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Protein

Presequence protease, mitochondrial

Gene

PITRM1

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

Functioni

Metalloendopeptidase of the mitochondrial matrix that functions in peptide cleavage and degradation rather than in protein processing (PubMed:10360838, PubMed:16849325, PubMed:19196155, PubMed:24931469). Has an ATP-independent activity (PubMed:16849325). Specifically cleaves peptides in the range of 5 to 65 residues (PubMed:19196155). Shows a preference for cleavage after small polar residues and before basic residues, but without any positional preference (PubMed:10360838, PubMed:19196155, PubMed:24931469). Degrades the transit peptides of mitochondrial proteins after their cleavage (PubMed:19196155). Also degrades other unstructured peptides (PubMed:19196155). It is also able to degrade amyloid-beta protein 40, one of the peptides produced by APP processing, when it accumulates in mitochondrion (PubMed:16849325, PubMed:24931469). It is a highly efficient protease, at least toward amyloid-beta protein 40 (PubMed:24931469). Cleaves that peptide at a specific position and is probably not processive, releasing digested peptides intermediates that can be further cleaved subsequently (PubMed:24931469).4 Publications

Cofactori

Zn2+1 PublicationNote: Binds 1 zinc ion per subunit.1 Publication

Enzyme regulationi

Mainly exists in a closed and catalytically competent conformation but a closed-to-open switch allows substrate entry into the catalytic chamber (PubMed:24931469). Substrate binding induces closure and dimerization (PubMed:24931469). A disulfide bond may lock the enzyme in a closed conformation preventing substrate entry into the catalytic chamber, participating in redox regulation of the enzyme (Probable). Inhibited by metal-chelating agents (PubMed:10360838). Inhibited by nickel and zinc excess, and slightly activated by manganese (PubMed:19196155).2 Publications3 Publications

Kineticsi

  1. KM=1.07 µM for leumorphin ARG-ARG-GLN-PHE-LYS-VAL-VAL-THR-ARG-SER-GLN peptide (at pH 7.5)1 Publication
  2. KM=0.5 µM for TYR-GLY-GLY-LEU-ARG-ARG-GLY-GLN peptide (at pH 7.5)1 Publication

    pH dependencei

    Optimum pH is 7.7.1 Publication

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Metal bindingi104Zinc; via tele nitrogen; catalyticCombined sources1 Publication1
    Active sitei107Proton acceptor2 Publications1
    Metal bindingi108Zinc; via tele nitrogen; catalyticCombined sources1 Publication1
    Metal bindingi205Zinc; catalyticCombined sources1 Publication1

    GO - Molecular functioni

    • enzyme activator activity Source: ProtInc
    • metalloendopeptidase activity Source: UniProtKB
    • metallopeptidase activity Source: Reactome
    • zinc ion binding Source: UniProtKB

    GO - Biological processi

    • protein targeting to mitochondrion Source: Reactome
    • proteolysis Source: UniProtKB

    Keywordsi

    Molecular functionHydrolase, Metalloprotease, Protease
    LigandMetal-binding, Zinc

    Enzyme and pathway databases

    ReactomeiR-HSA-1268020 Mitochondrial protein import
    SignaLinkiQ5JRX3

    Protein family/group databases

    MEROPSiM16.009

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Presequence protease, mitochondrial1 Publication (EC:3.4.24.-4 Publications)
    Short name:
    hPreP1 Publication
    Alternative name(s):
    Pitrilysin metalloproteinase 11 Publication
    Short name:
    Metalloprotease 11 Publication
    Short name:
    hMP11 Publication
    Gene namesi
    Name:PITRM1Imported
    Synonyms:KIAA1104Imported, MP11 Publication
    OrganismiHomo sapiens (Human)
    Taxonomic identifieri9606 [NCBI]
    Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
    Proteomesi
    • UP000005640 Componenti: Chromosome 10

    Organism-specific databases

    EuPathDBiHostDB:ENSG00000107959.15
    HGNCiHGNC:17663 PITRM1
    neXtProtiNX_Q5JRX3

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertionGraphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Mitochondrion

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Mutagenesisi1 – 15Missing : Loss of localization to the mitochondrion. 1 PublicationAdd BLAST15
    Mutagenesisi107E → Q: Loss of metalloendopeptidase activity. 2 Publications1
    Mutagenesisi119C → S: No loss of metalloendopeptidase activity under oxidizing conditions. 1 Publication1
    Mutagenesisi557L → E: Decreased metalloendopeptidase activity without effect on protein stability. 1 Publication1
    Mutagenesisi558P → G: Decreased metalloendopeptidase activity without effect on protein stability. 1 Publication1

    Organism-specific databases

    DisGeNETi10531
    OpenTargetsiENSG00000107959
    PharmGKBiPA134902269

    Chemistry databases

    ChEMBLiCHEMBL3124731

    Polymorphism and mutation databases

    BioMutaiPITRM1
    DMDMi485956568

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Transit peptidei1 – 28MitochondrionSequence analysisAdd BLAST28
    ChainiPRO_000024993129 – 1037Presequence protease, mitochondrialAdd BLAST1009

    Amino acid modifications

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Disulfide bondi119 ↔ 5561 Publication
    Modified residuei759N6-acetyllysineBy similarity1
    Modified residuei770N6-acetyllysine; alternateBy similarity1
    Modified residuei770N6-succinyllysine; alternateBy similarity1
    Modified residuei849N6-succinyllysineBy similarity1
    Modified residuei884N6-acetyllysineBy similarity1
    Modified residuei946N6-succinyllysineBy similarity1

    Post-translational modificationi

    A disulfide bond locks the enzyme in the closed conformation preventing substrate entry into the catalytic chamber.2 Publications

    Keywords - PTMi

    Acetylation, Disulfide bond

    Proteomic databases

    EPDiQ5JRX3
    MaxQBiQ5JRX3
    PaxDbiQ5JRX3
    PeptideAtlasiQ5JRX3
    PRIDEiQ5JRX3
    ProteomicsDBi63119
    63120 [Q5JRX3-2]

    PTM databases

    iPTMnetiQ5JRX3
    PhosphoSitePlusiQ5JRX3
    SwissPalmiQ5JRX3

    Expressioni

    Tissue specificityi

    Widely expressed. Expressed at higher level in muscle and heart compared to brain, pancreas, liver, lung and placenta.1 Publication

    Gene expression databases

    BgeeiENSG00000107959
    CleanExiHS_PITRM1
    ExpressionAtlasiQ5JRX3 baseline and differential
    GenevisibleiQ5JRX3 HS

    Organism-specific databases

    HPAiHPA006753
    HPA006754

    Interactioni

    Subunit structurei

    Monomer and homodimer; homodimerization is induced by binding of the substrate.1 Publication

    Protein-protein interaction databases

    BioGridi115786, 61 interactors
    DIPiDIP-52900N
    IntActiQ5JRX3, 8 interactors
    STRINGi9606.ENSP00000370377

    Chemistry databases

    BindingDBiQ5JRX3

    Structurei

    Secondary structure

    11037
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Helixi33 – 37Combined sources5
    Beta strandi49 – 57Combined sources9
    Helixi58 – 60Combined sources3
    Beta strandi62 – 69Combined sources8
    Turni70 – 72Combined sources3
    Beta strandi75 – 80Combined sources6
    Beta strandi84 – 93Combined sources10
    Beta strandi97 – 100Combined sources4
    Helixi102 – 109Combined sources8
    Helixi110 – 112Combined sources3
    Beta strandi114 – 116Combined sources3
    Helixi122 – 127Combined sources6
    Beta strandi133 – 135Combined sources3
    Beta strandi141 – 151Combined sources11
    Helixi156 – 168Combined sources13
    Helixi174 – 180Combined sources7
    Beta strandi183 – 188Combined sources6
    Beta strandi192 – 194Combined sources3
    Beta strandi196 – 199Combined sources4
    Helixi201 – 209Combined sources9
    Helixi213 – 225Combined sources13
    Helixi230 – 232Combined sources3
    Turni239 – 241Combined sources3
    Helixi242 – 244Combined sources3
    Helixi247 – 250Combined sources4
    Helixi253 – 257Combined sources5
    Helixi260 – 262Combined sources3
    Beta strandi263 – 271Combined sources9
    Helixi273 – 277Combined sources5
    Helixi280 – 283Combined sources4
    Turni284 – 286Combined sources3
    Beta strandi307 – 313Combined sources7
    Helixi322 – 324Combined sources3
    Beta strandi326 – 336Combined sources11
    Helixi340 – 354Combined sources15
    Turni360 – 362Combined sources3
    Turni366 – 369Combined sources4
    Beta strandi370 – 374Combined sources5
    Beta strandi379 – 381Combined sources3
    Beta strandi383 – 396Combined sources14
    Helixi398 – 400Combined sources3
    Helixi401 – 418Combined sources18
    Helixi422 – 430Combined sources9
    Helixi433 – 437Combined sources5
    Helixi443 – 456Combined sources14
    Helixi461 – 465Combined sources5
    Helixi468 – 480Combined sources13
    Helixi484 – 487Combined sources4
    Helixi490 – 494Combined sources5
    Beta strandi499 – 506Combined sources8
    Turni508 – 512Combined sources5
    Helixi515 – 520Combined sources6
    Helixi523 – 527Combined sources5
    Helixi531 – 539Combined sources9
    Helixi542 – 549Combined sources8
    Helixi562 – 564Combined sources3
    Beta strandi575 – 579Combined sources5
    Turni580 – 582Combined sources3
    Beta strandi583 – 589Combined sources7
    Beta strandi593 – 603Combined sources11
    Helixi609 – 614Combined sources6
    Helixi615 – 621Combined sources7
    Turni622 – 624Combined sources3
    Helixi632 – 641Combined sources10
    Beta strandi643 – 654Combined sources12
    Beta strandi661 – 673Combined sources13
    Helixi674 – 676Combined sources3
    Helixi677 – 689Combined sources13
    Helixi696 – 699Combined sources4
    Helixi706 – 712Combined sources7
    Turni713 – 717Combined sources5
    Helixi718 – 727Combined sources10
    Turni728 – 730Combined sources3
    Helixi732 – 741Combined sources10
    Helixi743 – 749Combined sources7
    Helixi752 – 754Combined sources3
    Helixi759 – 762Combined sources4
    Helixi766 – 772Combined sources7
    Beta strandi773 – 775Combined sources3
    Beta strandi778 – 784Combined sources7
    Turni786 – 788Combined sources3
    Helixi789 – 793Combined sources5
    Helixi796 – 802Combined sources7
    Beta strandi813 – 815Combined sources3
    Beta strandi817 – 821Combined sources5
    Beta strandi839 – 844Combined sources6
    Beta strandi855 – 858Combined sources4
    Beta strandi862 – 871Combined sources10
    Helixi878 – 883Combined sources6
    Helixi886 – 893Combined sources8
    Helixi895 – 899Combined sources5
    Turni900 – 903Combined sources4
    Beta strandi906 – 912Combined sources7
    Beta strandi916 – 926Combined sources11
    Helixi929 – 936Combined sources8
    Helixi939 – 942Combined sources4
    Helixi949 – 955Combined sources7
    Helixi958 – 963Combined sources6
    Helixi969 – 971Combined sources3
    Helixi974 – 979Combined sources6
    Helixi983 – 994Combined sources12
    Helixi1002 – 1008Combined sources7
    Turni1011 – 1013Combined sources3
    Beta strandi1016 – 1023Combined sources8
    Helixi1026 – 1029Combined sources4
    Beta strandi1034 – 1036Combined sources3

    3D structure databases

    ProteinModelPortaliQ5JRX3
    SMRiQ5JRX3
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Sequence similaritiesi

    Belongs to the peptidase M16 family. PreP subfamily.Curated

    Keywords - Domaini

    Transit peptide

    Phylogenomic databases

    eggNOGiKOG2019 Eukaryota
    COG1026 LUCA
    GeneTreeiENSGT00390000018381
    HOGENOMiHOG000008829
    HOVERGENiHBG082167
    InParanoidiQ5JRX3
    KOiK06972
    OMAiFTYGNFP
    OrthoDBiEOG091G0108
    TreeFamiTF300333

    Family and domain databases

    InterProiView protein in InterPro
    IPR011249 Metalloenz_LuxS/M16
    IPR011765 Pept_M16_N
    IPR007863 Peptidase_M16_C
    IPR013578 Peptidase_M16C_assoc
    PfamiView protein in Pfam
    PF08367 M16C_assoc, 1 hit
    PF00675 Peptidase_M16, 1 hit
    PF05193 Peptidase_M16_C, 2 hits
    SMARTiView protein in SMART
    SM01264 M16C_associated, 1 hit
    SUPFAMiSSF63411 SSF63411, 4 hits

    Sequences (3)i

    Sequence statusi: Complete.

    Sequence processingi: The displayed sequence is further processed into a mature form.

    This entry describes 3 isoformsi produced by alternative splicing. AlignAdd to basket

    Isoform 1 (identifier: Q5JRX3-1) [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
    MWRCGGRQGL CVLRRLSGGH AHHRAWRWNS NRACERALQY KLGDKIHGFT
    60 70 80 90 100
    VNQVTSVPEL FLTAVKLTHD DTGARYLHLA REDTNNLFSV QFRTTPMDST
    110 120 130 140 150
    GVPHILEHTV LCGSQKYPCR DPFFKMLNRS LSTFMNAFTA SDYTLYPFST
    160 170 180 190 200
    QNPKDFQNLL SVYLDATFFP CLRELDFWQE GWRLEHENPS DPQTPLVFKG
    210 220 230 240 250
    VVFNEMKGAF TDNERIFSQH LQNRLLPDHT YSVVSGGDPL CIPELTWEQL
    260 270 280 290 300
    KQFHATHYHP SNARFFTYGN FPLEQHLKQI HEEALSKFQK IEPSTVVPAQ
    310 320 330 340 350
    TPWDKPREFQ ITCGPDSFAT DPSKQTTISV SFLLPDITDT FEAFTLSLLS
    360 370 380 390 400
    SLLTSGPNSP FYKALIESGL GTDFSPDVGY NGYTREAYFS VGLQGIAEKD
    410 420 430 440 450
    IETVRSLIDR TIDEVVEKGF EDDRIEALLH KIEIQMKHQS TSFGLMLTSY
    460 470 480 490 500
    IASCWNHDGD PVELLKLGNQ LAKFRQCLQE NPKFLQEKVK QYFKNNQHKL
    510 520 530 540 550
    TLSMRPDDKY HEKQAQVEAT KLKQKVEALS PGDRQQIYEK GLELRSQQSK
    560 570 580 590 600
    PQDASCLPAL KVSDIEPTIP VTELDVVLTA GDIPVQYCAQ PTNGMVYFRA
    610 620 630 640 650
    FSSLNTLPEE LRPYVPLFCS VLTKLGCGLL DYREQAQQIE LKTGGMSASP
    660 670 680 690 700
    HVLPDDSHMD TYEQGVLFSS LCLDRNLPDM MQLWSEIFNN PCFEEEEHFK
    710 720 730 740 750
    VLVKMTAQEL ANGIPDSGHL YASIRAGRTL TPAGDLQETF SGMDQVRLMK
    760 770 780 790 800
    RIAEMTDIKP ILRKLPRIKK HLLNGDNMRC SVNATPQQMP QTEKAVEDFL
    810 820 830 840 850
    RSIGRSKKER RPVRPHTVEK PVPSSSGGDA HVPHGSQVIR KLVMEPTFKP
    860 870 880 890 900
    WQMKTHFLMP FPVNYVGECI RTVPYTDPDH ASLKILARLM TAKFLHTEIR
    910 920 930 940 950
    EKGGAYGGGA KLSHNGIFTL YSYRDPNTIE TLQSFGKAVD WAKSGKFTQQ
    960 970 980 990 1000
    DIDEAKLSVF STVDAPVAPS DKGMDHFLYG LSDEMKQAHR EQLFAVSHDK
    1010 1020 1030
    LLAVSDRYLG TGKSTHGLAI LGPENPKIAK DPSWIIQ
    Length:1,037
    Mass (Da):117,413
    Last modified:May 1, 2013 - v3
    Checksum:iF488389F0E219718
    GO
    Isoform 2 (identifier: Q5JRX3-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         664-664: Q → QV

    Note: No experimental confirmation available.
    Show »
    Length:1,038
    Mass (Da):117,512
    Checksum:i8A55B3A43B434A4E
    GO
    Isoform 3 (identifier: Q5JRX3-3) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-53: MWRCGGRQGLCVLRRLSGGHAHHRAWRWNSNRACERALQYKLGDKIHGFTVNQ → MRNVALRRAAGPVCAEAAERR
         624-689: Missing.

    Show »
    Length:939
    Mass (Da):106,065
    Checksum:i21E09CEE32236867
    GO

    Sequence cautioni

    The sequence AAH01150 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated
    The sequence CAI39997 differs from that shown. Reason: Erroneous gene model prediction.Curated

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti121D → N in AAC67244 (PubMed:10360838).Curated1
    Sequence conflicti211T → V in CAI40001 (PubMed:15164054).Curated1
    Sequence conflicti212D → N in CAI40001 (PubMed:15164054).Curated1
    Sequence conflicti373D → E in AAC67244 (PubMed:10360838).Curated1
    Sequence conflicti418 – 420KGF → TRI in AAC67244 (PubMed:10360838).Curated3
    Sequence conflicti883 – 884LK → FE in AAH95422 (PubMed:15489334).Curated2

    Natural variant

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Natural variantiVAR_0275178Q → R1 PublicationCorresponds to variant dbSNP:rs11818724Ensembl.1
    Natural variantiVAR_027518145L → V1 PublicationCorresponds to variant dbSNP:rs9423502Ensembl.1
    Natural variantiVAR_027519169F → S1 PublicationCorresponds to variant dbSNP:rs3814596Ensembl.1
    Natural variantiVAR_027520328I → V3 PublicationsCorresponds to variant dbSNP:rs4242746Ensembl.1
    Natural variantiVAR_027521397A → V3 PublicationsCorresponds to variant dbSNP:rs3182535Ensembl.1
    Natural variantiVAR_027522516Q → H. Corresponds to variant dbSNP:rs3765101Ensembl.1
    Natural variantiVAR_057059554A → D. Corresponds to variant dbSNP:rs12248937Ensembl.1
    Natural variantiVAR_027523621V → I1 PublicationCorresponds to variant dbSNP:rs2388556Ensembl.1
    Natural variantiVAR_057060805R → Q. Corresponds to variant dbSNP:rs34837384Ensembl.1
    Natural variantiVAR_027524952I → M. Corresponds to variant dbSNP:rs2279219Ensembl.1
    Natural variantiVAR_027525963V → I1 PublicationCorresponds to variant dbSNP:rs17849904Ensembl.1
    Natural variantiVAR_027526969P → L. Corresponds to variant dbSNP:rs2279218Ensembl.1
    Natural variantiVAR_0275271037Q → RCombined sources4 PublicationsCorresponds to variant dbSNP:rs6901Ensembl.1

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0464941 – 53MWRCG…FTVNQ → MRNVALRRAAGPVCAEAAER R in isoform 3. 1 PublicationAdd BLAST53
    Alternative sequenceiVSP_046495624 – 689Missing in isoform 3. 1 PublicationAdd BLAST66
    Alternative sequenceiVSP_020597664Q → QV in isoform 2. 1 Publication1

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF061243 mRNA Translation: AAC67244.1
    AK002061 mRNA Translation: BAG51008.1
    AK303406 mRNA Translation: BAG64460.1
    AL451164 Genomic DNA Translation: CAI40001.1
    AL451164 Genomic DNA Translation: CAI39997.1 Sequence problems.
    BC001150 mRNA Translation: AAH01150.1 Different initiation.
    BC005025 mRNA Translation: AAH05025.1
    BC095422 mRNA Translation: AAH95422.1
    BC111987 mRNA Translation: AAI11988.1
    BC113369 mRNA Translation: AAI13370.1
    AB029027 mRNA Translation: BAA83056.2
    CCDSiCCDS55699.1 [Q5JRX3-2]
    CCDS55700.1 [Q5JRX3-3]
    CCDS59208.1 [Q5JRX3-1]
    RefSeqiNP_001229236.1, NM_001242307.1 [Q5JRX3-2]
    NP_001229238.1, NM_001242309.1 [Q5JRX3-3]
    NP_055704.2, NM_014889.3 [Q5JRX3-1]
    UniGeneiHs.528300

    Genome annotation databases

    EnsembliENST00000224949; ENSP00000224949; ENSG00000107959 [Q5JRX3-1]
    ENST00000380989; ENSP00000370377; ENSG00000107959 [Q5JRX3-2]
    ENST00000451104; ENSP00000401201; ENSG00000107959 [Q5JRX3-3]
    GeneIDi10531
    KEGGihsa:10531
    UCSCiuc001igt.3 human [Q5JRX3-1]

    Keywords - Coding sequence diversityi

    Alternative splicing, Polymorphism

    Similar proteinsi

    Entry informationi

    Entry nameiPREP_HUMAN
    AccessioniPrimary (citable) accession number: Q5JRX3
    Secondary accession number(s): B3KMJ6
    , B4E0J8, C9JSL2, E7ES23, O95204, Q2M2G6, Q4VBR1, Q5JRW7, Q7L5Z7, Q9BSI6, Q9BVJ5, Q9UPP8
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: September 19, 2006
    Last sequence update: May 1, 2013
    Last modified: July 18, 2018
    This is version 130 of the entry and version 3 of the sequence. See 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 10
      Human chromosome 10: 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    5. Peptidase families
      Classification of peptidase families and list of entries
    6. SIMILARITY comments
      Index of protein domains and families

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