YRC Public Data Repository - Protein Structure Prediction

Protein:	DNA2
Organism:	Saccharomyces cerevisiae
Length:	1522 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 DNA2.

Description	E-value	Query Range	Subject Range
DNA2_YEAST - DNA replication ATP-dependent helicase/nuclease DNA2 OS=Saccharomyces cerevisiae (strain ATCC 204508... DNA2 - Tripartite DNA replication factor with single-stranded DNA-dependent ATPase, ATP-dependent nuclease,...	0.0	[1..1522]	[1..1522]
DNA2 - DNA replication helicase 2 homolog (yeast)	0.0	[453..1471]	[97..1063]
gi\|15221015 - gi\|15221015\|ref\|NP_172361.1\| emb2411 (embryo defective 2411); ATP binding / ATP-dependent DNA helica...	0.0	[439..1473]	[334..1295]
DNA2_XENLA - DNA replication ATP-dependent helicase/nuclease DNA2 OS=Xenopus laevis GN=dna2 PE=1 SV=1	0.0	[453..1477]	[85..1053]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[453..1521]	[393..1396]
DNA2_SCHPO - DNA replication ATP-dependent helicase dna2 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) G... dna2 - DNA replication endonuclease-helicase Dna2	0.0	[453..1521]	[394..1397]
gi\|24640930, gi\|... - gi\|7291108\|gb\|AAF46543.1\| CG2990-PA, isoform A [Drosophila melanogaster], gi\|24640930\|ref\|NP_572597....	0.0	[446..1474]	[98..1104]
gi\|19483918 - gi\|19483918\|gb\|AAH25182.1\| Dna2 protein [Mus musculus]	0.0	[642..1471]	[1..786]

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Predicted Domain #1

Region A:
Residues: [1-435]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPGTPQKNKR SASISVSPAK KTEEKEIIQN DSKAILSKQT KRKKKYAFAP INNLNGKNTK  60
   61 VSNASVLKSI AVSQVRNTSR TKDINKAVSK SVKQLPNSQV KPKREMSNLS RHHDFTQDED 120
  121 GPMEEVIWKY SPLQRDMSDK TTSAAEYSDD YEDVQNPSST PIVPNRLKTV LSFTNIQVPN 180
  181 ADVNQLIQEN GNEQVRPKPA EISTRESLRN IDDILDDIEG DLTIKPTITK FSDLPSSPIK 240
  241 APNVEKKAEV NAEEVDKMDS TGDSNDGDDS LIDILTQKYV EKRKSESQIT IQGNTNQKSG 300
  301 AQESCGKNDN TKSRGEIEDH ENVDNQAKTG NAFYENEEDS NCQRIKKNEK IEYNSSDEFS 360
  361 DDSLIELLNE TQTQVEPNTI EQDLDKVEKM VSDDLRIATD STLSAYALRA KSGAPRDGVV 420
  421 RLVIVSLRSV ELPKI

[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: [436-754]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GTQKILECID GKGEQSSVVV RHPWVYLEFE VGDVIHIIEG KNIENKRLLS DDKNPKTQLA  60
   61 NDNLLVLNPD VLFSATSVGS SVGCLRRSIL QMQFQDPRGE PSLVMTLGNI VHELLQDSIK 120
  121 YKLSHNKISM EIIIQKLDSL LETYSFSIII CNEEIQYVKE LVMKEHAENI LYFVNKFVSK 180
  181 SNYGCYTSIS GTRRTQPISI SNVIDIEENI WSPIYGLKGF LDATVEANVE NNKKHIVPLE 240
  241 VKTGKSRSVS YEVQGLIYTL LLNDRYEIPI EFFLLYFTRD KNMTKFPSVL HSIKHILMSR 300
  301 NRMSMNFKHQ LQEVFGQAQ

[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: [755-882]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SRFELPPLLR DSSCDSCFIK ESCMVLNKLL EDGTPEESGL VEGEFEILTN HLSQNLANYK  60
   61 EFFTKYNDLI TKEESSITCV NKELFLLDGS TRESRSGRCL SGLVVSEVVE HEKTEGAYIY 120
  121 CFSRRRND

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [970-1023]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IDKNDIQQSL SLARFNLLSL FLPAVSPGVD IVDERSKLCR KTKRSDGGNE ILRS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.221849
Match:	1gm5A_
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [883-969]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NNSQSMLSSQ IAANDFVIIS DEEGHFCLCQ GRVQFINPAK IGISVKRKLL NNRLLDKEKG  60
   61 VTTIQSVVES ELEQSSLIAT QNLVTYR

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [1024-1231]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LLVDNRAPKF RDANDDPVIP YKLSKDTTLN LNQKEAIDKV MRAEDYALIL GMPGTGKTTV  60
   61 IAEIIKILVS EGKRVLLTSY THSAVDNILI KLRNTNISIM RLGMKHKVHP DTQKYVPNYA 120
  121 SVKSYNDYLS KINSTSVVAT TCLGINDILF TLNEKDFDYV ILDEASQISM PVALGPLRYG 180
  181 NRFIMVGDHY QLPPLVKNDA ARLGGLEE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	9.221849
Match:	1gm5A_
Description:	RecG, N-terminal domain; RecG "wedge" domain; RecG helicase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [1232-1423]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SLFKTFCEKH PESVAELTLQ YRMCGDIVTL SNFLIYDNKL KCGNNEVFAQ SLELPMPEAL  60
   61 SRYRNESANS KQWLEDILEP TRKVVFLNYD NCPDIIEQSE KDNITNHGEA ELTLQCVEGM 120
  121 LLSGVPCEDI GVMTLYRAQL RLLKKIFNKN VYDGLEILTA DQFQGRDKKC IIISMVRRNS 180
  181 QLNGGALLKE LR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	64.69897
Match:	1pjr__
Description:	DEXX box DNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [1424-1522]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RVNVAMTRAK SKLIIIGSKS TIGSVPEIKS FVNLLEERNW VYTMCKDALY KYKFPDRSNA  60
   61 IDEARKGCGK RTGAKPITSK SKFVSDKPII KEILQEYES

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2.39794
Match:	1qhhD_
Description:	STRUCTURE OF DNA HELICASE WITH ADPNP
Matching Structure (courtesy of the PDB):

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