YRC Public Data Repository - Protein Structure Prediction

Protein:	PHD1
Organism:	Saccharomyces cerevisiae
Length:	366 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 PHD1.

Description	E-value	Query Range	Subject Range
gi\|151941502 - gi\|151941502\|gb\|EDN59865.1\| transcriptional activator that enhances pseudohyphal growth [Saccharomyc... PHD1 - Transcriptional activator that enhances pseudohyphal growth; regulates expression of FLO11, an adhes... PHD1_YEAST - Putative transcription factor PHD1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PHD1 ...	2.0E-86	[1..366]	[1..366]
STUA_EMENI - Cell pattern formation-associated protein stuA OS=Emericella nidulans GN=stuA PE=2 SV=2 STUA_EMENI - Cell pattern formation-associated protein stuA OS=Emericella nidulans (strain FGSC A4 / ATCC 38163 /...	5.0E-46	[41..361]	[1..324]
RES1_SCHPO - Cell division cycle-related protein res1/sct1 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843)... res1 - MBF transcription factor complex subunit Res1	6.0E-42	[199..347]	[16..156]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	3.0E-40	[3..189]	[1484..1673]
gi\|28949997, gi\|... - gi\|32412854\|ref\|XP_326907.1\| hypothetical protein ( (U51117) ascospore maturation 1 protein [Neurosp... STUA_NEUCR - Cell pattern formation-associated protein asm-1 OS=Neurospora crassa (strain ATCC 24698 / 74-OR23-1A...	2.0E-38	[71..344]	[2..298]
gi\|83767526, gi\|... - gi\|9955855\|dbj\|BAB12227.1\| RNA polymerase II largest subunit [Aspergillus oryzae], gi\|83767526\|dbj\|B... gi\|169770395 - gi\|169770395\|ref\|XP_001819667.1\| hypothetical protein [Aspergillus oryzae RIB40]	2.0E-36	[7..189]	[1565..1740]
gi\|7494259 - pir\|\|T18492 hypothetical protein C0805w - malaria parasite (Plasmodium falciparum) gi\|124505021, gi... - gi\|3758846\|emb\|CAB11131.1\| DNA-directed RNA polymerase II, putative [Plasmodium falciparum 3D7], gi\|...	1.0E-35	[11..188]	[2221..2388]
MBP1_KLULA - Transcription factor MBP1 OS=Kluyveromyces lactis GN=MBP1 PE=4 SV=2 MBP1_KLULA - Transcription factor MBP1 OS=Kluyveromyces lactis (strain ATCC 8585 / CBS 2359 / DSM 70799 / NBRC 12...	3.0E-35	[196..336]	[13..139]

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Predicted Domain #1

Region A:
Residues: [1-194]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MYHVPEMRLH YPLVNTQSNA AITPTRSYDN TLPSFNELSH QSTINLPFVQ RETPNAYANV  60
   61 AQLATSPTQA KSGYYCRYYA VPFPTYPQQP QSPYQQAVLP YATIPNSNFQ PSSFPVMAVM 120
  121 PPEVQFDGSF LNTLHPHTEL PPIIQNTNDT SVARPNNLKS IAAASPTVTA TTRTPGVSST 180
  181 SVLKPRVITT MWED

[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: [195-289]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ENTICYQVEA NGISVVRRAD NNMINGTKLL NVTKMTRGRR DGILRSEKVR EVVKIGSMHL  60
   61 KGVWIPFERA YILAQREQIL DHLYPLFVKD IESIV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	85.28043
Match:	1bm8__
Description:	DNA-binding domain of Mlu1-box binding protein MBP1
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
transcription regulator activity	4.36949648004482	bayes_pls_golite062009
DNA binding	4.06494205639151	bayes_pls_golite062009
nucleic acid binding	3.98559547948274	bayes_pls_golite062009
transcription factor activity	3.87642218322379	bayes_pls_golite062009
sequence-specific DNA binding	3.19892138828988	bayes_pls_golite062009
binding	2.79149251200147	bayes_pls_golite062009
protein binding	1.55473080522232	bayes_pls_golite062009
transcription repressor activity	0.838109968340069	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [290-366]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DARKPSNKAS LTPKSSPAPI KQEPSDNKHE IATEIKPKSI DALSNGASTQ GAGELPHLKI  60
   61 NHIDTEAQTS RAKNELS

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.367	0.859	specific RNA polymerase II transcription factor activity	a.4.1	Homeodomain-like

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: