Protein Overview: TOM1

General Information:
Name(s) found:	TOM1 / YDR457W [SGD]
Description(s) found: SHOW ONLY BEST	gi\|927738\|gb\|AAB64910.1\| Tom1p; CAI: 0.16 [Saccharomyces cerevisiae] [NCBI NR] gi\|6320665\|ref\|NP_010745.1\| E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; Tom1p [Saccharomyces cerevisiae] [NCBI NR] gi\|50401412\|sp\|Q03280.1\|TOM1_YEAST RecName: Full=E3 ubiquitin-protein ligase TOM1; AltName: Full=Temperature-dependent organization in mitotic nucleus protein 1; AltName: Full=Suppressor of snRNA protein 2 [NCBI NR] pir\|\|S69625 hypothetical protein YDR457w - yeast (Saccharomyces cerevisiae) [NCBI NR] E3 ubiquitin-protein ligase TOM1 OS=Saccharomyces cerevisiae GN=TOM1 PE=1 SV=1 [Swiss-Prot] TOM1 E3 ubiqitin ligase required for G2/M transition [mips] E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones [SGD] TOM1, Chr IV from 1369779-1379585 [yeast_orfs2] Chr IV from 1369779-1379585 [yeastorf3.fasta] Chr IV from 1369778-1379584 [yeastorf4.fasta] >Q03280 (Q03280) D8035.1P (Ubiquitin ligase) [4932.FASTACCERV.txt] TOM1 SGDID:S0002865, Chr IV from 1369778-1379584, Verified ORF [yeastflysequest.fasta] TOM1 SGDID:S0002865, Chr IV from 1369780-1379586, Verified ORF [10112005cervSGD.fasta] Tom1p; CAI: 0.16 [Saccharomyces cerevisiae]gi\|6320665\|ref\|NP_010745.1\| Temperature dependent Organization in Mitotic nucleus; hect-domain-containing protein, containing kinase motifs; similar to Rsp5 [Saccharomyces cerevisiae]gi\|2131505\|pir\|\|S69625 hypo [nrdb_11152004_Chlamydomonas] (Q03280) E3 ubiquitin protein ligase TOM1 (EC 6.3.2.-) (Temperature dependent-organization in mitotic nucleus protein 1) (Suppressor of snRNA protein 2) [cerv4932.FASTAC] TOM1 SGDID:S000002865, Chr IV from 1369780-1379586, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] TOM1 SGDID:S000002865, Chr IV from 1369782-1379588, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators" [yeast-contam.fasta] TOM1 SGDID:S000002865, Chr IV from 1369783-1379589, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators" [SGD_S-cerevisiae_na_08-19-2008_con_reversed.fasta] E3 ubiquitin protein ligase TOM1 (Temperature-dependent organization in mitotic nucleus protein 1) (Suppressor of snRNA protein 2) [nr-271106-contam.fasta] E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; Tom1p [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Tom1p; CAI: 0.16 [Saccharomyces cerevisiae] [nr-271106-contam.fasta] TOM1 SGDID:S000002865, Chr IV from 1369783-1379589, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones" [SGD_S-cerevisiae_na_01-05-2010_reversed.fasta] [chemostatdb.fasta] E3 ubiquitin-protein ligase TOM1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TOM1 PE=1 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] TOM1 SGDID:S000002865, Chr IV from 1369790-1379596, Genome Release 64-1-1, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones" [yeast-030211-contam.fasta] TOM1 SGDID:S000002865, Chr IV from 1369790-1379596, Genome Release 64-2-1, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones; interacts with Dia2p and is required for Dia2p degradation; required to target Cdc6p for ubiquitin-mediated destruction during G1 phase" [20141208_orf_trans.fasta] YDR457W SGDID:S000002865, Chr IV from 1369790-1379596, Genome Release 64-1-1, Verified ORF, "E3 ubiquitin ligase of the hect-domain class; has a role in mRNA export from the nucleus and may regulate transcriptional coactivators; involved in degradation of excess histones" [2016-01-SGD_Yeast_Contam_Riffle_20140507-Ska-Hec-110-tubulin.fasta]
Organism:	Saccharomyces cerevisiae
Length:	3268 amino acids
Gene Ontology:
Cellular Component:	nucleus [IDA] nucleolus [IDA]
Biological Process:	nucleocytoplasmic transport [IMP] protein polyubiquitination [TAS] regulation of cell size [IMP] mitosis [IMP] protein monoubiquitination [TAS] nucleus organization [IMP]
Molecular Function:	ubiquitin-protein ligase activity [TAS]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      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 FGMSLGNGSF SQVPQHLEAR DFLAIIFMEN PPYEYFTSVA 780
  781 ISNVTEVLQY LDEKYEDYAF MDVMKVLNDQ LENLNDFLNS PNDRSFFLER DGENSVRSCH 840
  841 SKLCRLAAIL NIVTNVYIDL TTLSCKRIMQ IYSYFDKRGF SLIKNLKLLF QKCALEEMYI 900
  901 RQHMPDSVIT ETMPLPIVDV SGDGPPLQIY IDDPKKGDQK GKITSVKTRN TLQMRTILYT 960
  961 LQSNTAILFR CFLRLSHSRN MDLEHKDLTT EVHIFENVVE NVIEMLKATE LEGHLPYILV1020
 1021 LLNFNTFVFT IPKASPNSTE ILQTIPAYIF YQKGGYLLYL HIIRDLFTRM TKIKDLSSLD1080
 1081 NINYIDESNG ILTLSCLINA LTFYNKSMQT ETMENVQSIG KYYVSIDDDY NIMKALTVPI1140
 1141 KVMALAMILD LDKSDSLFKT QSRNVPYSVF KQLLSMLKNI FTNVNIYTKE LYELHWDLIF1200
 1201 PPIKKISLFE QVGIPGDVAA NYLTDTGDDL PADNSIGLFS PEQWEKYKKL IGEDKSIYYP1260
 1261 QPMQAQYYKG CSSKELDELR DTFFNDGLPS RIFTVLPFYP KLVNAFAKTL LQIFTKYDEP1320
 1321 TEVFAGRILD RILETDLDDP ATLSSLIHLF GIFLNEKYIY QKASHLMQRF IEYLEKSLKP1380
 1381 EHVNTPWFSK ALYVYEIILA KSELPHLEEL SKDVLLRYPL LSMAKVFRIP DPMKQKLFDI1440
 1441 LIRVSDISNF YSALATSRIL IFYSRDELYA NNIARSGILS RLLKVIGSFQ KLDKINFLES1500
 1501 SFLLLTRRCF ETTENVDALI RAEINRSFTA RPLGGGDDAV RELTTILEEK AHVVMRSPSQ1560
 1561 FIDVLCETAR FHEFDDQGAL VDYSLKRFLG EKDKNTQASS TEKSDIYERT GIMHLLLSQL1620
 1621 MAASEKDWLS EPANSSDLPE NKKAQLDPSR NPVCAYMIFL LKLLVELVSS YNQCKFEFLT1680
 1681 FSRRNTYAER PRPRTTAINF FLYRLLDKPV GTDHDKHEAK RREVIGMLAR SVIIGFLATV1740
 1741 QDDRTTKTDV KLADPHMNFI RKFAIEAIIK AIRNATSSSK LLESNHLKLD MWFRIITSMV1800
 1801 YVQAPYLRQL LDSNKVEADQ YQLCKLVIDL GLPSVITEAM ASIDLNYPFS KKIFNVAVEA1860
 1861 LNTISSTRNN FSEHFKIEDH DEVEDEVDES DKEEIPDMFK NSALGMYDVE DIEEDDDDDT1920
 1921 SLIGDDDAMA FVDSDNGFEV VFSDEDDDMG EEDADDARSD SEENELSSEM QSSTADGTDV1980
 1981 DYEVDDADGL IINIDQPSGD DEEMADYDAN ISHSSHSENE DDASMDVIEV YDDELSSGYD2040
 2041 VDLSDYDVDE SDWDSGLSSL SISDEDSESS EDEPINSTRM GDSRRRWLIA EGVELTDDSQ2100
 2101 GESEEDDRGV FRGIEHIFSN ENEPLFRVHD EMRHRNHHRS INRTHFHSAM SAPSLSLLNR2160
 2161 GRRNQSNLIN PLGPTGLEQV ENDISDQVTV AGSGSRPRSH HLHFSEVLVS GSFFDEPVLD2220
 2221 GIILKSTVSR WKDIFDMFYD SKTYANCIIP TVINRLYKVS LALQKDLENK REQEKLKNKN2280
 2281 LLFNEAKVES HNSSDAISVE QDDIQESNVT HDDHEPVYVT IQGSEVDIGG TDIDPEFMNA2340
 2341 LPDDIRADVF AQHVRERRAE ARLNSDHNVH SREIDSDFLE AIPEDIREGI LDTEAEEQRM2400
 2401 FGRIGSSADV IRADDDVSNN DEEVENGLDH GNSNDRNNAD PEKKKPARIY FAPLIDRAGI2460
 2461 ASLMKSVFIS KPYIQREIYH ELFYRLCSSK QNRNDLMNTF LFILSEGIID QHSLEKVYNI2520
 2521 ISSRAMGHAK TTTVRQLPSD CTPLTVANQT IEILQSLIDA DSRLKYFLIA EHDNLIVNKA2580
 2581 NNKSRKEALP DKKLRWPLWH LFSLLDRKLI TDESVLMDLL TRILQVCTKT LAVLSTSSNG2640
 2641 KENLSKKFHL PSFDEDDLMK ILSIIMLDSC TTRVFQQTLN IIYNLSKLQG CMSIFTKHLV2700
 2701 SLAISIMSKL KSALDGLSRE VGTITTGMEI NSELLQKFTL PSSDQAKLLK ILTTVDFLYT2760
 2761 HKRKEEERNV KDLQSLYDKM NGGPVWSSLS ECLSQFEKSQ AINTSATILL PLIESLMVVC2820
 2821 RRSDLSQNRN TAVKYEDAKL LDFSKTRVEN LFFPFTDAHK KLLNQMIRSN PKLMSGPFAL2880
 2881 LVKNPKVLDF DNKRYFFNAK LKSDNQERPK LPITVRREQV FLDSYRALFF KTNDEIKNSK2940
 2941 LEITFKGESG VDAGGVTREW YQVLSRQMFN PDYALFLPVP SDKTTFHPNR TSGINPEHLS3000
 3001 FFKFIGMIIG KAIRDQCFLD CHFSREVYKN ILGRPVSLKD MESLDPDYYK SLVWILENDI3060
 3061 TDIIEETFSV ETDDYGEHKV INLIEGGKDI IVTEANKQDY VKKVVEYKLQ TSVKEQMDNF3120
 3121 LVGFYALISK DLITIFDEQE LELLISGLPD IDVDDWKNNT TYVNYTATCK EVSYFWRAVR3180
 3181 SFDAEERAKL LQFVTGTSKV PLNGFKELSG VNGVCKFSIH RDFGSSERLP SSHTCFNQLN3240
 3241 LPPYESYETL RGSLLLAINE GHEGFGLA

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Krogan NJ, et al. (2006)		LAG2 TOM1
View Details	Gavin AC, et al. (2006)		ADE3 CSE1 MAE1 PRS3 TDH1 TOM1 YDR341C
View Details	Ho Y, et al. (2002)		BCY1 CAR2 CPR6 ESS1 HEF3 HSP104 HXT6 MDN1 PUP2 RPB3 RPN1 RPO21 SPT5 TFG1 TOM1 UTP22 YHR033W

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	DAD1	Dam1-765 complex purified from yeast with Dad1-TAP	Shimogawa MM, et al. (2006)
View Run	CEP3	sample cbf3 from feb 2005	Sandall S, et all (2006)
View Run	ASF1	3912: TAP-tagged, strain background includes hpc2(delta)	Green EM, et al (2005)
View Run	ASF1	3829 - low filter	Green EM, et al (2005)
View Run	ZDS1	Sample 2- cpn2 from june 2005	McCusker D, et al (2007)
View Run	BOI1	Sample boi 1 with ha tag from october 2005	McCusker D, et al (2007)
View Run	MLP2	#29 Asynchronous Prep5-TiO2 Flowthrough	Keck JM, et al. (2011)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	RBG1	TOM1	1	Unpublished Fields Lab Data
View Screen	LIA1	TOM1	1	Unpublished Fields Lab Data
View Screen	LOS1	TOM1	1	Unpublished Fields Lab Data
View Screen	YLR415C	TOM1	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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	PROTEIN(S)	PUBLICATION
View Data	TOM1	Huh WK, et al. (2003)
View Data	TOM1 and NOP56	Huh WK, et al. (2003)

Protein Structure Data

[What does the above image mean?]
[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..746]	MSA	2.005001	View MSA. No confident structure predictions are available.
2	View Details	[747..1651]	deduced	N/A	No confident structure predictions are available.
3	View Details	[1652..1845]	MSA	1.30299	View MSA. No confident structure predictions are available.
4	View Details	[1846..2170]	MSA	29.460997	View MSA. No confident structure predictions are available.
5	View Details	[2171..2767]	deduced	N/A	No confident structure predictions are available.
6	View Details	[2768..2873]	PSI-BLAST	2.30103	Ubiquitin ligase NEDD4 WWIII domain
7	View Details	[2874..2951]	PSI-BLAST	578.9691	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
8	View Details	[2952..3049] [3105..3147]	PSI-BLAST	578.9691	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)
9	View Details	[3050..3104] [3148..3268]	PSI-BLAST	578.9691	Ubiquitin-protein ligase E3a, Hect catalytic domain (E6ap)

Functions predicted (by domain):

Gene Ontology predictions

No functions predicted.

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

No functions predicted.

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

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.97

Source: Reynolds et al. (2008)

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