YRC Public Data Repository - Protein Structure Prediction

Protein:	HMO1
Organism:	Saccharomyces cerevisiae
Length:	246 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 HMO1.

Description	E-value	Query Range	Subject Range
gi\|185134049, gi... - gi\|185134049\|ref\|NP_001117742.1\| SOX9 alpha2 [Oncorhynchus mykiss], gi\|12003242\|gb\|AAG43497.1\|AF2098...	1.0E-44	[4..227]	[5..234]
gi\|14290107 - gi\|14290107\|gb\|AAK59254.1\| HMG box transcription factor Sox9a1 [Monopterus albus]	1.0E-44	[4..227]	[5..229]
gi\|7707826 - gi\|7707826\|dbj\|BAA95427.1\| sox9 alpha [Rana rugosa]	4.0E-44	[4..227]	[5..232]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	7.0E-44	[4..227]	[5..232]
SOX9_MOUSE - Transcription factor SOX-9 OS=Mus musculus GN=Sox9 PE=1 SV=2	9.0E-44	[4..227]	[5..232]
SOX9_CALJA - Transcription factor SOX-9 OS=Callithrix jacchus GN=SOX9 PE=2 SV=1	1.0E-43	[4..227]	[5..232]
SOX9_CHICK - Transcription factor SOX-9 OS=Gallus gallus GN=SOX9 PE=1 SV=3	1.0E-43	[4..227]	[5..232]
gi\|16945893, gi\|... - gi\|33415940\|gb\|AAQ18507.1\| transcription factor Sox9a [Takifugu rubripes], gi\|16945893\|gb\|AAL32172.1...	1.0E-43	[4..227]	[5..229]
SOX9_PONPY - Transcription factor SOX-9 OS=Pongo pygmaeus GN=SOX9 PE=2 SV=1 gi\|55645881 - ref\|XP_511651.1\| PREDICTED: transcription factor SOX9 [Pan troglodytes] SOX9_MACMU - Transcription factor SOX-9 OS=Macaca mulatta GN=SOX9 PE=2 SV=1 gi\|60656361, gi\|... - gi\|60656361\|gb\|AAX32744.1\| SRY-box [synthetic construct], gi\|168277508\|dbj\|BAG10732.1\| transcription... SOX9 - SRY (sex determining region Y)-box 9	2.0E-43	[4..227]	[5..232]
gi\|12698702 - gi\|12698702\|gb\|AAK01648.1\| SOX9 [Hylobates sp. TIB-201]	2.0E-43	[4..227]	[5..232]

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Predicted Domain #1

Region A:
Residues: [1-92]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTTDPSVKLK SAKDSLVSSL FELSKAANQT ASSIVDFYNA IGDDEEEKIE AFTTLTESLQ  60
   61 TLTSGVNHLH GISSELVNPI DDDKDAIIAA PV

