YRC Public Data Repository - Protein Structure Prediction

Protein:	NAF1
Organism:	Saccharomyces cerevisiae
Length:	492 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 NAF1.

Description	E-value	Query Range	Subject Range
NAF1 - RNA-binding protein required for the assembly of box H/ACA snoRNPs and thus for pre-rRNA processing,... NAF1_YEAST - H/ACA ribonucleoprotein complex non-core subunit NAF1 OS=Saccharomyces cerevisiae (strain ATCC 20450...	4.0E-78	[1..467]	[1..467]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	6.0E-67	[147..483]	[1378..1688]
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\|...	5.0E-52	[136..481]	[2016..2411]
gi\|4808166 - gi\|4808166\|emb\|CAB42797.1\| largest subunit of the RNA polymerase II complex [Drosophila pseudoobscur...	9.0E-52	[187..463]	[1485..1805]
gi\|12642614 - gi\|12642614\|gb\|AAK00311.1\|AF315821_1 DNA-dependent RNA polymerase II largest subunit RPB1 [Monosiga ...	1.0E-51	[135..462]	[1357..1738]
gi\|40217297, gi\|... - gi\|4808164\|emb\|CAB42795.1\| largest subunit of the RNA polymerase II complex [Drosophila guanche], gi...	2.0E-51	[187..463]	[1563..1883]
gi\|9943, gi\|66976 - gi\|9943\|emb\|CAA34560.1\| unnamed protein product [Plasmodium falciparum], pir\|\|RNZQ2L DNA-directed RN... RPB1_PLAFD - DNA-directed RNA polymerase II subunit RPB1 OS=Plasmodium falciparum (isolate CDC / Honduras) GN=RPI...	2.0E-50	[136..481]	[2018..2406]
NAF1_SCHPO - H/ACA ribonucleoprotein complex non-core subunit NAF1 OS=Schizosaccharomyces pombe (strain 972 / ATC... SPBC30D10.15 - snoRNP assembly factor	3.0E-49	[4..385]	[119..514]

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Predicted Domain #1

Region A:
Residues: [1-126]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSDDLFSKAL ENPDQDLNVE LPKDDVDLGL LGDGGNERKT DEPVADAERS TGLGSGSSES  60
   61 ESDSGSDSDS DSGSSGSEDD SADQDVEGED EGGDAIENED EDEDPSPSGP ILSKNEILEE 120
  121 TVPELP

[Run NCBI BLAST on this sequence.]

Detection Method:

deduced

Shown below are all of our de novo (Rosetta) predictions for this domain.
Click here to view only most confident match.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.291	c.23.1	CheY-like

Predicted Domain #2

Region A:
Residues: [127-291]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EDYEISEKTI ITPIGVLKSA FENNIIIHAT MSGEKRVLKE GSIFCLEDRT LIGMLTEVFG  60
   61 PLQNPFYRIK LPDSKKNLFD ELKVRLGEKA FIVTPDAHWI DTFELKRNKG TDASNGYDEE 120
  121 LPEEEQEFSD DEKEALFKKM KKQQRQRKKR DNRKLANDSD NVKVK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.0
Match:	1k83A_
Description:	RBP1
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [292-492]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RARQPKANSL PKLVPPLGMS SNAPMQHGYK SRNARENIKR ESSATSNRNG SSPVPITQHH  60
   61 QQQFSANNYP FPQQPNGMPY PPYSPFPQPT NFQYPPPPFG QATPAQFSNT VPYGSLPPAY 120
  121 NNMSPPTQQS FMPMTQSQPP LPYGVPPMNQ MQNPMYIQPP PQAPPQGNGN FQQVMELHQI 180
  181 LLQQQQQQHQ YQHQHQQDPR T

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #4

Region A:
Residues: [390-492]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FGQATPAQFS NTVPYGSLPP AYNNMSPPTQ QSFMPMTQSQ PPLPYGVPPM NQMQNPMYIQ  60
   61 PPPQAPPQGN GNFQQVMELH QILLQQQQQQ HQYQHQHQQD PRT

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no 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