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Protein

Vesicle-associated membrane protein-associated protein A

Gene

VAPA

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

May play a role in vesicle trafficking.2 Publications

GO - Molecular functioni

  • FFAT motif binding Source: UniProtKB
  • microtubule binding Source: UniProtKB
  • protein domain specific binding Source: UniProtKB
  • protein heterodimerization activity Source: UniProtKB
  • signal transducer activity Source: UniProtKB

GO - Biological processi

  • cell death Source: UniProtKB
  • COPII-coated vesicle budding Source: UniProtKB
  • ER to Golgi vesicle-mediated transport Source: UniProtKB
  • membrane fusion Source: ProtInc
  • negative regulation by host of viral genome replication Source: AgBase
  • neuron projection development Source: UniProtKB
  • positive regulation by host of viral genome replication Source: AgBase
  • positive regulation by host of viral release from host cell Source: AgBase
  • positive regulation of I-kappaB kinase/NF-kappaB signaling Source: UniProtKB
  • protein localization to endoplasmic reticulum Source: UniProtKB
  • signal transduction Source: GOC
  • small molecule metabolic process Source: Reactome
  • sphingolipid biosynthetic process Source: Reactome
  • sphingolipid metabolic process Source: Reactome
Complete GO annotation...

Enzyme and pathway databases

ReactomeiREACT_115810. Sphingolipid de novo biosynthesis.

Names & Taxonomyi

Protein namesi
Recommended name:
Vesicle-associated membrane protein-associated protein A
Short name:
VAMP-A
Short name:
VAMP-associated protein A
Short name:
VAP-A
Alternative name(s):
33 kDa VAMP-associated protein
Short name:
VAP-33
Gene namesi
Name:VAPA
Synonyms:VAP33
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 18

Organism-specific databases

HGNCiHGNC:12648. VAPA.

Subcellular locationi

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Topological domaini1 – 227227CytoplasmicSequence AnalysisAdd
BLAST
Transmembranei228 – 24821Helical; Anchor for type IV membrane proteinSequence AnalysisAdd
BLAST

GO - Cellular componenti

  • endoplasmic reticulum Source: UniProtKB
  • endoplasmic reticulum membrane Source: Reactome
  • Golgi membrane Source: GOC
  • integral component of membrane Source: UniProtKB-KW
  • microtubule cytoskeleton Source: Ensembl
  • plasma membrane Source: UniProtKB
  • vesicle Source: UniProtKB
Complete GO annotation...

Keywords - Cellular componenti

Endoplasmic reticulum, Membrane

Pathology & Biotechi

Mutagenesis

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Mutagenesisi94 – 941K → D: Alters interaction with ZFYVE27; when associated with D-96. 1 Publication
Mutagenesisi96 – 961M → D: Alters interaction with ZFYVE27; when associated with D-94. 1 Publication

Organism-specific databases

PharmGKBiPA37272.

Polymorphism and mutation databases

BioMutaiVAPA.
DMDMi122066680.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 249249Vesicle-associated membrane protein-associated protein APRO_0000213470Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei125 – 1251N6-acetyllysine1 Publication
Modified residuei214 – 2141Phosphoserine1 Publication

Keywords - PTMi

Acetylation, Phosphoprotein

Proteomic databases

MaxQBiQ9P0L0.
PaxDbiQ9P0L0.
PRIDEiQ9P0L0.

PTM databases

PhosphoSiteiQ9P0L0.

Miscellaneous databases

PMAP-CutDBQ9P0L0.

Expressioni

Tissue specificityi

Ubiquitous.

Gene expression databases

BgeeiQ9P0L0.
CleanExiHS_VAPA.
ExpressionAtlasiQ9P0L0. baseline and differential.
GenevestigatoriQ9P0L0.

Organism-specific databases

HPAiHPA009174.

Interactioni

Subunit structurei

Homodimer, and heterodimer with VAPB. Interacts with VAMP1, VAMP2, STX1A, BET1, SEC22C and with the C-terminal domain of OCLN. Interacts with OSBPL1A. Interacts (via MSP domain) with ZFYVE27; may retain ZFYVE27 in the endoplasmic reticulum and regulate its function in cell projections formation. Interacts with OSBP. Interacts (via C-terminus) with RSAD2/viperin (via C-terminus). Interacts with HCV protein NS5A and NS5B. Interacts with IFITM3.7 Publications

Binary interactionsi

WithEntry#Exp.IntActNotes
P279587EBI-1059156,EBI-8753518From a different organism.
Q034634EBI-1059156,EBI-8803426From a different organism.
EGFRP005332EBI-1059156,EBI-297353
OPRM1P353723EBI-1059156,EBI-2624570
STARD3Q14849-14EBI-1059156,EBI-9819369
VAPBO95292-12EBI-1059156,EBI-9350848
ZFYVE27Q5T4F45EBI-1059156,EBI-3892947

Protein-protein interaction databases

BioGridi114651. 58 interactions.
DIPiDIP-41135N.
IntActiQ9P0L0. 47 interactions.
MINTiMINT-109415.
STRINGi9606.ENSP00000345656.

Structurei

Secondary structure

1
249
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Beta strandi14 – 218Combined sources
Beta strandi23 – 275Combined sources
Beta strandi33 – 408Combined sources
Beta strandi43 – 453Combined sources
Beta strandi47 – 548Combined sources
Turni56 – 583Combined sources
Beta strandi59 – 635Combined sources
Beta strandi65 – 684Combined sources
Beta strandi73 – 808Combined sources
Beta strandi94 – 1018Combined sources
Helixi109 – 1157Combined sources
Turni118 – 1203Combined sources
Beta strandi122 – 13110Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2RR3NMR-A11-135[»]
ProteinModelPortaliQ9P0L0.
SMRiQ9P0L0. Positions 9-135.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9P0L0.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini14 – 131118MSPPROSITE-ProRule annotationAdd
BLAST

Coiled coil

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Coiled coili169 – 20537Sequence AnalysisAdd
BLAST

Sequence similaritiesi

Contains 1 MSP domain.PROSITE-ProRule annotation

Keywords - Domaini

Coiled coil, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiCOG5066.
GeneTreeiENSGT00390000006947.
HOGENOMiHOG000293182.
HOVERGENiHBG028551.
InParanoidiQ9P0L0.
KOiK06096.
OMAiFEMPSEN.
OrthoDBiEOG7CK389.
PhylomeDBiQ9P0L0.
TreeFamiTF317024.

Family and domain databases

Gene3Di2.60.40.360. 1 hit.
InterProiIPR000535. MSP_dom.
IPR008962. PapD-like.
IPR016763. VAP.
IPR030229. VAPA.
[Graphical view]
PANTHERiPTHR10809. PTHR10809. 1 hit.
PTHR10809:SF40. PTHR10809:SF40. 1 hit.
PfamiPF00635. Motile_Sperm. 1 hit.
[Graphical view]
PIRSFiPIRSF019693. VAMP-associated. 1 hit.
SUPFAMiSSF49354. SSF49354. 1 hit.
PROSITEiPS50202. MSP. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q9P0L0-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MASASGAMAK HEQILVLDPP TDLKFKGPFT DVVTTNLKLR NPSDRKVCFK
60 70 80 90 100
VKTTAPRRYC VRPNSGIIDP GSTVTVSVML QPFDYDPNEK SKHKFMVQTI
110 120 130 140 150
FAPPNTSDME AVWKEAKPDE LMDSKLRCVF EMPNENDKLN DMEPSKAVPL
160 170 180 190 200
NASKQDGPMP KPHSVSLNDT ETRKLMEECK RLQGEMMKLS EENRHLRDEG
210 220 230 240
LRLRKVAHSD KPGSTSTASF RDNVTSPLPS LLVVIAAIFI GFFLGKFIL
Length:249
Mass (Da):27,893
Last modified:January 9, 2007 - v3
Checksum:i68B603F3A9FA5475
GO
Isoform 2 (identifier: Q9P0L0-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     139-139: L → LGITPPGNAPTVTSMSSINNTVATPASYHTKDDPRGLSVLKQEKQK

Show »
Length:294
Mass (Da):32,614
Checksum:i8B2D033706621878
GO

Sequence cautioni

The sequence AAD09742.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence AAF72105.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
The sequence BG488667 differs from that shown. Reason: Frameshift at positions 72, 207 and 241. Curated

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti10 – 112KH → ND in AAC26508 (PubMed:9657962).Curated
Sequence conflicti10 – 112KH → ND in AAV38424 (Ref. 8) Curated
Sequence conflicti160 – 1601P → S in AAF72105 (Ref. 2) Curated

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti8 – 81M → T.
Corresponds to variant rs1044163 [ dbSNP | Ensembl ].
VAR_050440
Natural varianti104 – 1041P → L.
Corresponds to variant rs1127666 [ dbSNP | Ensembl ].
VAR_050441

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei139 – 1391L → LGITPPGNAPTVTSMSSINN TVATPASYHTKDDPRGLSVL KQEKQK in isoform 2. 1 PublicationVSP_038648

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF044670 mRNA. Translation: AAD09742.1. Different initiation.
AF154847 mRNA. Translation: AAF72105.1. Different initiation.
AC006238 Genomic DNA. No translation available.
CH471113 Genomic DNA. Translation: EAX01591.1.
CH471113 Genomic DNA. Translation: EAX01592.1.
BC002992 mRNA. Translation: AAH02992.2.
BG488667 mRNA. No translation available.
AF057358 mRNA. Translation: AAC26508.1.
AF086627 mRNA. Translation: AAD13576.1.
BT019618 mRNA. Translation: AAV38424.1.
CCDSiCCDS11847.2. [Q9P0L0-2]
CCDS11848.2. [Q9P0L0-1]
RefSeqiNP_003565.4. NM_003574.5. [Q9P0L0-2]
NP_919415.2. NM_194434.2. [Q9P0L0-1]
UniGeneiHs.165195.

Genome annotation databases

EnsembliENST00000340541; ENSP00000345656; ENSG00000101558. [Q9P0L0-2]
ENST00000400000; ENSP00000382880; ENSG00000101558. [Q9P0L0-1]
GeneIDi9218.
KEGGihsa:9218.
UCSCiuc002koj.3. human. [Q9P0L0-2]
uc002kok.3. human. [Q9P0L0-1]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF044670 mRNA. Translation: AAD09742.1. Different initiation.
AF154847 mRNA. Translation: AAF72105.1. Different initiation.
AC006238 Genomic DNA. No translation available.
CH471113 Genomic DNA. Translation: EAX01591.1.
CH471113 Genomic DNA. Translation: EAX01592.1.
BC002992 mRNA. Translation: AAH02992.2.
BG488667 mRNA. No translation available.
AF057358 mRNA. Translation: AAC26508.1.
AF086627 mRNA. Translation: AAD13576.1.
BT019618 mRNA. Translation: AAV38424.1.
CCDSiCCDS11847.2. [Q9P0L0-2]
CCDS11848.2. [Q9P0L0-1]
RefSeqiNP_003565.4. NM_003574.5. [Q9P0L0-2]
NP_919415.2. NM_194434.2. [Q9P0L0-1]
UniGeneiHs.165195.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
2RR3NMR-A11-135[»]
ProteinModelPortaliQ9P0L0.
SMRiQ9P0L0. Positions 9-135.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi114651. 58 interactions.
DIPiDIP-41135N.
IntActiQ9P0L0. 47 interactions.
MINTiMINT-109415.
STRINGi9606.ENSP00000345656.

PTM databases

PhosphoSiteiQ9P0L0.

Polymorphism and mutation databases

BioMutaiVAPA.
DMDMi122066680.

Proteomic databases

MaxQBiQ9P0L0.
PaxDbiQ9P0L0.
PRIDEiQ9P0L0.

Protocols and materials databases

DNASUi9218.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000340541; ENSP00000345656; ENSG00000101558. [Q9P0L0-2]
ENST00000400000; ENSP00000382880; ENSG00000101558. [Q9P0L0-1]
GeneIDi9218.
KEGGihsa:9218.
UCSCiuc002koj.3. human. [Q9P0L0-2]
uc002kok.3. human. [Q9P0L0-1]

Organism-specific databases

CTDi9218.
GeneCardsiGC18P009904.
H-InvDBHIX0115359.
HGNCiHGNC:12648. VAPA.
HPAiHPA009174.
MIMi605703. gene.
neXtProtiNX_Q9P0L0.
PharmGKBiPA37272.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiCOG5066.
GeneTreeiENSGT00390000006947.
HOGENOMiHOG000293182.
HOVERGENiHBG028551.
InParanoidiQ9P0L0.
KOiK06096.
OMAiFEMPSEN.
OrthoDBiEOG7CK389.
PhylomeDBiQ9P0L0.
TreeFamiTF317024.

Enzyme and pathway databases

ReactomeiREACT_115810. Sphingolipid de novo biosynthesis.

Miscellaneous databases

ChiTaRSiVAPA. human.
EvolutionaryTraceiQ9P0L0.
GeneWikiiVAPA.
GenomeRNAii9218.
NextBioi34557.
PMAP-CutDBQ9P0L0.
PROiQ9P0L0.
SOURCEiSearch...

Gene expression databases

BgeeiQ9P0L0.
CleanExiHS_VAPA.
ExpressionAtlasiQ9P0L0. baseline and differential.
GenevestigatoriQ9P0L0.

Family and domain databases

Gene3Di2.60.40.360. 1 hit.
InterProiIPR000535. MSP_dom.
IPR008962. PapD-like.
IPR016763. VAP.
IPR030229. VAPA.
[Graphical view]
PANTHERiPTHR10809. PTHR10809. 1 hit.
PTHR10809:SF40. PTHR10809:SF40. 1 hit.
PfamiPF00635. Motile_Sperm. 1 hit.
[Graphical view]
PIRSFiPIRSF019693. VAMP-associated. 1 hit.
SUPFAMiSSF49354. SSF49354. 1 hit.
PROSITEiPS50202. MSP. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "VAP-33 localizes to both an intracellular vesicle population and with occludin at the tight junction."
    Lapierre L.A., Tuma P.L., Navarre J., Goldenring J.R., Anderson J.M.
    J. Cell Sci. 112:3723-3732(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1), SUBCELLULAR LOCATION, INTERACTION WITH OCLN.
    Tissue: Liver.
  2. "Cloning and isolating human 33kDa Vamp-associated protein cDNA."
    Zhou H.J., Huang X.W., Zhou Y., Hu S.L., Yuan J.G., Qiang B.Q.
    Submitted (MAY-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1), NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 1-199 (ISOFORM 2).
    Tissue: Lung.
  6. "Identification of a human homologue of the vesicle-associated membrane protein (VAMP)-associated protein of 33 kDa (VAP-33): a broadly expressed protein that binds to VAMP."
    Weir M.L., Klip A., Trimble W.S.
    Biochem. J. 333:247-251(1998) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 8-249 (ISOFORM 1), INTERACTION WITH VAMP1 AND VAMP2.
    Tissue: Pancreatic islet.
  7. "Molecular cloning and characterization of mammalian homologues of vesicle-associated membrane protein-associated (VAMP-associated) proteins."
    Nishimura Y., Hayashi M., Inada H., Tanaka T.
    Biochem. Biophys. Res. Commun. 254:21-26(1999) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 8-249 (ISOFORM 1).
    Tissue: B-cell.
  8. "Cloning of human full-length CDSs in BD Creator(TM) system donor vector."
    Kalnine N., Chen X., Rolfs A., Halleck A., Hines L., Eisenstein S., Koundinya M., Raphael J., Moreira D., Kelley T., LaBaer J., Lin Y., Phelan M., Farmer A.
    Submitted (OCT-2004) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 8-249 (ISOFORM 1).
  9. Cited for: FUNCTION, INTERACTION WITH VAPB; VAMP1; VAMP2; STX1A; BET1 AND SEC22C.
  10. "Promotion of neurite extension by protrudin requires its interaction with vesicle-associated membrane protein-associated protein."
    Saita S., Shirane M., Natume T., Iemura S., Nakayama K.I.
    J. Biol. Chem. 284:13766-13777(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, INTERACTION WITH ZFYVE27, MUTAGENESIS OF LYS-94 AND MET-96, SUBCELLULAR LOCATION.
  11. "Lysine acetylation targets protein complexes and co-regulates major cellular functions."
    Choudhary C., Kumar C., Gnad F., Nielsen M.L., Rehman M., Walther T.C., Olsen J.V., Mann M.
    Science 325:834-840(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: ACETYLATION [LARGE SCALE ANALYSIS] AT LYS-125, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  12. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  13. "Viperin inhibits hepatitis C virus replication by interfering with binding of NS5A to host protein hVAP-33."
    Wang S., Wu X., Pan T., Song W., Wang Y., Zhang F., Yuan Z.
    J. Gen. Virol. 93:83-92(2012) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH RSAD2 AND HCV PROTEIN NS5A AND NS5B.
  14. "The antiviral effector IFITM3 disrupts intracellular cholesterol homeostasis to block viral entry."
    Amini-Bavil-Olyaee S., Choi Y.J., Lee J.H., Shi M., Huang I.C., Farzan M., Jung J.U.
    Cell Host Microbe 13:452-464(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH IFITM3.
  15. "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome."
    Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L., Ye M., Zou H.
    J. Proteomics 96:253-262(2014) [PubMed] [Europe PMC] [Abstract]
    Cited for: PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-214, IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
    Tissue: Liver.
  16. "Electrostatic interaction between oxysterol-binding protein and VAMP-associated protein A revealed by NMR and mutagenesis studies."
    Furuita K., Jee J., Fukada H., Mishima M., Kojima C.
    J. Biol. Chem. 285:12961-12970(2010) [PubMed] [Europe PMC] [Abstract]
    Cited for: STRUCTURE BY NMR OF 11-135, INTERACTION WITH OSBP.

Entry informationi

Entry nameiVAPA_HUMAN
AccessioniPrimary (citable) accession number: Q9P0L0
Secondary accession number(s): A6NDZ0
, D3DUI3, O75453, Q5U0E7, Q9UBZ2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 2002
Last sequence update: January 9, 2007
Last modified: April 29, 2015
This is version 141 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 18
    Human chromosome 18: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.