YRC Public Data Repository - Protein Structure Prediction

Protein:	SUV3
Organism:	Saccharomyces cerevisiae
Length:	737 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 SUV3.

Description	E-value	Query Range	Subject Range
SUV3 - ATP-dependent RNA helicase, component of the mitochondrial degradosome along with the RNase Dss1p; t... SUV3_YEAST - ATP-dependent RNA helicase SUV3, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S28... gi\|190407918 - gi\|190407918\|gb\|EDV11183.1\| ATP-dependent RNA helicase SUV3, mitochondrial precursor [Saccharomyces ...	0.0	[1..737]	[1..737]
SUV3_SACDO - ATP-dependent RNA helicase SUV3, mitochondrial OS=Saccharomyces douglasii GN=SUV3 PE=3 SV=1 SUV3_SACPA - ATP-dependent RNA helicase SUV3, mitochondrial OS=Saccharomyces paradoxus GN=SUV3 PE=3 SV=1	0.0	[1..737]	[1..737]
Q66FY3\|Q66FY3_YERPS - ATP-dependent DNA helicase - Yersinia pseudotuberculosis gi\|167048747, gi... - gi\|167401854\|ref\|ZP_02307342.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Antiqua str.... gi\|89104204, gi\|... - gi\|89104204\|ref\|ZP_01176754.1\| COG0514: Superfamily II DNA helicase [Yersinia pestis biovar Oriental... gi\|166213635, gi... - gi\|166213635\|ref\|ZP_02239670.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Antiqua str.... gi\|108806187, gi... - gi\|108806187\|ref\|YP_650103.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis Antiqua], gi\|10877810... gi\|167054800, gi... - gi\|167426281\|ref\|ZP_02318034.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Mediaevalis ... gi\|229682488, gi... - gi\|229900469\|ref\|ZP_04515598.1\| ATP-dependent DNA helicase [Yersinia pestis Nepal516], gi\|229682488\|... gi\|167421077, gi... - gi\|167421077\|ref\|ZP_02312830.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Orientalis s... gi\|167469646 - gi\|167469646\|ref\|ZP_02334350.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis FV-1] gi\|21957085, gi\|... - gi\|22124312\|ref\|NP_667735.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis KIM], gi\|21957085\|gb\|A... gi\|25290798 - pir\|\|AI0466 ATP-dependent DNA helicase (EC 3.6.1.-) [imported] - Yersinia pestis (strain CO92) gi\|51594557, gi\|... - gi\|51594557\|ref\|YP_068748.1\| ATP-dependent DNA helicase RecQ [Yersinia pseudotuberculosis IP 32953],... gi\|45442967, gi\|... - gi\|45442967\|ref\|NP_994506.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Microtus str. 9... gi\|16123968, gi\|... - gi\|218930836\|ref\|YP_002348711.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis CO92], gi\|16123968... gi\|162418857, gi... - gi\|162418857\|ref\|YP_001605148.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis Angola], gi\|162351... gi\|229706105, gi... - gi\|229837162\|ref\|ZP_04457327.1\| ATP-dependent DNA helicase [Yersinia pestis Pestoides A], gi\|2297061... gi\|229695888, gi... - gi\|229839522\|ref\|ZP_04459681.1\| ATP-dependent DNA helicase [Yersinia pestis biovar Orientalis str. P... gi\|77630731, gi\|... - gi\|77630731\|ref\|ZP_00793317.1\| COG0514: Superfamily II DNA helicase [Yersinia pseudotuberculosis IP ... gi\|149289417, gi... - gi\|153997111\|ref\|ZP_02022244.1\| ATP-dependent DNA helicase [Yersinia pestis CA88-4125], gi\|149289417... gi\|165989444, gi... - gi\|166011675\|ref\|ZP_02232573.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Antiqua str.... gi\|229900085, gi... - gi\|229900085\|ref\|ZP_04515222.1\| ATP-dependent DNA helicase [Yersinia pestis biovar Orientalis str. I... gi\|145600700, gi... - gi\|145600700\|ref\|YP_001164776.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis Pestoides F], gi\|1... gi\|165921764, gi... - gi\|165926240\|ref\|ZP_02222072.1\| ATP-dependent DNA helicase RecQ [Yersinia pestis biovar Orientalis s...	0.0	[205..735]	[13..537]
gi\|153825932, gi... - gi\|153825932\|ref\|ZP_01978599.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae MZO-2], gi\|14974034... gi\|121548208, gi... - gi\|121587570\|ref\|ZP_01677336.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae 2740-80], gi\|121548... gi\|124118769, gi... - gi\|153222629\|ref\|ZP_01953333.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae MAK 757], gi\|124118... gi\|124123627, gi... - gi\|153800796\|ref\|ZP_01955382.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae MZO-3], gi\|12412362... gi\|126510885, gi... - gi\|153818546\|ref\|ZP_01971213.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae NCTC 8457], gi\|1265... gi\|126520877, gi... - gi\|229509372\|ref\|ZP_04398855.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae B33], gi\|229353687\|... gi\|229369165, gi... - gi\|229606510\|ref\|YP_002877158.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae MJ-1236], gi\|22936... gi\|229346745, gi... - gi\|229516319\|ref\|ZP_04405767.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae RC9], gi\|229346745\|... gi\|229350488, gi... - gi\|229512489\|ref\|ZP_04401961.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae TMA 21], gi\|2293504... gi\|229507002, gi... - gi\|229507002\|ref\|ZP_04396510.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae BX 330286], gi\|2293... gi\|227080417, gi... - gi\|227080417\|ref\|YP_002808968.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae M66-2], gi\|2270083... gi\|15640226, gi\|... - gi\|9654602\|gb\|AAF93372.1\| ATP-dependent DNA helicase RecQ [Vibrio cholerae O1 biovar El Tor str. N16... gi\|11354421 - pir\|\|E82351 ATP-dependent DNA helicase RecQ VC0196 [imported] - Vibrio cholerae (strain N16961 serog... gi\|75830228, gi\|... - gi\|75830228\|ref\|ZP_00759510.1\| COG0514: Superfamily II DNA helicase [Vibrio cholerae MO10], gi\|25485... gi\|75816541, gi\|... - gi\|75816541\|ref\|ZP_00747008.1\| COG0514: Superfamily II DNA helicase [Vibrio cholerae V52], gi\|121728...	0.0	[185..736]	[6..556]
gi\|27360504, gi\|... - gi\|27364385\|ref\|NP_759913.1\| ATP-dependent DNA helicase RecQ [Vibrio vulnificus CMCP6], gi\|27360504\|...	0.0	[201..736]	[12..547]
gi\|28198526, gi\|... - gi\|28198526\|ref\|NP_778840.1\| ATP-dependent DNA helicase [Xylella fastidiosa Temecula1], gi\|28056610\|...	0.0	[209..719]	[11..516]
gi\|56480445, gi\|... - gi\|56480445\|ref\|NP_709628.2\| ATP-dependent DNA helicase RecQ [Shigella flexneri 2a str. 301], gi\|563... gi\|30064881, gi\|... - gi\|30064881\|ref\|NP_839052.1\| ATP-dependent DNA helicase RecQ [Shigella flexneri 2a str. 2457T], gi\|3...	0.0	[203..735]	[13..537]
gi\|188015421, gi... - gi\|188015421\|gb\|EDU53543.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC4113], ... gi\|168763952, gi... - gi\|189365963\|gb\|EDU84379.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC4501], ... gi\|168753724, gi... - gi\|189358975\|gb\|EDU77394.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC4401], ... gi\|187768838, gi... - gi\|187768838\|gb\|EDU32682.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC4196], ... gi\|168768108, gi... - gi\|189362723\|gb\|EDU81142.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC4486], ... gi\|83569341, gi\|... - gi\|83569341\|ref\|ZP_00920796.1\| COG0514: Superfamily II DNA helicase [Shigella dysenteriae 1012], gi\|... gi\|189373237, gi... - gi\|189373237\|gb\|EDU91653.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC869], g... gi\|192926687, gi... - gi\|75256254\|ref\|ZP_00727932.1\| COG0514: Superfamily II DNA helicase [Escherichia coli E22], gi\|19306... gi\|168780726, gi... - gi\|189001596\|gb\|EDU70582.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC4076], ... gi\|193068067, gi... - gi\|193068067\|ref\|ZP_03049032.1\| ATP-dependent DNA helicase RecQ [Escherichia coli E110019], gi\|19295... gi\|168801109, gi... - gi\|189376685\|gb\|EDU95101.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC508], g... gi\|208806062, gi... - gi\|208806062\|ref\|ZP_03248399.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC420... gi\|195938114 - gi\|195938114\|ref\|ZP_03083496.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC402... gi\|208821321, gi... - gi\|208821321\|ref\|ZP_03261641.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC404... tr\|A0A0G3HRF1\|A0... - ATP-dependent DNA helicase protein OS=Escherichia coli (strain K12) GN=recQ PE=4 SV=1 gi\|208812810, gi... - gi\|208812810\|ref\|ZP_03254139.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC404... gi\|217321505, gi... - gi\|217325284\|ref\|ZP_03441368.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. TW145... gi\|209400089, gi... - gi\|209400089\|ref\|YP_002273341.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. EC41... gi\|115515205, gi... - gi\|117626081\|ref\|YP_859404.1\| ATP-dependent DNA helicase RecQ [Escherichia coli APEC O1], gi\|1155152... gi\|227888592, gi... - gi\|227888592\|ref\|ZP_04006397.1\| ATP-dependent DNA helicase RecQ [Escherichia coli 83972], gi\|2278344... gi\|226903003, gi... - gi\|237702832\|ref\|ZP_04533313.1\| ATP-dependent DNA helicase recQ [Escherichia sp. 3_2_53FAA], gi\|2269... gi\|75512622 - gi\|75512622\|ref\|ZP_00735134.1\| COG0514: Superfamily II DNA helicase [Escherichia coli 53638] gi\|209753170, gi... - pir\|\|F86069 ATP-dependent DNA helicase [imported] - Escherichia coli (strain O157:H7, substrain EDL... gi\|15834006, gi\|... - gi\|15834006\|ref\|NP_312779.1\| ATP-dependent DNA helicase [Escherichia coli O157:H7], gi\|13364228\|dbj\|... gi\|26250563, gi\|... - gi\|26250563\|ref\|NP_756603.1\| ATP-dependent DNA helicase RecQ [Escherichia coli CFT073], gi\|26110993\|... gi\|91074922, gi\|... - gi\|91213348\|ref\|YP_543334.1\| ATP-dependent DNA helicase RecQ [Escherichia coli UTI89], gi\|91074922\|g... gi\|15834006, gi\|... - gi\|15834006\|ref\|NP_312779.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 str. Sakai], ... gi\|15804414, gi\|... - gi\|15804414\|ref\|NP_290454.1\| ATP-dependent DNA helicase RecQ [Escherichia coli O157:H7 EDL933], gi\|1...	0.0	[203..735]	[13..537]
gi\|15837982, gi\|... - gi\|9106386\|gb\|AAF84190.1\|AE003969_7 DNA helicase [Xylella fastidiosa 9a5c], gi\|15837982\|ref\|NP_29867... gi\|11267478 - pir\|\|A82689 DNA helicase XF1381 [imported] - Xylella fastidiosa (strain 9a5c)	0.0	[209..736]	[56..585]

