YRC Public Data Repository - Protein Structure Prediction

Protein:	SPB4
Organism:	Saccharomyces cerevisiae
Length:	606 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 SPB4.

Description	E-value	Query Range	Subject Range
SPB4_YEAST - ATP-dependent rRNA helicase SPB4 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=SPB4 PE... SPB4_YEAS7 - ATP-dependent rRNA helicase SPB4 OS=Saccharomyces cerevisiae (strain YJM789) GN=SPB4 PE=3 SV=1 SPB4 - Putative ATP-dependent RNA helicase, nucleolar protein required for synthesis of 60S ribosomal subun...	0.0	[1..606]	[1..606]
gi\|5059027, gi\|5... - gi\|5059032\|gb\|AAD38877.1\|AF110009_1 p68 RNA helicase [Molgula oculata], gi\|5059027\|gb\|AAD38874.1\|AF1...	0.0	[6..409]	[148..533]
gi\|13514813, gi\|... - gi\|2580552\|gb\|AAC51830.1\| dead box, X isoform [Homo sapiens], gi\|2580550\|gb\|AAC51829.1\| dead box, X ...	0.0	[6..408]	[181..579]
DDX3L_MOUSE - Putative ATP-dependent RNA helicase Pl10 OS=Mus musculus GN=D1Pas1 PE=1 SV=1	0.0	[6..431]	[180..602]
gi\|10177293 - gi\|10177293\|dbj\|BAB10554.1\| ATP-dependent RNA helicase-like protein [Arabidopsis thaliana]	0.0	[3..405]	[135..518]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[5..406]	[194..589]
gi\|10039327 - gi\|10039327\|dbj\|BAB13306.1\| PL10-related protein CnPL10 [Hydra magnipapillata]	0.0	[6..422]	[172..583]
gi\|5059030 - gi\|5059030\|gb\|AAD38876.1\|AF110008_1 p68 RNA helicase [Molgula occulta]	0.0	[7..409]	[151..535]

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Predicted Domain #1

Region A:
Residues: [1-231]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MSKSLEWDNL GFSLLPWIRT GLDVMGFETM TPVQASTIPM LAGNKDVVVD SVTGSGKTAA  60
   61 FVIPVLEKVV KEEANTSKFK KAHFHSLIIA PTRELSRQIE SVVLSFLEHY PSDLFPIKCQ 120
  121 LLVGTNEATV RDDVSNFLRN RPQILIGTPG RVLDFLQMPA VKTSACSMVV MDEADRLLDM 180
  181 SFIKDTEKIL RLLPKQRRTG LFSATMRSAG SDIFKTGLRN PVRITVNSKN Q

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	431.0
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [232-388]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 APSSLKLNYC VVNPAEKLQL LVSILNNYKF KKCIVYFPTC VSVSYFYSFI QYLGKRNILV  60
   61 NEVEIFSLHG KLQTSARTKT LTAFTDSLSN SVLFTTDVAA RGIDIPDVDL VIQLDPPTNT 120
  121 DMFMHRCGRT GRANRVGKAI TFLNEGREED FIPFMQV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	431.0
Match:	1hv8A_
Description:	Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [389-519]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KNVELEELDL EVKGITTNFY EDFRNWILED RDRFDKGVKA YVAFIKYYSN HSATSIFRLQ  60
   61 SLDYVGIAKL YGLFRLPRMP EITKYLATEK QEGIFPGNWL VDPPVNMDEY KYKDKKREKE 120
  121 RQETLKNISL I

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	10.0
Match:	1d9xA_
Description:	Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [520-606]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NDKKKLKSEL KKKNLAWSDK TLTKERKLER KEKMSLKRKA IEEELKAEEL DENAEEERIK  60
   61 EDWKEIVLQN KRKKVSSKAI QGNFDDL

[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	0.604	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.705	a.64.1	Saposin
View	Download	0.776	a.28.3	Retrovirus capsid protein C-terminal domain
View	Download	0.631	a.126.1	Serum albumin-like
View	Download	0.611	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.580	a.64.1	Saposin
View	Download	0.576	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.495	a.36.1	Signal peptide-binding domain
View	Download	0.444	a.4.1	Homeodomain-like
View	Download	0.443	a.118.13	Arp2/3 complex 16 kDa subunit ARPC5
View	Download	0.440	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.421	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.387	a.121.1	Tetracyclin repressor-like, C-terminal domain
View	Download	0.359	a.4.1	Homeodomain-like
View	Download	0.347	a.77.1	DEATH domain
View	Download	0.333	d.43.1	Elongation factor Ts (EF-Ts), dimerisation domain
View	Download	0.333	a.57.1	Protein HNS-dependent expression A; HdeA
View	Download	0.322	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.321	a.12.1	Kix domain of CBP (creb binding protein)
View	Download	0.305	f.1.5	Exotoxin A, middle domain
View	Download	0.304	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.292	a.60.1	SAM/Pointed domain
View	Download	0.291	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.285	a.138.1	Multiheme cytochromes
View	Download	0.277	a.4.2	Methylated DNA-protein cysteine methyltransferase, C-terminal domain
View	Download	0.275	a.22.1	Histone-fold
View	Download	0.272	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.264	d.54.1	Enolase N-terminal domain-like
View	Download	0.262	c.102.1	Cell-division inhibitor MinC, N-terminal domain
View	Download	0.261	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.259	a.158.1	F-box domain
View	Download	0.250	a.46.2	Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
View	Download	0.245	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.240	a.24.15	FAD-dependent thiol oxidase
View	Download	0.231	a.77.1	DEATH domain
View	Download	0.230	a.118.14	FliG
View	Download	0.227	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.226	a.112.1	Description not found.
View	Download	0.225	d.87.2	CO dehydrogenase flavoprotein C-terminal domain-like
View	Download	0.224	a.74.1	Cyclin-like
View	Download	0.223	a.24.17	Group V grass pollen allergen
View	Download	0.221	a.3.1	Cytochrome c
View	Download	0.221	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.221	a.144.1	PABC (PABP) domain
View	Download	0.219	a.77.1	DEATH domain
View	Download	0.213	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.211	a.2.7	tRNA-binding arm
View	Download	0.208	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.202	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.200	a.4.5	"Winged helix" DNA-binding 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