YRC Public Data Repository - Protein Structure Prediction

Protein:	NDE2
Organism:	Saccharomyces cerevisiae
Length:	545 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 NDE2.

Description	E-value	Query Range	Subject Range
gi\|151941917 - gi\|151941917\|gb\|EDN60273.1\| type II NAD(P)H:quinone oxidoreductase [Saccharomyces cerevisiae YJM789] gi\|190405091 - gi\|190405091\|gb\|EDV08358.1\| type II NAD(P)H:quinone oxidoreductase [Saccharomyces cerevisiae RM11-1a... NDH2_YEAST - External NADH-ubiquinone oxidoreductase 2, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 20... NDE2 - Mitochondrial external NADH dehydrogenase, catalyzes the oxidation of cytosolic NADH; Nde1p and Nde2...	0.0	[1..545]	[1..545]
NDH1_SCHPO - Probable NADH-ubiquinone oxidoreductase C3A11.07, mitochondrial OS=Schizosaccharomyces pombe (strain... SPAC3A11.07 - NADH dehydrogenase	1.0E-98	[86..544]	[80..549]
gi\|3718005, gi\|4... - gi\|49651726\|emb\|CAG78667.1\| YALI0F25135p [Yarrowia lipolytica], gi\|3718005\|emb\|CAA07265.1\| alternati... NDH2_YARLI - External alternative NADH-ubiquinone oxidoreductase, mitochondrial OS=Yarrowia lipolytica (strain CL...	7.0E-92	[8..544]	[36..580]
DLDH1_ARATH - Dihydrolipoyl dehydrogenase 1, mitochondrial OS=Arabidopsis thaliana GN=LPD1 PE=1 SV=2	3.0E-89	[50..524]	[1..466]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	2.0E-87	[86..524]	[26..460]
gi\|4688668 - gi\|4688668\|emb\|CAB41413.1\| NADH dehydrogenase [Corynebacterium glutamicum] gi\|62390348, gi\|... - gi\|62390348\|ref\|YP_225750.1\| NADH dehydrogenase [Corynebacterium glutamicum ATCC 13032], gi\|41325685...	4.0E-87	[97..542]	[12..424]

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Predicted Domain #1

Region A:
Residues: [1-87]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MLPRLGFART ARSIHRFKMT QISKPFFHST EVGKPGPQQK LSKSYTAVFK KWFVRGLKLT  60
   61 FYTTLAGTLY VSYELYKESN PPKQVPQ

[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: [88-210]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 STAFANGLKK KELVILGTGW GAISLLKKLD TSLYNVTVVS PRSFFLFTPL LPSTPVGTIE  60
   61 MKSIVEPVRS IARRTPGEVH YIEAEALDVD PKAKKVMVQS VSEDEYFVSS LSYDYLVVSV 120
  121 GAK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [368-445]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NEPIDFSKTL MSRIPEQTNR RGLLINDKLE LLGSENSIYA IGDCTAHTGF FPTAQVAHQE  60
   61 GEYLAKILDK KLQIEQLE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	85.221849
Match:	1dxlA_
Description:	Dihydrolipoamide dehydrogenase
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [211-367]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TTTFNIPGVY GNANFLKEIE DAQNIRMKLM KTIEQASSFP VNDPERKRLL TFVVVGGGPT  60
   61 GVEFAAELQD YINQDLRKWM PDLSKEMKVI LIEALPNILN MFDKTLIKYA EDLFARDEID 120
  121 LQVNTAVKVV EPTYIRTLQN GQTNTDIEYG MLVWATG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [446-545]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WDMLNSTDET EVSRLQKEVN LRKSKLDKFN YKHMGALAYI GSETAIADLH MGDSSYQLKG  60
   61 MFAFLFWKSA YLAMCLSIRN RILIAMDWTK VYFLGRDSSV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	85.221849
Match:	1dxlA_
Description:	Dihydrolipoamide dehydrogenase
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