[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	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.892	0.014	RNA polymerase I transcription factor activity	a.47.2	t-snare proteins
View	Download	0.892	0.014	RNA polymerase I transcription factor activity	a.47.2	t-snare proteins
View	Download	0.820	0.014	RNA polymerase I transcription factor activity	a.2.7	tRNA-binding arm
View	Download	0.820	0.014	RNA polymerase I transcription factor activity	a.2.7	tRNA-binding arm
View	Download	0.932	0.014	RNA polymerase I transcription factor activity	a.7.5	Tubulin chaperone cofactor A
View	Download	0.932	0.014	RNA polymerase I transcription factor activity	a.7.5	Tubulin chaperone cofactor A
View	Download	0.900	0.014	RNA polymerase I transcription factor activity	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.900	0.014	RNA polymerase I transcription factor activity	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.828	0.014	RNA polymerase I transcription factor activity	a.47.2	t-snare proteins
View	Download	0.828	0.014	RNA polymerase I transcription factor activity	a.47.2	t-snare proteins
View	Download	0.810	0.014	RNA polymerase I transcription factor activity	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.755	0.014	RNA polymerase I transcription factor activity	a.7.8	GAT domain
View	Download	0.702	0.014	RNA polymerase I transcription factor activity	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.651	0.014	RNA polymerase I transcription factor activity	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.647	0.014	RNA polymerase I transcription factor activity	a.133.1	Phospholipase A2, PLA2
View	Download	0.561	0.014	RNA polymerase I transcription factor activity	a.30.1	ROP protein
View	Download	0.553	0.014	RNA polymerase I transcription factor activity	a.2.7	tRNA-binding arm
View	Download	0.549	0.014	RNA polymerase I transcription factor activity	a.7.6	Ribosomal protein S20
View	Download	0.549	0.014	RNA polymerase I transcription factor activity	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.537	0.014	RNA polymerase I transcription factor activity	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.522	0.014	RNA polymerase I transcription factor activity	f.14.1	Voltage-gated potassium channels
View	Download	0.514	0.014	RNA polymerase I transcription factor activity	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.512	0.014	RNA polymerase I transcription factor activity	a.7.1	Spectrin repeat
View	Download	0.509	0.014	RNA polymerase I transcription factor activity	f.15.1	Small-conductance potassium channel
View	Download	0.496	0.014	RNA polymerase I transcription factor activity	a.30.2	Homodimeric domain of signal transducing histidine kinase
View	Download	0.481	0.014	RNA polymerase I transcription factor activity	a.24.10	Histidine-containing phosphotransfer domain, HPT domain
View	Download	0.470	0.014	RNA polymerase I transcription factor activity	a.112.1	Description not found.
View	Download	0.445	0.014	RNA polymerase I transcription factor activity	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.437	0.014	RNA polymerase I transcription factor activity	a.118.16	Testis/brain RNA-binding protein (TB-RBP)
View	Download	0.434	0.014	RNA polymerase I transcription factor activity	f.13.1	Family A G protein-coupled receptor-like
View	Download	0.423	0.014	RNA polymerase I transcription factor activity	a.118.1	ARM repeat
View	Download	0.422	0.014	RNA polymerase I transcription factor activity	a.25.1	Ferritin-like
View	Download	0.420	0.014	RNA polymerase I transcription factor activity	a.62.1	Hepatitis B viral capsid (hbcag)
View	Download	0.410	0.014	RNA polymerase I transcription factor activity	a.2.6	Effector domain of the protein kinase pkn/prk1
View	Download	0.403	0.014	RNA polymerase I transcription factor activity	a.30.2	Homodimeric domain of signal transducing histidine kinase
View	Download	0.402	0.014	RNA polymerase I transcription factor activity	a.64.1	Saposin
View	Download	0.394	0.014	RNA polymerase I transcription factor activity	a.126.1	Serum albumin-like
View	Download	0.381	0.014	RNA polymerase I transcription factor activity	i.1.1	Ribosome and ribosomal fragments
View	Download	0.376	0.014	RNA polymerase I transcription factor activity	d.150.1	4'-phosphopantetheinyl transferase
View	Download	0.376	0.014	RNA polymerase I transcription factor activity	a.24.3	Cytochromes
View	Download	0.376	0.014	RNA polymerase I transcription factor activity	a.2.3	Chaperone J-domain
View	Download	0.375	0.014	RNA polymerase I transcription factor activity	a.48.2	Transferrin receptor ectodomain, C-terminal domain
View	Download	0.371	0.014	RNA polymerase I transcription factor activity	a.46.1	Methionine synthase domain
View	Download	0.366	0.014	RNA polymerase I transcription factor activity	a.26.1	4-helical cytokines
View	Download	0.361	0.014	RNA polymerase I transcription factor activity	a.83.1	Guanido kinase N-terminal domain
View	Download	0.360	0.014	RNA polymerase I transcription factor activity	a.47.2	t-snare proteins
View	Download	0.355	0.014	RNA polymerase I transcription factor activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.343	0.014	RNA polymerase I transcription factor activity	f.36.1	Neurotransmitter-gated ion-channel pransmembrane pore
View	Download	0.334	0.014	RNA polymerase I transcription factor activity	f.17.2	Cytochrome c oxidase subunit II-like, transmembrane region
View	Download	0.334	0.014	RNA polymerase I transcription factor activity	a.39.1	EF-hand
View	Download	0.331	0.014	RNA polymerase I transcription factor activity	a.77.1	DEATH domain
View	Download	0.324	0.014	RNA polymerase I transcription factor activity	f.21.2	Fumarate reductase respiratory complex transmembrane subunits
View	Download	0.317	0.014	RNA polymerase I transcription factor activity	d.58.20	NAD-binding domain of HMG-CoA reductase
View	Download	0.316	0.014	RNA polymerase I transcription factor activity	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.314	0.014	RNA polymerase I transcription factor activity	a.2.1	GreA transcript cleavage protein, N-terminal domain
View	Download	0.310	0.014	RNA polymerase I transcription factor activity	a.16.1	S15/NS1 RNA-binding domain
View	Download	0.307	0.014	RNA polymerase I transcription factor activity	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.306	0.014	RNA polymerase I transcription factor activity	a.47.2	t-snare proteins
View	Download	0.306	0.014	RNA polymerase I transcription factor activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.304	0.014	RNA polymerase I transcription factor activity	a.1.1	Globin-like
View	Download	0.299	0.014	RNA polymerase I transcription factor activity	a.7.1	Spectrin repeat
View	Download	0.296	0.014	RNA polymerase I transcription factor activity	a.13.1	alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View	Download	0.283	0.014	RNA polymerase I transcription factor activity	a.5.3	N-terminal domain of phosphatidylinositol transfer protein sec14p
View	Download	0.278	0.014	RNA polymerase I transcription factor activity	a.64.1	Saposin
View	Download	0.274	0.014	RNA polymerase I transcription factor activity	c.47.1	Thioredoxin-like
View	Download	0.272	0.014	RNA polymerase I transcription factor activity	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.272	0.014	RNA polymerase I transcription factor activity	d.52.3	Prokaryotic type KH domain (KH-domain type II)
View	Download	0.269	0.014	RNA polymerase I transcription factor activity	a.7.7	BAG domain
View	Download	0.258	0.014	RNA polymerase I transcription factor activity	a.2.5	Prefoldin
View	Download	0.257	0.014	RNA polymerase I transcription factor activity	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.256	0.014	RNA polymerase I transcription factor activity	a.29.5	alpha-ketoacid dehydrogenase kinase, N-terminal domain
View	Download	0.256	0.014	RNA polymerase I transcription factor activity	d.58.11	EF-G/eEF-2 domains III and V
View	Download	0.255	0.014	RNA polymerase I transcription factor activity	d.58.16	Poly(A) polymerase, C-terminal domain
View	Download	0.252	0.014	RNA polymerase I transcription factor activity	a.57.1	Protein HNS-dependent expression A; HdeA
View	Download	0.252	0.014	RNA polymerase I transcription factor activity	a.29.2	Bromodomain
View	Download	0.250	0.014	RNA polymerase I transcription factor activity	f.28.1	Nonheme 11 kDa protein of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
View	Download	0.249	0.014	RNA polymerase I transcription factor activity	a.25.1	Ferritin-like
View	Download	0.248	0.014	RNA polymerase I transcription factor activity	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.247	0.014	RNA polymerase I transcription factor activity	a.24.9	alpha-catenin/vinculin
View	Download	0.245	0.014	RNA polymerase I transcription factor activity	a.25.1	Ferritin-like
View	Download	0.241	0.014	RNA polymerase I transcription factor activity	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac
View	Download	0.235	0.014	RNA polymerase I transcription factor activity	a.26.1	4-helical cytokines
View	Download	0.230	0.014	RNA polymerase I transcription factor activity	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.225	0.014	RNA polymerase I transcription factor activity	a.24.3	Cytochromes
View	Download	0.224	0.014	RNA polymerase I transcription factor activity	b.36.1	PDZ domain-like
View	Download	0.224	0.014	RNA polymerase I transcription factor activity	a.5.4	Elongation factor TFIIS domain 2
View	Download	0.221	0.014	RNA polymerase I transcription factor activity	a.144.2	Ribosomal protein L20
View	Download	0.219	0.014	RNA polymerase I transcription factor activity	b.82.4	Regulatory protein AraC
View	Download	0.216	0.014	RNA polymerase I transcription factor activity	a.37.1	A DNA-binding domain in eukaryotic transcription factors
View	Download	0.216	0.014	RNA polymerase I transcription factor activity	a.8.3	Families 57/38 glycoside transferase middle domain
View	Download	0.211	0.014	RNA polymerase I transcription factor activity	d.96.1	Tetrahydrobiopterin biosynthesis enzymes-like
View	Download	0.211	0.014	RNA polymerase I transcription factor activity	f.25.1	Cytochrome c oxidase subunit III-like
View	Download	0.210	0.014	RNA polymerase I transcription factor activity	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.209	0.014	RNA polymerase I transcription factor activity	a.118.1	ARM repeat
View	Download	0.208	0.014	RNA polymerase I transcription factor activity	d.15.2	CAD & PB1 domains
View	Download	0.208	0.014	RNA polymerase I transcription factor activity	d.58.49	YajQ-like
View	Download	0.208	0.014	RNA polymerase I transcription factor activity	a.144.1	PABC (PABP) domain
View	Download	0.205	0.014	RNA polymerase I transcription factor activity	d.110.4	SNARE-like
View	Download	0.202	0.014	RNA polymerase I transcription factor activity	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.201	0.014	RNA polymerase I transcription factor activity	a.2.9	C-terminal UvrC-binding domain of UvrB

Predicted Domain #2

Region A:
Residues: [93-246]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KAVRRKIERD PNAPKKPLTV FFAYSAYVRQ ELREDRQKAG LPPLSSTEIT QEISKKWKEL  60
   61 SDNEKEKWKQ AYNVELENYQ REKSKYLEAK KNGTLPPASL ENGPTHAPVP IPFSLQHAAE 120
  121 PPVEKRPHDD DGSSEKKKKK KKKDKKKDKS NSSI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	44.325697
Match:	1k99A_
Description:	Upstream binding factor
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
DNA binding	5.15324651287773	bayes_pls_golite062009
nucleic acid binding	5.01228762819617	bayes_pls_golite062009
transcription regulator activity	4.9607192917135	bayes_pls_golite062009
transcription factor activity	3.82658263870186	bayes_pls_golite062009
binding	3.6211482127468	bayes_pls_golite062009
sequence-specific DNA binding	2.96229555092695	bayes_pls_golite062009
RNA polymerase II transcription factor activity	2.75319687398598	bayes_pls_golite062009
chromatin binding	1.64428658020027	bayes_pls_golite062009
transcription activator activity	1.62744929149746	bayes_pls_golite062009
transcription repressor activity	1.53825678633232	bayes_pls_golite062009
protein binding	1.131658134984	bayes_pls_golite062009
transcription factor binding	1.10315330167937	bayes_pls_golite062009
DNA bending activity	0.87985209274756	bayes_pls_golite062009
RNA polymerase II transcription factor activity, enhancer binding	0.261169200304829	bayes_pls_golite062009
RNA polymerase I transcription factor activity	0.0772111539778018	bayes_pls_golite062009

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: