YRC Public Data Repository - Protein Structure Prediction

Protein:	MOD5
Organism:	Saccharomyces cerevisiae
Length:	428 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 MOD5.

Description	E-value	Query Range	Subject Range
gi\|151945358 - gi\|151945358\|gb\|EDN63601.1\| tRNA isopentenyltransferase [Saccharomyces cerevisiae YJM789] MOD5 - Delta 2-isopentenyl pyrophosphate:tRNA isopentenyl transferase, required for biosynthesis of the mod... MOD5_YEAST - tRNA dimethylallyltransferase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c...	0.0	[1..428]	[1..428]
TRIT1 - tRNA isopentenyltransferase 1	0.0	[9..412]	[18..428]
SPAC343.15 - tRNA isopentenyltransferase MOD5_SCHPO - tRNA dimethylallyltransferase, mitochondrial OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) ...	0.0	[12..417]	[1..424]
gi\|15602770, gi\|... - gi\|15602770\|ref\|NP_245842.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Pasteurella multoci...	0.0	[2..334]	[30..352]
IPT2_ARATH - tRNA dimethylallyltransferase 2 OS=Arabidopsis thaliana GN=IPT2 PE=1 SV=2	0.0	[10..428]	[16..464]
MIAA_ECOLI - tRNA delta(2)-isopentenylpyrophosphate transferase (EC 2.5.1.8) (IPP transferase) (Isopentenyl-dipho... gi\|85676922, gi\|... - gi\|89110891\|ref\|AP_004671.1\| delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase [Escherich... MIAA_ECODH - tRNA dimethylallyltransferase OS=Escherichia coli (strain K12 / DH10B) GN=miaA PE=3 SV=1 gi\|194434582, gi... - gi\|194434582\|ref\|ZP_03066839.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Shigella dysente... MIAA_ECOSE - tRNA dimethylallyltransferase OS=Escherichia coli (strain SE11) GN=miaA PE=3 SV=1 gi\|75234280, gi\|... - gi\|75234280\|ref\|ZP_00718668.1\| COG0324: tRNA delta(2)-isopentenylpyrophosphate transferase [Escheric... MIAA_ECOHS - tRNA dimethylallyltransferase OS=Escherichia coli O9:H4 (strain HS) GN=miaA PE=3 SV=1 MIAA_ECO24 - tRNA dimethylallyltransferase OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=miaA PE=3 SV=1 gi\|194439532, gi... - gi\|83585091\|ref\|ZP_00923744.1\| COG0324: tRNA delta(2)-isopentenylpyrophosphate transferase [Escheric... MIAA_SHIBS - tRNA dimethylallyltransferase OS=Shigella boydii serotype 4 (strain Sb227) GN=miaA PE=3 SV=1 MIAA_SHISS - tRNA dimethylallyltransferase OS=Shigella sonnei (strain Ss046) GN=miaA PE=3 SV=1 gi\|75515410, gi\|... - gi\|75515410\|ref\|ZP_00737567.1\| COG0324: tRNA delta(2)-isopentenylpyrophosphate transferase [Escheric... gi\|192926358, gi... - gi\|75255898\|ref\|ZP_00727630.1\| COG0324: tRNA delta(2)-isopentenylpyrophosphate transferase [Escheric... MIAA_ECO8A - tRNA dimethylallyltransferase OS=Escherichia coli O8 (strain IAI1) GN=miaA PE=3 SV=1 EG10595 - delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase / Dimethylallyl diphosphate:tRNA dimeth... MIAA_ECO55 - tRNA dimethylallyltransferase OS=Escherichia coli (strain 55989 / EAEC) GN=miaA PE=3 SV=1 MIAA_ECOBW - tRNA dimethylallyltransferase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=miaA PE=3 SV=1 gi\|251787420, gi... - gi\|251787420\|ref\|YP_003001724.1\| hypothetical protein B21_04000 [Escherichia coli BL21], gi\|24237969... gi\|253326248, gi... - gi\|254290850\|ref\|YP_003056598.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia col... gi\|226840291, gi... - gi\|254037185\|ref\|ZP_04871262.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia sp. ... gi\|254164100, gi... - gi\|254164100\|ref\|YP_003047208.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia col... MIAA_SHIF8 - tRNA dimethylallyltransferase OS=Shigella flexneri serotype 5b (strain 8401) GN=miaA PE=3 SV=2 MIAA_ECOLC - tRNA dimethylallyltransferase OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=miaA PE=... gi\|2506034 - gi\|2506034\|dbj\|BAA22627.1\| tRNA delta 2-isopentenylpyrophosphate transferase [Shigella flexneri] EG10595 - delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase / Dimethylallyl diphosphate:tRNA dimeth...	0.0	[13..329]	[9..309]
gi\|188014483, gi... - gi\|188014483\|gb\|EDU52605.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... MIAA_ECO57 - tRNA dimethylallyltransferase OS=Escherichia coli O157:H7 GN=miaA PE=3 SV=1 gi\|12519156, gi\|... - gi\|15804760\|ref\|NP_290801.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O1... gi\|25324127, gi\|... - pir\|\|C86113 hypothetical protein miaA [imported] - Escherichia coli (strain O157:H7, substrain EDL9... gi\|254595590, gi... - gi\|254796190\|ref\|YP_003081027.1\| delta(2)-isopentenylpyrophosphate tRNA-adenosine transferase [Esche... gi\|217326156, gi... - gi\|217326156\|ref\|ZP_03442240.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli... gi\|15834401, gi\|... - gi\|15834401\|ref\|NP_313174.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O1... gi\|208726374, gi... - gi\|208806573\|ref\|ZP_03248910.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli... gi\|208812724, gi... - gi\|208812724\|ref\|ZP_03254053.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli... gi\|208819068, gi... - gi\|208819068\|ref\|ZP_03259388.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli... MIAA_ECO5E - tRNA dimethylallyltransferase OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=miaA PE=3 SV=1 gi\|168780601, gi... - gi\|189001749\|gb\|EDU70735.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... gi\|168784806, gi... - gi\|189374757\|gb\|EDU93173.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... gi\|168801824, gi... - gi\|189376077\|gb\|EDU94493.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... gi\|195935961 - gi\|195935961\|ref\|ZP_03081343.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli... gi\|189357893, gi... - gi\|189357893\|gb\|EDU76312.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... gi\|168760410, gi... - gi\|189368991\|gb\|EDU87407.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... gi\|168766448, gi... - gi\|189364314\|gb\|EDU82733.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15... gi\|168774118, gi... - gi\|187770326\|gb\|EDU34170.1\| tRNA delta(2)-isopentenylpyrophosphate transferase [Escherichia coli O15...	0.0	[13..329]	[9..309]
MIAA_HAEIN - tRNA dimethylallyltransferase OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd) ... MIAA_HAEIN - tRNA dimethylallyltransferase OS=Haemophilus influenzae GN=miaA PE=3 SV=1	0.0	[12..334]	[1..308]

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Predicted Domain #1

Region A:
Residues: [1-128]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLKGPLKGCL NMSKKVIVIA GTTGVGKSQL SIQLAQKFNG EVINSDSMQV YKDIPIITNK  60
   61 HPLQEREGIP HHVMNHVDWS EEYYSHRFET ECMNAIEDIH RRGKIPIVVG GTHYYLQTLF 120
  121 NKRVDTKS

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.3
Match:	1iqpA
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [129-195]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SERKLTRKQL DILESTDPDV IYNTLVKCDP DIATKYHPND YRRVQRMLEI YYKTGKKPSE  60
   61 TFNEQKI

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.3
Match:	1iqpA
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	3.37529385176635	bayes_pls_golite062009
DNA binding	3.3049326844117	bayes_pls_golite062009
nucleic acid binding	3.24981360535232	bayes_pls_golite062009
binding	2.79894364685962	bayes_pls_golite062009
transcription factor activity	2.44389510173662	bayes_pls_golite062009
RNA polymerase II transcription factor activity	1.57041104288348	bayes_pls_golite062009
transcription activator activity	1.20323819132961	bayes_pls_golite062009
protein binding	0.852654490075478	bayes_pls_golite062009
RNA binding	0.84315767580466	bayes_pls_golite062009
sequence-specific DNA binding	0.732558534458316	bayes_pls_golite062009
transcription repressor activity	0.686318575498149	bayes_pls_golite062009
chromatin binding	0.626365497850853	bayes_pls_golite062009
transcription factor binding	0.515821187939278	bayes_pls_golite062009
catalytic activity	0.263007611601737	bayes_pls_golite062009
specific RNA polymerase II transcription factor activity	0.200483461579207	bayes_pls_golite062009
transcription cofactor activity	0.113925660147477	bayes_pls_golite062009
structure-specific DNA binding	0.0855506955761403	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [196-305]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TLKFDTLFLW LYSKPEPLFQ RLDDRVDDML ERGALQEIKQ LYEYYSQNKF TPEQCENGVW  60
   61 QVIGFKEFLP WLTGKTDDNT VKLEDCIERM KTRTRQYAKR QVKWIKKMLI

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	14.3
Match:	1iqpA
Description:	Replication factor C
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [306-428]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PDIKGDIYLL DATDLSQWDT NASQRAIAIS NDFISNRPIK QERAPKALEE LLSKGETTMK  60
   61 KLDDWTHYTC NVCRNADGKN VVAIGEKYWK IHLGSRRHKS NLKRNTRQAD FEKWKINKKE 120
  121 TVE

[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.

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: