YRC Public Data Repository - Protein Structure Prediction

Protein:	PAF1
Organism:	Saccharomyces cerevisiae
Length:	445 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 PAF1.

Description	E-value	Query Range	Subject Range
gi\|207347468 - gi\|207347468\|gb\|EDZ73625.1\| YBR279Wp-like protein [Saccharomyces cerevisiae AWRI1631] PAF1_YEAST - RNA polymerase II-associated protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=P... gi\|190408572 - gi\|190408572\|gb\|EDV11837.1\| RNA polymerase-associated protein 1 [Saccharomyces cerevisiae RM11-1a] gi\|151946664 - gi\|151946664\|gb\|EDN64886.1\| RNA polymerase-associated factor [Saccharomyces cerevisiae YJM789] PAF1 - Component of the Paf1p complex that binds to and modulates the activity of RNA polymerases I and II;...	0.0	[1..435]	[1..435]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[1..435]	[1..434]
gi\|123981872, gi... - gi\|123996701\|gb\|ABM85952.1\| Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae) [synt... PAF1 - Paf1, RNA polymerase II associated factor, homolog (S. cerevisiae)	0.0	[1..425]	[23..452]
gi\|7715600 - gi\|7715600\|gb\|AAF68118.1\|AC010793_13 F20B17.16 [Arabidopsis thaliana]	0.0	[1..388]	[188..593]
gi\|12857167 - gi\|12857167\|dbj\|BAB30913.1\| unnamed protein product [Mus musculus]	1.0E-98	[1..350]	[23..377]
atms-PA, FBpp0306920 - The gene antimeros is referred to in FlyBase by the symbol Dmel\atms (CG2503, FBgn0010750). It is a ... gi\|220946232, gi... - gi\|220955924\|gb\|ACL90505.1\| atms-PA [synthetic construct], gi\|220946232\|gb\|ACL85659.1\| atms-PA [synt...	3.0E-82	[3..337]	[24..363]
SPAC664.03 - RNA polymerase II associated Paf1 complex PAF1_SCHPO - RNA polymerase II-associated protein 1 homolog OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843...	3.0E-81	[2..350]	[4..364]

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Predicted Domain #1

Region A:
Residues: [1-193]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKKQEYIAP IKYQNSLPVP QLPPKLLVYP ESPETNADSS QLINSLYIKT NVTNLIQQDE  60
   61 DLGMPVDLMK FPGLLNKLDS KLLYGFDNVK LDKDDRILLR DPRIDRLTKT DISKVTFLRR 120
  121 TEYVSNTIAA HDNTSLKRKR RLDDGDSDDE NLDVNHIISR VEGTFNKTDK WQHPVKKGVK 180
  181 MVKKWDLLPD TAS

[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 #2

Region A:
Residues: [194-445]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDQVYFILKF MGSASLDTKE KKSLNTGIFR PVELEEDEWI SMYATDHKDS AILENELEKG  60
   61 MDEMDDDSHE GKIYKFKRIR DYDMKQVAEK PMTELAIRLN DKDGIAYYKP LRSKIELRRR 120
  121 RVNDIIKPLV KEHDIDQLNV TLRNPSTKEA NIRDKLRMKF DPINFATVDE EDDEDEEQPE 180
  181 DVKKESEGDS KTEGSEQEGE NEKDEEIKQE KENEQDEENK QDENRAADTP ETSDAVHTEQ 240
  241 KPEEEKETLQ EE

[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 #3

Region A:
Residues: [311-445]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RRRRVNDIIK PLVKEHDIDQ LNVTLRNPST KEANIRDKLR MKFDPINFAT VDEEDDEDEE  60
   61 QPEDVKKESE GDSKTEGSEQ EGENEKDEEI KQEKENEQDE ENKQDENRAA DTPETSDAVH 120
  121 TEQKPEEEKE TLQEE

[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.

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