398431  Cd Length: 213  Bit Score: 152.54  E-value: 1.15e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910  26 QDSLMSAVRPGLQHIAKILAesnPQRYgtLWRWFDEIYSLFDLLLQQHFLAKASASFSENFYSLKRVVleshkspHSLAS 105
Cdd:pfam04757   1 DEELESLLRPQLRYILRLLA---GQRF--PLNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVS-------DRDGG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910 106 TGLPKGHHWRSLLFLVLVPYLKVKLEKLVSRLREEDDYSIHLPASPWKKFYKAFLAAYPFVNMAWEGWFLSQQLRYILGK 185
Cdd:pfam04757  69 RLLSRRRRLLSLLLLVLLPYLLRKLDSLLPRLSANDLESRNARDSLKSRLKRYLLKLYPFLESLYKLLNLHLFLFYLTGK 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910 186 aqHHSPLLSMAGVQLVRLTSEDIQameqreasvavSQQSAHSLNNKLRRAVKRALGSItlsfSTGLSVGVFFLQFLDWWY 265
Cdd:pfam04757 149 --YYSLSKRLLGIRYVRLKPLDIF-----------SNERRVSYEQLLWNAFSELLGFL----LPLLLAVILFLKLLEWWY 211


                  ..
gi 1694579910 266 SS 267
Cdd:pfam04757 212 SS 213
mRING_PEX12 cd16451
Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as ...
 302-355 7.37e-33

Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as peroxisome assembly protein 12 or peroxisome assembly factor 3 (PAF-3), is a RING finger domain-containing integral membrane peroxin required for protein import into peroxisomes. Mutations in human PEX12 result in the peroxisome deficiency Zellweger syndrome of complementation group III (CG-III), a lethal neurological disorder. PEX12 also functions as an E3-ubiquitin ligase that facilitates the PEX4-dependent monoubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. PEX12 contains a modified RING finger that lacks the third, fourth, and eighth zinc-binding residues of the consensus RING finger motif, suggesting PEX12 may only bind one zinc ion.


:

Pssm-ID: 438115 [Multi-domain]  Cd Length: 54  Bit Score: 116.57  E-value: 7.37e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1694579910 302 TVCPLCRKIRANDTALSTSGYVFCYRCAYYYVKHHQRCPVTGYPTELQHLVKLY 355
Cdd:cd16451     1 GICPLCRKKRTNPTALATSGYVFCYPCIYRYVKEHGRCPVTGYPASLDHLIKLY 54
 
Name Accession Description Interval E-value
Pex2_Pex12 pfam04757
Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of ...
 26-267 1.15e-44

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.


Pssm-ID: 398431  Cd Length: 213  Bit Score: 152.54  E-value: 1.15e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910  26 QDSLMSAVRPGLQHIAKILAesnPQRYgtLWRWFDEIYSLFDLLLQQHFLAKASASFSENFYSLKRVVleshkspHSLAS 105
Cdd:pfam04757   1 DEELESLLRPQLRYILRLLA---GQRF--PLNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVS-------DRDGG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910 106 TGLPKGHHWRSLLFLVLVPYLKVKLEKLVSRLREEDDYSIHLPASPWKKFYKAFLAAYPFVNMAWEGWFLSQQLRYILGK 185
Cdd:pfam04757  69 RLLSRRRRLLSLLLLVLLPYLLRKLDSLLPRLSANDLESRNARDSLKSRLKRYLLKLYPFLESLYKLLNLHLFLFYLTGK 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910 186 aqHHSPLLSMAGVQLVRLTSEDIQameqreasvavSQQSAHSLNNKLRRAVKRALGSItlsfSTGLSVGVFFLQFLDWWY 265
Cdd:pfam04757 149 --YYSLSKRLLGIRYVRLKPLDIF-----------SNERRVSYEQLLWNAFSELLGFL----LPLLLAVILFLKLLEWWY 211


                  ..
gi 1694579910 266 SS 267
Cdd:pfam04757 212 SS 213
mRING_PEX12 cd16451
Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as ...
 302-355 7.37e-33

Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as peroxisome assembly protein 12 or peroxisome assembly factor 3 (PAF-3), is a RING finger domain-containing integral membrane peroxin required for protein import into peroxisomes. Mutations in human PEX12 result in the peroxisome deficiency Zellweger syndrome of complementation group III (CG-III), a lethal neurological disorder. PEX12 also functions as an E3-ubiquitin ligase that facilitates the PEX4-dependent monoubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. PEX12 contains a modified RING finger that lacks the third, fourth, and eighth zinc-binding residues of the consensus RING finger motif, suggesting PEX12 may only bind one zinc ion.


Pssm-ID: 438115 [Multi-domain]  Cd Length: 54  Bit Score: 116.57  E-value: 7.37e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1694579910 302 TVCPLCRKIRANDTALSTSGYVFCYRCAYYYVKHHQRCPVTGYPTELQHLVKLY 355
Cdd:cd16451     1 GICPLCRKKRTNPTALATSGYVFCYPCIYRYVKEHGRCPVTGYPASLDHLIKLY 54
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 304-341 2.85e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 37.87  E-value: 2.85e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1694579910  304 CPLCRKIRANDTALSTSGYVFCYRCAYYYVK-HHQRCPV 341
Cdd:smart00184   1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLEsGNNTCPI 39
 
Name Accession Description Interval E-value
Pex2_Pex12 pfam04757
Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of ...
 26-267 1.15e-44

Pex2 / Pex12 amino terminal region; This region is found at the N terminal of a number of known and predicted peroxins including Pex2, Pex10 and Pex12. This conserved region is usually associated with a C terminal ring finger (pfam00097) domain.


Pssm-ID: 398431  Cd Length: 213  Bit Score: 152.54  E-value: 1.15e-44
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910  26 QDSLMSAVRPGLQHIAKILAesnPQRYgtLWRWFDEIYSLFDLLLQQHFLAKASASFSENFYSLKRVVleshkspHSLAS 105
Cdd:pfam04757   1 DEELESLLRPQLRYILRLLA---GQRF--PLNYFDEIKLLLDLLYFRLTLLRGNATLGEEYYGLKRVS-------DRDGG 68

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910 106 TGLPKGHHWRSLLFLVLVPYLKVKLEKLVSRLREEDDYSIHLPASPWKKFYKAFLAAYPFVNMAWEGWFLSQQLRYILGK 185
Cdd:pfam04757  69 RLLSRRRRLLSLLLLVLLPYLLRKLDSLLPRLSANDLESRNARDSLKSRLKRYLLKLYPFLESLYKLLNLHLFLFYLTGK 148

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1694579910 186 aqHHSPLLSMAGVQLVRLTSEDIQameqreasvavSQQSAHSLNNKLRRAVKRALGSItlsfSTGLSVGVFFLQFLDWWY 265
Cdd:pfam04757 149 --YYSLSKRLLGIRYVRLKPLDIF-----------SNERRVSYEQLLWNAFSELLGFL----LPLLLAVILFLKLLEWWY 211


                  ..
gi 1694579910 266 SS 267
Cdd:pfam04757 212 SS 213
mRING_PEX12 cd16451
Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as ...
 302-355 7.37e-33

Modified RING finger found in peroxin-12 (PEX12) and similar proteins; PEX12, also known as peroxisome assembly protein 12 or peroxisome assembly factor 3 (PAF-3), is a RING finger domain-containing integral membrane peroxin required for protein import into peroxisomes. Mutations in human PEX12 result in the peroxisome deficiency Zellweger syndrome of complementation group III (CG-III), a lethal neurological disorder. PEX12 also functions as an E3-ubiquitin ligase that facilitates the PEX4-dependent monoubiquitination of PEX5, a key player in peroxisomal matrix protein import, to control PEX5 receptor recycling or degradation. PEX12 contains a modified RING finger that lacks the third, fourth, and eighth zinc-binding residues of the consensus RING finger motif, suggesting PEX12 may only bind one zinc ion.


Pssm-ID: 438115 [Multi-domain]  Cd Length: 54  Bit Score: 116.57  E-value: 7.37e-33
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1694579910 302 TVCPLCRKIRANDTALSTSGYVFCYRCAYYYVKHHQRCPVTGYPTELQHLVKLY 355
Cdd:cd16451     1 GICPLCRKKRTNPTALATSGYVFCYPCIYRYVKEHGRCPVTGYPASLDHLIKLY 54
RING smart00184
Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and ...
 304-341 2.85e-04

Ring finger; E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)


Pssm-ID: 214546 [Multi-domain]  Cd Length: 40  Bit Score: 37.87  E-value: 2.85e-04
                           10        20        30
                   ....*....|....*....|....*....|....*....
gi 1694579910  304 CPLCRKIRANDTALSTSGYVFCYRCAYYYVK-HHQRCPV 341
Cdd:smart00184   1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLEsGNNTCPI 39
RING-HC cd16449
HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type ...
 304-341 8.99e-04

HC subclass of RING (RING-HC) finger and its variants; The RING finger is a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc. It is defined by the "cross-brace" motif that chelates zinc atoms by eight amino acid residues, typically Cys or His, arranged in a characteristic spacing. Canonical RING motifs have been categorized into two major subclasses, RING-HC (C3HC4-type) and RING-H2 (C3H2C3-type), according to their Cys/His content. There are also many variants of RING fingers. Some have a different Cys/His pattern. Some lack a single Cys or His residue at typical Zn ligand positions, especially, the fourth or eighth zinc ligand is prevalently exchanged for an Asp, which can chelate Zn in a RING finger as well. This family corresponds to the HC subclass of RING (RING-HC) fingers that are characterized by containing C3HC4-type canonical RING-HC fingers or noncanonical RING-HC finger variants, including C4C4-, C3HC3D-, C2H2C4-, and C3HC5-type modified RING-HC fingers. The canonical RING-HC finger has been defined as C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C. It binds two Zn ions in a unique "cross-brace" arrangement, which distinguishes it from tandem zinc fingers and other similar motifs. RING-HC fingers can be found in a group of diverse proteins with a variety of cellular functions, including oncogenesis, development, viral replication, signal transduction, the cell cycle, and apoptosis. Many of them are ubiquitin-protein ligases (E3s) that serve as scaffolds for binding to ubiquitin-conjugating enzymes (E2s, also referred to as ubiquitin carrier proteins or UBCs) in close proximity to substrate proteins, which enables efficient transfer of ubiquitin from E2 to the substrates.


Pssm-ID: 438113 [Multi-domain]  Cd Length: 41  Bit Score: 36.69  E-value: 8.99e-04
                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1694579910 304 CPLCRKiRANDTALSTSGYVFCYRCAYYYVKH-HQRCPV 341
Cdd:cd16449     3 CPICLE-RLKDPVLLPCGHVFCRECIRRLLESgSIKCPI 40
RING-HC_PEX10 cd16527
RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known ...
 304-354 1.45e-03

RING finger, HC subclass, found in peroxin-10 (PEX10) and similar proteins; PEX10, also known as peroxisome biogenesis factor 10, peroxisomal biogenesis factor 10, peroxisome assembly protein 10, or RING finger protein 69 (RNF69), is an integral peroxisomal membrane protein with two transmembrane regions and a C3HC4-type RING-HC finger within its cytoplasmically exposed C-terminus. It plays an essential role in peroxisome assembly, import of target substrates, and recycling or degradation of protein complexes and amino acids. It is an essential component of the spinal locomotor circuit, and thus its mutations may be involved in peroxisomal biogenesis disorders (PBD). Mutations in human PEX10 also result in autosomal recessive ataxia. Moreover, PEX10 functions as an E3-ubiquitin ligase with an E2, UBCH5C. It mono- or poly-ubiquitinates PEX5, a key player in peroxisomal matrix protein import, in a UBC4-dependent manner, to control PEX5 receptor recycling or degradation. It also links the E2 ubiquitin conjugating enzyme PEX4 to the protein import machinery of the peroxisome.


Pssm-ID: 438190 [Multi-domain]  Cd Length: 52  Bit Score: 36.44  E-value: 1.45e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1694579910 304 CPLCRKIRANDTALSTsGYVFCYRCAYYYVKHHQRCPVTGYPTELQHLVKL 354
Cdd:cd16527     3 CSLCLEERRHPTATPC-GHLFCWSCITEWCNEKPECPLCREPFQPQRLVPL 52
 
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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