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Predicted Domain #1

Region A:
Residues: [1-135]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MALVKYSTVF FPLRSLRLFV SIKKAYYHSE PHSIDLFHDK DWIVKRPKFL NLPKNEHSKL  60
   61 DIFQFNFNKS ESNNVYLQDS SFKDNLDKAM QFIYNDKLSS LDAKQVPIKN LAWLKLRDYI 120
  121 YQQLKDPKLQ AKTYV

[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	0.450	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.429	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.629	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.629	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.471	d.54.1	Enolase N-terminal domain-like
View	Download	0.471	d.54.1	Enolase N-terminal domain-like
View	Download	0.450	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.445	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.445	c.2.1	NAD(P)-binding Rossmann-fold domains
View	Download	0.429	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.401	a.1.1	Globin-like
View	Download	0.383	a.1.1	Globin-like
View	Download	0.380	a.1.1	Globin-like
View	Download	0.379	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.378	c.55.3	Ribonuclease H-like
View	Download	0.377	d.87.1	FAD/NAD-linked reductases, dimerisation (C-terminal) domain
View	Download	0.376	d.112.1	Phoshotransferase/anion transport protein
View	Download	0.362	f.21.2	Fumarate reductase respiratory complex transmembrane subunits
View	Download	0.362	d.20.1	UBC-like
View	Download	0.341	a.131.1	Peridinin-chlorophyll protein
View	Download	0.337	a.39.1	EF-hand
View	Download	0.335	c.16.1	Lumazine synthase
View	Download	0.334	c.23.1	CheY-like
View	Download	0.333	d.87.1	FAD/NAD-linked reductases, dimerisation (C-terminal) domain
View	Download	0.322	a.133.1	Phospholipase A2, PLA2
View	Download	0.296	d.6.1	Prion-like
View	Download	0.294	d.211.1	Ankyrin repeat
View	Download	0.262	a.177.1	Sigma2 domain of RNA polymerase sigma factors
View	Download	0.255	d.153.1	N-terminal nucleophile aminohydrolases (Ntn hydrolases)
View	Download	0.246	a.118.1	ARM repeat
View	Download	0.239	a.26.1	4-helical cytokines
View	Download	0.231	a.24.4	Hemerythrin
View	Download	0.227	a.142.1	PTS-regulatory domain, PRD

Predicted Domain #2

Region A:
Residues: [136-542]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PSVSEIIHPS SPGNLISLLI NCNKISNLVW KSVLKYSLSN NITTLDKFIH VLQQTFDHVY  60
   61 EQEILPMMTN TDDTDGAHNV DITNPAEWFP EARKIRRHII MHIGPTNSGK TYRALQKLKS 120
  121 VDRGYYAGPL RLLAREVYDR FHAEKIRCNL LTGEEVIRDL DDRGNSAGLT SGTVEMVPIN 180
  181 QKFDVVVLDE IQMMSDGDRG WAWTNALLGV VSKEVHLCGE KSVLPLVKSI VKMTGDKLTI 240
  241 NEYERLGKLS VEEKPIKDGI KGLRKGDCVV AFSKKKILDL KLKIEKDTNL KVAVIYGSLP 300
  301 PETRVQQAAL FNNGEYDIMV ASDAIGMGLN LSIDRVVFTT NMKYNGEELM EMTSSQIKQI 360
  361 GGRAGRFKSR SASGGVPQGF ITSFESKVLK SVRKAIEAPV EYLKTAV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	84.30103
Match:	1fuuA_
Description:	Initiation factor 4a
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
hydrolase activity	2.18454736627863	bayes_pls_golite062009
binding	1.62320027057768	bayes_pls_golite062009
nucleic acid binding	1.02467925786178	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
DNA binding	0.526183203901145	bayes_pls_golite062009
ribonuclease activity	0.436561333238012	bayes_pls_golite062009
transcription regulator activity	0.390949264169589	bayes_pls_golite062009
helicase activity	0.32448546535964	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	0.22341412535263	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	0.222180491809685	bayes_pls_golite062009
pyrophosphatase activity	0.219296317139543	bayes_pls_golite062009
nucleoside-triphosphatase activity	0.194147556947887	bayes_pls_golite062009
nucleotide binding	0.114848452385726	bayes_pls_golite062009
purine nucleotide binding	0.10713474095071	bayes_pls_golite062009
purine ribonucleotide binding	0.0916519414118148	bayes_pls_golite062009
ribonucleotide binding	0.0915913646217636	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [543-655]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TWPTDEICAQ LMTQFPPGTP TSVLLQTISD ELEKSSDNLF TLSDLKSKLK VIGLFEHMED  60
   61 IPFFDKLKLS NAPVKDMPMV TKAFTKFCET IAKRHTRGLL SYRLPFNLLD YNC

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	7.0
Match:	1d2mA_
Description:	Nucleotide excision repair enzyme UvrB
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [656-737]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IPNESYSLEV YESLYNIITL YFWLSNRYPN YFIDMESAKD LKYFCEMIIF EKLDRLKKNP  60
   61 YAHKPFGSTR GHLSSSRRRL RT

[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	0.244	a.39.1	EF-hand
View	Download	0.508	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.259	b.40.2	Bacterial enterotoxins
View	Download	0.240	a.61.1	Retroviral matrix proteins
View	Download	0.220	a.40.1	Calponin-homology domain, CH-domain
View	Download	0.208	a.2.3	Chaperone J-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

Predicted functions: