YRC Public Data Repository - Protein Structure Prediction

Protein:	MSK1
Organism:	Saccharomyces cerevisiae
Length:	576 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 MSK1.

Description	E-value	Query Range	Subject Range
MSK1 - Mitochondrial lysine-tRNA synthetase, required for import of both aminoacylated and deacylated forms... SYKM_YEAST - Lysine--tRNA ligase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MSK1 ...	0.0	[1..576]	[1..576]
SYK2_ECO57 - (P0A8N6) Lysyl-tRNA synthetase, heat inducible (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS) SYK2_ECOLI - (P0A8N5) Lysyl-tRNA synthetase, heat inducible (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS)	0.0	[32..574]	[1..504]
SYK2_ECOLI - Lysyl-tRNA synthetase, heat inducible (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS) - Escherichia coli SYK2_ECO57 - Lysine--tRNA ligase, heat inducible OS=Escherichia coli O157:H7 GN=lysU PE=3 SV=2 EG10553 - lysine tRNA synthetase, inducible / Lysine--tRNA ligase, heat inducible; Ap4A and Ap3A synthase gi\|15804722, gi\|... - gi\|15804722\|ref\|NP_290763.1\| lysyl-tRNA synthetase [Escherichia coli O157:H7 EDL933], gi\|12519106\|gb... gi\|15834365, gi\|... - gi\|15834365\|ref\|NP_313138.1\| lysyl-tRNA synthetase [Escherichia coli O157:H7 str. Sakai], gi\|1336458... gi\|238861695, gi... - gi\|238903238\|ref\|YP_002929034.1\| lysine tRNA synthetase, inducible [Escherichia coli BW2952], gi\|238... gi\|254796152, gi... - gi\|254796152\|ref\|YP_003080989.1\| lysine tRNA synthetase, inducible [Escherichia coli O157:H7 str. TW... gi\|170083579, gi... - gi\|170083579\|ref\|YP_001732899.1\| lysine tRNA synthetase, inducible [Escherichia coli str. K-12 subst... gi\|189379164, gi... - gi\|189379164\|gb\|EDU97580.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC508], gi\|168... gi\|208726904, gi... - gi\|208807103\|ref\|ZP_03249440.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4206], g... EG10553 - lysine tRNA synthetase, inducible / Lysine--tRNA ligase, heat inducible; Ap4A and Ap3A synthase gi\|195935919 - gi\|195935919\|ref\|ZP_03081301.1\| lysyl-tRNA synthetase [Escherichia coli O157:H7 str. EC4024] gi\|208819932, gi... - gi\|208819932\|ref\|ZP_03260252.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4042], g... gi\|208735239, gi... - gi\|208813962\|ref\|ZP_03255291.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4045], g... gi\|209921620, gi... - gi\|209921620\|ref\|YP_002295704.1\| lysyl-tRNA synthetase [Escherichia coli SE11], gi\|209914879\|dbj\|BAG... gi\|209162047, gi... - gi\|209400647\|ref\|YP_002273676.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4115], ... gi\|188017408, gi... - gi\|188017408\|gb\|EDU55530.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4113], gi\|16... gi\|168760993, gi... - gi\|189368520\|gb\|EDU86936.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4501], gi\|16... gi\|168755314, gi... - gi\|189357458\|gb\|EDU75877.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4401], gi\|16... gi\|168774502, gi... - gi\|187769884\|gb\|EDU33728.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4196], gi\|16... gi\|168766403, gi... - gi\|189364021\|gb\|EDU82440.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4486], gi\|16... gi\|189375037, gi... - gi\|189375037\|gb\|EDU93453.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC869], gi\|168... gi\|189001831, gi... - gi\|189001831\|gb\|EDU70817.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. EC4076], gi\|16... gi\|89110851, gi\|... - gi\|89110851\|ref\|AP_004631.1\| lysine tRNA synthetase, inducible [Escherichia coli str. K-12 substr. W... gi\|218363451, gi... - gi\|218556682\|ref\|YP_002389596.1\| lysyl-tRNA synthetase [Escherichia coli IAI1], gi\|218363451\|emb\|CAR... gi\|188488978, gi... - gi\|75514889\|ref\|ZP_00737118.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli 53638], g... gi\|217326188, gi... - gi\|217326188\|ref\|ZP_03442272.1\| lysyl-tRNA synthetase LysU [Escherichia coli O157:H7 str. TW14588], ... gi\|192931307, gi... - gi\|75259047\|ref\|ZP_00730415.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli E22], gi\|... gi\|75212057, gi\|... - gi\|75212057\|ref\|ZP_00712112.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli B171], gi... gi\|218697832, gi... - gi\|218697832\|ref\|YP_002405499.1\| lysyl-tRNA synthetase [Escherichia coli 55989], gi\|218354564\|emb\|CA... gi\|157069275, gi... - gi\|75197980\|ref\|ZP_00708050.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli HS], gi\|1...	0.0	[32..574]	[2..505]
gi\|54035540 - gb\|AAH84042.1\| Unknown (protein for MGC:98393) [Xenopus laevis] SYK_MOUSE - Lysine--tRNA ligase OS=Mus musculus GN=Kars PE=1 SV=1	0.0	[5..575]	[22..576]
gi\|227888438, gi... - gi\|227888438\|ref\|ZP_04006243.1\| lysine tRNA synthetase, constitutive [Escherichia coli 83972], gi\|22... gi\|237706467, gi... - gi\|237706467\|ref\|ZP_04536948.1\| lysyl-tRNA synthetase [Escherichia sp. 3_2_53FAA], gi\|226899507\|gb\|E... gi\|238861694, gi... - gi\|238902015\|ref\|YP_002927811.1\| lysine tRNA synthetase, constitutive [Escherichia coli BW2952], gi\|... gi\|242378422, gi... - gi\|251786149\|ref\|YP_003000453.1\| hypothetical protein B21_02685 [Escherichia coli BL21], gi\|24237842... gi\|253323313, gi... - gi\|254289562\|ref\|YP_003055310.1\| lysine tRNA synthetase, constitutive [Escherichia coli BL21(DE3)], ... gi\|254037933, gi... - gi\|254037933\|ref\|ZP_04871991.1\| lysyl-tRNA synthetase [Escherichia sp. 1_1_43], gi\|226839557\|gb\|EEH7... gi\|254162802, gi... - gi\|254162802\|ref\|YP_003045910.1\| lysine tRNA synthetase, constitutive [Escherichia coli B str. REL60... EG10552 - lysine tRNA synthetase, constitutive / Lysine--tRNA ligase, constitutive SYK1_ECOL6 - Lysine--tRNA ligase OS=Escherichia coli O6 GN=lysS PE=3 SV=2 SYK1_ECOLI - Lysyl-tRNA synthetase (EC 6.1.1.6) (Lysine--tRNA ligase) (LysRS) - Escherichia coli SYK1_ECOL6 - Lysine--tRNA ligase OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN=lysS PE=3 SV=2 gi\|91073842, gi\|... - gi\|91212268\|ref\|YP_542254.1\| lysyl-tRNA synthetase [Escherichia coli UTI89], gi\|91073842\|gb\|ABE08723... EG10552 - lysine tRNA synthetase, constitutive / Lysine--tRNA ligase, constitutive gi\|110344630, gi... - gi\|110643038\|ref\|YP_670768.1\| lysyl-tRNA synthetase [Escherichia coli 536], gi\|110344630\|gb\|ABG70867... gi\|188493495, gi... - gi\|75515328\|ref\|ZP_00737512.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli 53638], g... gi\|89109669, gi\|... - gi\|89109669\|ref\|AP_003449.1\| lysine tRNA synthetase, constitutive [Escherichia coli str. K-12 substr... gi\|115514245, gi... - gi\|117625121\|ref\|YP_854109.1\| lysyl-tRNA synthetase [Escherichia coli APEC O1], gi\|115514245\|gb\|ABJ0... gi\|124502308, gi... - gi\|124526204\|ref\|ZP_01698209.1\| lysyl-tRNA synthetase [Escherichia coli B], gi\|124502308\|gb\|EAY49768... gi\|218691015, gi... - gi\|218691015\|ref\|YP_002399227.1\| lysyl-tRNA synthetase [Escherichia coli ED1a], gi\|218428579\|emb\|CAR... gi\|218366652, gi... - gi\|218559883\|ref\|YP_002392796.1\| lysyl-tRNA synthetase [Escherichia coli S88], gi\|218366652\|emb\|CAR0... gi\|218706396, gi... - gi\|218706396\|ref\|YP_002413915.1\| lysyl-tRNA synthetase [Escherichia coli UMN026], gi\|218433493\|emb\|C... gi\|218371585, gi... - gi\|218701599\|ref\|YP_002409228.1\| lysyl-tRNA synthetase [Escherichia coli IAI39], gi\|218371585\|emb\|CA... gi\|75196841, gi\|... - gi\|75196841\|ref\|ZP_00706911.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli HS], gi\|1... gi\|191173251, gi... - gi\|75239233\|ref\|ZP_00723206.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli F11], gi\|... gi\|83587715, gi\|... - gi\|83587715\|ref\|ZP_00926342.1\| COG1190: Lysyl-tRNA synthetase (class II) [Escherichia coli 101-1], g... gi\|169753792, gi... - gi\|170018864\|ref\|YP_001723818.1\| lysyl-tRNA synthetase [Escherichia coli ATCC 8739], gi\|169753792\|gb... gi\|209920344, gi... - gi\|209920344\|ref\|YP_002294428.1\| lysyl-tRNA synthetase [Escherichia coli SE11], gi\|209913603\|dbj\|BAG... gi\|170082451, gi... - gi\|170082451\|ref\|YP_001731771.1\| lysine tRNA synthetase, constitutive [Escherichia coli str. K-12 su...	0.0	[44..574]	[14..505]
gi\|221321410 - gi\|221321410\|ref\|ZP_03602704.1\| lysyl-tRNA synthetase [Bacillus subtilis subsp. subtilis str. SMY] gi\|221317147 - gi\|221317147\|ref\|ZP_03598441.1\| lysyl-tRNA synthetase [Bacillus subtilis subsp. subtilis str. JH642] gi\|221312214 - gi\|221312214\|ref\|ZP_03594019.1\| lysyl-tRNA synthetase [Bacillus subtilis subsp. subtilis str. NCIB 3... SYK_BACSU - Lysine--tRNA ligase OS=Bacillus subtilis (strain 168) GN=lysS PE=3 SV=1 SYK_BACSU - Lysine--tRNA ligase OS=Bacillus subtilis GN=lysS PE=3 SV=1	0.0	[39..571]	[5..497]
gi\|11095909 - gi\|11095909\|gb\|AAG30114.1\|AF285758_1 lysyl-tRNA synthetase [Homo sapiens]	0.0	[5..575]	[51..606]
gi\|25293037 - pir\|\|F89818 lysyl-tRNA synthetase [imported] - Staphylococcus aureus (strain N315) SYK_STAA3 - Lysine--tRNA ligase OS=Staphylococcus aureus (strain USA300) GN=lysS PE=3 SV=1 SYK_STAA8 - Lysine--tRNA ligase OS=Staphylococcus aureus (strain NCTC 8325) GN=lysS PE=3 SV=1 SYK_STAAB - Lysine--tRNA ligase OS=Staphylococcus aureus (strain bovine RF122 / ET3-1) GN=lysS PE=3 SV=1 SYK_STAAC - Lysine--tRNA ligase OS=Staphylococcus aureus (strain COL) GN=lysS PE=3 SV=1 gi\|255005310 - gi\|255005310\|ref\|ZP_05143911.2\| lysyl-tRNA synthetase [Staphylococcus aureus subsp. aureus Mu50-omeg... gi\|253315214 - gi\|253315214\|ref\|ZP_04838427.1\| lysyl-tRNA synthetase [Staphylococcus aureus subsp. aureus str. CF-M... gi\|221142291 - gi\|221142291\|ref\|ZP_03566784.1\| lysyl-tRNA synthetase [Staphylococcus aureus subsp. aureus str. JKD6... gi\|221138566 - gi\|221138566\|ref\|ZP_03563368.1\| lysyl-tRNA synthetase [Staphylococcus aureus subsp. aureus str. JKD6... gi\|87127414\|gb\|A... - lysyl-tRNA synthetase [Staphylococcus aureus subsp. aureus USA300], lysyl-tRNA synthetase [Staphyloc... gi\|269202138\|ref... - lysyl-tRNA synthetase [Staphylococcus aureus subsp. aureus ED98] SYK_STAAM - Lysine--tRNA ligase OS=Staphylococcus aureus (strain Mu50 / ATCC 700699) GN=lysS PE=3 SV=1 SYK_STAA1 - Lysine--tRNA ligase OS=Staphylococcus aureus (strain Mu3 / ATCC 700698) GN=lysS PE=3 SV=1 SYK_STAAN - Lysine--tRNA ligase OS=Staphylococcus aureus (strain N315) GN=lysS PE=1 SV=1	0.0	[42..573]	[1..495]

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Predicted Domain #1

Region A:
Residues: [1-204]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MNVLLKRRSL TFAPRWLWCK CRSSRSRPYS LAHAVDTSKM EATRRNGQIV KDLGRYYPSM  60
   61 SESALHDLCQ EYKEVTIADF NERFLGNPAT LHHEDNPNLL LSINGRIKSI RFSGQKIVFI 120
  121 DLYNGSSGLK NDTQLQLIVN YNKIGGSSED KANFSEYMNF LKKGDYIKAL GYPGFSQSRV 180
  181 KMLSLICNKL PIVLSVSQLP LPSR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	633.0103
Match:	1e1oA_
Description:	Lysyl-tRNA synthetase (LysRS)
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
ligase activity, forming aminoacyl-tRNA and related compounds	7.89468709683036	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	7.89468709683036	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	7.88410036819636	bayes_pls_golite062009
ligase activity	6.92073480193262	bayes_pls_golite062009
lysine-tRNA ligase activity	5.79033103181143	bayes_pls_golite062009
phenylalanine-tRNA ligase activity	2.99105702052936	bayes_pls_golite062009
serine-tRNA ligase activity	2.46505535069103	bayes_pls_golite062009
structural constituent of ribosome	2.43759174701552	bayes_pls_golite062009
glycine-tRNA ligase activity	2.29229136935761	bayes_pls_golite062009
threonine-tRNA ligase activity	2.18642354927	bayes_pls_golite062009
structural molecule activity	2.08258913217268	bayes_pls_golite062009
catalytic activity	1.99372273395202	bayes_pls_golite062009
alanine-tRNA ligase activity	1.82594054955281	bayes_pls_golite062009
histidine-tRNA ligase activity	1.72215103383322	bayes_pls_golite062009
transcription regulator activity	1.67362693618722	bayes_pls_golite062009
binding	1.54403712698597	bayes_pls_golite062009
nucleic acid binding	1.48056625237411	bayes_pls_golite062009
DNA binding	1.44496421928708	bayes_pls_golite062009
translation initiation factor activity	0.96756670903925	bayes_pls_golite062009
asparagine-tRNA ligase activity	0.921492123574877	bayes_pls_golite062009
transcription factor activity	0.825973629967327	bayes_pls_golite062009
sequence-specific DNA binding	0.77755643935497	bayes_pls_golite062009
ribonuclease activity	0.702449673647117	bayes_pls_golite062009
nuclease activity	0.111225677144242	bayes_pls_golite062009
aspartate-tRNA ligase activity	0.00572514744734753	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [205-576]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LNDETKIKSN RVVDYQLNGT QTLLVRARII KLLRKFLDDR NFVEVETPIL SSKSNGAMAK  60
   61 PFITSSKDFD HLELRIAPEL WLKRLIISGL QKVYEIGKVF RNEGIDSTHN AEFSTLEFYE 120
  121 TYMSMDDIVT RTEDLFKFLI TNLQKFFQDT RLPVPKTFSE LHLALSENNW KFRKVEFLPT 180
  181 LNKELGIDLM NSGLDINKPS ELLKALPKDI AKKYFPSADN TGQLSSLQIL NKLSDVFLEQ 240
  241 RHCQSTLPTV IYHQPAILSP LAKTDPQNKQ VTKRFEVFIK GKEYINAYEE ENCPQLQLQK 300
  301 FLQQKQINEL TGNKTETLSP VIDYQYVETM KYGMPPVGGF GLGIDRLCML FCDKKRIEEV 360
  361 LPFGCVDDVN RQ

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	633.0103
Match:	1e1oA_
Description:	Lysyl-tRNA synthetase (LysRS)
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits

Predicted functions: