YRC Public Data Repository - Protein Structure Prediction

Protein:	TOM1
Organism:	Saccharomyces cerevisiae
Length:	3268 amino acids
Reference:	Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

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Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for TOM1.

Description	E-value	Query Range	Subject Range
gi\|25406003, gi\|... - gi\|8778329\|gb\|AAF79338.1\|AC002304_31 F14J16.10 [Arabidopsis thaliana], pir\|\|H96599 protein F14J16.10...	0.0	[2077..3268]	[2688..4056]
TOM1_YEAST - E3 ubiquitin-protein ligase TOM1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TOM1 PE... TOM1 - E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may reg...	0.0	[1..3268]	[1..3268]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[2225..3268]	[2798..3839]

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Predicted Domain #1

Region A:
Residues: [1-746]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVLFTRCEKA RKEKLAAGYK PLVDYLIDCD TPTFLERIEA IQEWDRSRDD LYVWIPILDR  60
   61 MDGLLLKVAE KYKYKQDPKK ECEVKLVEME AHDVDYCLKM LKFTRRLLLN TENRFVYSSG 120
  121 DVLMYLLNCP NFTIKLAVMR ILAILGERFV IAREKIVAHN IFGDHNLRKK TLKLALSLSS 180
  181 SVMDEDGEHF SLVDLYFDKK KVPQKWRKLR FTHYTSNDFK KSSQQKNNIN ETQTSIKKVT 240
  241 MTTQELCEHS LQQIFDKGMA LLPAESWFDF SIKASVAKAF SDDSGENIDL RNIIIETKLN 300
  301 AIAFVNTIFS PPQVSSKLFE LDPYAFNSLT DLISLSETKI PKELRTDALF TLECISLKHV 360
  361 WCSDIIRNLG GNISHGLLFQ ILRYIAKTLR EATDEIDEEY NVRFFYLISN LADVKPLHES 420
  421 LFAAGLIPTL LEIVSIRNCP YKRTLASATH LLETFIDNSE TTTEFIENDG FTMLITSVAN 480
  481 EIDFTLAHPE TWQPPKYSVV YYSISFRELA YIRSLLKLVL KLLSTDSGDR IRNLIDSPIL 540
  541 VSLKKILENK LVFGLTLITY TLDVVQKVIN SEPTIYPVLV EAGLIPYVID NFPKLIGPSA 600
  601 ELLSLLPDVV SAICLNPEGL KQVKEKGLIN NLFDFLLDAD HARILTGGDR STEYGTDIDE 660
  661 LARHYPDLKA NIVEALCNVI RKMPSTFRNE REFLFTSPKD QKYFFHRKNE EILTDKEEHE 720
  721 PAYWELLDKG TMLDTFTSVL FGMSLG

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [747-1651]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NGSFSQVPQH LEARDFLAII FMENPPYEYF TSVAISNVTE VLQYLDEKYE DYAFMDVMKV  60
   61 LNDQLENLND FLNSPNDRSF FLERDGENSV RSCHSKLCRL AAILNIVTNV YIDLTTLSCK 120
  121 RIMQIYSYFD KRGFSLIKNL KLLFQKCALE EMYIRQHMPD SVITETMPLP IVDVSGDGPP 180
  181 LQIYIDDPKK GDQKGKITSV KTRNTLQMRT ILYTLQSNTA ILFRCFLRLS HSRNMDLEHK 240
  241 DLTTEVHIFE NVVENVIEML KATELEGHLP YILVLLNFNT FVFTIPKASP NSTEILQTIP 300
  301 AYIFYQKGGY LLYLHIIRDL FTRMTKIKDL SSLDNINYID ESNGILTLSC LINALTFYNK 360
  361 SMQTETMENV QSIGKYYVSI DDDYNIMKAL TVPIKVMALA MILDLDKSDS LFKTQSRNVP 420
  421 YSVFKQLLSM LKNIFTNVNI YTKELYELHW DLIFPPIKKI SLFEQVGIPG DVAANYLTDT 480
  481 GDDLPADNSI GLFSPEQWEK YKKLIGEDKS IYYPQPMQAQ YYKGCSSKEL DELRDTFFND 540
  541 GLPSRIFTVL PFYPKLVNAF AKTLLQIFTK YDEPTEVFAG RILDRILETD LDDPATLSSL 600
  601 IHLFGIFLNE KYIYQKASHL MQRFIEYLEK SLKPEHVNTP WFSKALYVYE IILAKSELPH 660
  661 LEELSKDVLL RYPLLSMAKV FRIPDPMKQK LFDILIRVSD ISNFYSALAT SRILIFYSRD 720
  721 ELYANNIARS GILSRLLKVI GSFQKLDKIN FLESSFLLLT RRCFETTENV DALIRAEINR 780
  781 SFTARPLGGG DDAVRELTTI LEEKAHVVMR SPSQFIDVLC ETARFHEFDD QGALVDYSLK 840
  841 RFLGEKDKNT QASSTEKSDI YERTGIMHLL LSQLMAASEK DWLSEPANSS DLPENKKAQL 900
  901 DPSRN

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #3

Region A:
Residues: [1652-1845]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PVCAYMIFLL KLLVELVSSY NQCKFEFLTF SRRNTYAERP RPRTTAINFF LYRLLDKPVG  60
   61 TDHDKHEAKR REVIGMLARS VIIGFLATVQ DDRTTKTDVK LADPHMNFIR KFAIEAIIKA 120
  121 IRNATSSSKL LESNHLKLDM WFRIITSMVY VQAPYLRQLL DSNKVEADQY QLCKLVIDLG 180
  181 LPSVITEAMA SIDL

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [1846-2170]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NYPFSKKIFN VAVEALNTIS STRNNFSEHF KIEDHDEVED EVDESDKEEI PDMFKNSALG  60
   61 MYDVEDIEED DDDDTSLIGD DDAMAFVDSD NGFEVVFSDE DDDMGEEDAD DARSDSEENE 120
  121 LSSEMQSSTA DGTDVDYEVD DADGLIINID QPSGDDEEMA DYDANISHSS HSENEDDASM 180
  181 DVIEVYDDEL SSGYDVDLSD YDVDESDWDS GLSSLSISDE DSESSEDEPI NSTRMGDSRR 240
  241 RWLIAEGVEL TDDSQGESEE DDRGVFRGIE HIFSNENEPL FRVHDEMRHR NHHRSINRTH 300
  301 FHSAMSAPSL SLLNRGRRNQ SNLIN

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below is our most confident prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #5

Region A:
Residues: [2171-2767]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PLGPTGLEQV ENDISDQVTV AGSGSRPRSH HLHFSEVLVS GSFFDEPVLD GIILKSTVSR  60
   61 WKDIFDMFYD SKTYANCIIP TVINRLYKVS LALQKDLENK REQEKLKNKN LLFNEAKVES 120
  121 HNSSDAISVE QDDIQESNVT HDDHEPVYVT IQGSEVDIGG TDIDPEFMNA LPDDIRADVF 180
  181 AQHVRERRAE ARLNSDHNVH SREIDSDFLE AIPEDIREGI LDTEAEEQRM FGRIGSSADV 240
  241 IRADDDVSNN DEEVENGLDH GNSNDRNNAD PEKKKPARIY FAPLIDRAGI ASLMKSVFIS 300
  301 KPYIQREIYH ELFYRLCSSK QNRNDLMNTF LFILSEGIID QHSLEKVYNI ISSRAMGHAK 360
  361 TTTVRQLPSD CTPLTVANQT IEILQSLIDA DSRLKYFLIA EHDNLIVNKA NNKSRKEALP 420
  421 DKKLRWPLWH LFSLLDRKLI TDESVLMDLL TRILQVCTKT LAVLSTSSNG KENLSKKFHL 480
  481 PSFDEDDLMK ILSIIMLDSC TTRVFQQTLN IIYNLSKLQG CMSIFTKHLV SLAISIMSKL 540
  541 KSALDGLSRE VGTITTGMEI NSELLQKFTL PSSDQAKLLK ILTTVDFLYT HKRKEEE

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #6

Region A:
Residues: [2768-2873]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RNVKDLQSLY DKMNGGPVWS SLSECLSQFE KSQAINTSAT ILLPLIESLM VVCRRSDLSQ  60
   61 NRNTAVKYED AKLLDFSKTR VENLFFPFTD AHKKLLNQMI RSNPKL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2.30103
Match:	1i5hW_
Description:	Ubiquitin ligase NEDD4 WWIII domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	2.86383554738706	bayes_pls_golite062009
binding	2.62219069341981	bayes_pls_golite062009
ubiquitin-protein ligase activity	2.59532734096591	bayes_pls_golite062009
small conjugating protein ligase activity	2.41863405676058	bayes_pls_golite062009
transcription activator activity	2.14675042199891	bayes_pls_golite062009
transcription factor binding	2.10967934447529	bayes_pls_golite062009
transcription cofactor activity	1.96062029508094	bayes_pls_golite062009
histone methyltransferase activity	1.90194027965368	bayes_pls_golite062009
transcription coactivator activity	1.85689339141637	bayes_pls_golite062009
acid-amino acid ligase activity	1.6967322982151	bayes_pls_golite062009
protein binding	1.46903005775608	bayes_pls_golite062009
protein-lysine N-methyltransferase activity	1.14806422628668	bayes_pls_golite062009
histone-lysine N-methyltransferase activity	1.14806422628668	bayes_pls_golite062009
lysine N-methyltransferase activity	1.14806422628668	bayes_pls_golite062009
protein methyltransferase activity	1.121001087082	bayes_pls_golite062009
ligase activity, forming carbon-nitrogen bonds	0.568363753662296	bayes_pls_golite062009
catalytic activity	0.210712504691113	bayes_pls_golite062009
histone methyltransferase activity (H3-K36 specific)	0.173723075520888	bayes_pls_golite062009
transcription repressor activity	0.0876845006692102	bayes_pls_golite062009

Predicted Domain #7

Region A:
Residues: [2874-2951]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSGPFALLVK NPKVLDFDNK RYFFNAKLKS DNQERPKLPI TVRREQVFLD SYRALFFKTN  60
   61 DEIKNSKLEI TFKGESGV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	578.9691
Match:	1c4zA_
Description:	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [2952-3049]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DAGGVTREWY QVLSRQMFNP DYALFLPVPS DKTTFHPNRT SGINPEHLSF FKFIGMIIGK  60
   61 AIRDQCFLDC HFSREVYKNI LGRPVSLKDM ESLDPDYY

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [3105-3147]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VEYKLQTSVK EQMDNFLVGF YALISKDLIT IFDEQELELL ISG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	578.9691
Match:	1c4zA_
Description:	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
Matching Structure (courtesy of the PDB):

Predicted Domain #9

Region A:
Residues: [3050-3104]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KSLVWILEND ITDIIEETFS VETDDYGEHK VINLIEGGKD IIVTEANKQD YVKKV

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [3148-3268]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPDIDVDDWK NNTTYVNYTA TCKEVSYFWR AVRSFDAEER AKLLQFVTGT SKVPLNGFKE  60
   61 LSGVNGVCKF SIHRDFGSSE RLPSSHTCFN QLNLPPYESY ETLRGSLLLA INEGHEGFGL 120
  121 A

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	578.9691
Match:	1c4zA_
Description:	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
Matching Structure (courtesy of the PDB):

TMHMM	pre 2.0c	PSIPRED	pre v2.61
SignalP	pre 3.0	COILS	1999
DISOPRED	pre v0.2	NCBI nr	circa 2005
PSI-BLAST	~2.2.10	FFAS	ffas
PDB	~2005	Pfam	16
HMMER	2.3.1

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: