YRC Public Data Repository - Protein Structure Prediction

Protein:	PAM1
Organism:	Saccharomyces cerevisiae
Length:	830 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 PAM1.

Description	E-value	Query Range	Subject Range
PAM1_YEAST - Protein PAM1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=PAM1 PE=1 SV=2 PAM1 - Essential protein of unknown function; exhibits variable expression during colony morphogenesis; ove...	0.0	[1..814]	[1..814]
STC2_STAAU - Staphylocoagulase OS=Staphylococcus aureus PE=1 SV=1	1.0E-93	[463..758]	[402..703]
mug72 - ketopantoate reductase MUG72_SCHPO - Meiotically up-regulated gene 72 protein OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=m...	2.0E-71	[2..343]	[6..336]
PANE_LACLA - Putative 2-dehydropantoate 2-reductase OS=Lactococcus lactis subsp. lactis (strain IL1403) GN=LL1323... PANE_LACLA - Putative 2-dehydropantoate 2-reductase OS=Lactococcus lactis subsp. lactis GN=LL1323 PE=3 SV=1	3.0E-69	[5..346]	[1..312]
gi\|15923220, gi\|... - gi\|15923220\|ref\|NP_370754.1\| staphylocoagulase precursor [Staphylococcus aureus subsp. aureus Mu50],... gi\|15925933, gi\|... - gi\|15925933\|ref\|NP_373466.1\| staphylocoagulase precursor [Staphylococcus aureus subsp. aureus N315],... gi\|156720695, gi... - gi\|156978560\|ref\|YP_001440819.1\| staphylocoagulase precursor [Staphylococcus aureus subsp. aureus Mu... gi\|238549995, gi... - pir\|\|A89786 staphylocoagulase precursor [imported] - Staphylococcus aureus (strain N315), gi\|238549... gi\|255005025 - gi\|255005025\|ref\|ZP_05143626.2\| staphylocoagulase precursor [Staphylococcus aureus subsp. aureus Mu5...	7.0E-69	[356..712]	[299..655]
gi\|18144446, gi\|... - gi\|18309768\|ref\|NP_561702.1\| 2-dehydropantoate 2-reductase [Clostridium perfringens str. 13], gi\|181...	8.0E-68	[5..344]	[1..308]

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Predicted Domain #1

Region A:
Residues: [1-213]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTSALRVLVC GDHPNLILYT SRFQHAKNIE FYLVNNSKNA NYEVSSLFYG TERFQIQNHF  60
   61 QSLLDLVDLN NENGGLVFDL IIMSASSLQE IPQVLRDIKP MMNKTTKILF ESSGFIYLEP 120
  121 FIKASVDLSL SNIFSIFTDY DIRRLDNGSY KQFTTANAKS FSVSIGQTTS VHENSYSSDI 180
  181 IPILNTFQKL FQKLFPRDVV TLYDHSPSAF LAK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.154902
Match:	1ks9A_
Description:	Ketopantoate reductase PanE
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [214-371]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EWELALPQIC FDPLLIILEE KNPSTLDDHV LAKPLISGLL GESLLIIKKM GIAMNNPNFQ  60
   61 NEQTILKHWK NKCEDLPDGP ALLYNFIHKA SSLNIDLLLL QPILLADDFG VKTPYLECLF 120
  121 TMMTQYQLLN KGDSEWFIRK DENTALTRVD DLQNSIAL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	39.154902
Match:	1ks9A_
Description:	Ketopantoate reductase PanE
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [372-461]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KDGKIMQLQN SESTLKNEIK ELQSQVLSLK QEVSSSKANN GQELEILKKK VQMGDNSLFD  60
   61 RPNSNTNGIS PSDNIVDVDL NYERSDQGNN

[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	0.416	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.417	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.437	a.144.1	PABC (PABP) domain
View	Download	0.482	a.24.4	Hemerythrin
View	Download	0.689	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.412	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.390	a.118.8	TPR-like
View	Download	0.365	a.7.6	Ribosomal protein S20
View	Download	0.351	a.71.1	Endoplasmic reticulum protein ERP29, C-domain
View	Download	0.338	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.334	a.24.17	Group V grass pollen allergen
View	Download	0.326	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.326	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.316	a.23.4	Mitochondrial import receptor subunit Tom20
View	Download	0.309	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.309	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.307	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.293	a.7.7	BAG domain
View	Download	0.290	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.288	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.286	a.144.1	PABC (PABP) domain
View	Download	0.281	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.271	a.24.4	Hemerythrin
View	Download	0.267	f.15.1	Small-conductance potassium channel
View	Download	0.264	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.261	a.159.1	Protein serine/threonine phosphatase 2C, C-terminal domain
View	Download	0.254	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.251	a.7.2	Enzyme IIa from lactose specific PTS, IIa-lac
View	Download	0.251	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.250	f.17.1	F1F0 ATP synthase subunit C
View	Download	0.244	a.77.1	DEATH domain
View	Download	0.233	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.233	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.233	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.223	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.223	a.64.1	Saposin
View	Download	0.222	a.76.1	Iron-dependent represor protein, dimerization domain
View	Download	0.222	f.14.1	Voltage-gated potassium channels
View	Download	0.222	f.14.1	Voltage-gated potassium channels
View	Download	0.220	a.163.1	Crustacean CHH/MIH/GIH neurohormone
View	Download	0.220	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.220	b.40.4	Nucleic acid-binding proteins
View	Download	0.219	f.15.1	Small-conductance potassium channel
View	Download	0.216	f.34.1	Mechanosensitive channel protein MscS (YggB), transmembrane region
View	Download	0.214	a.21.1	HMG-box
View	Download	0.213	d.58.16	Poly(A) polymerase, C-terminal domain
View	Download	0.213	a.2.8	Eukaryotic DNA topoisomerase I, dispensable insert domain
View	Download	0.211	a.47.2	t-snare proteins
View	Download	0.209	a.144.1	PABC (PABP) domain
View	Download	0.200	a.76.1	Iron-dependent represor protein, dimerization domain

Predicted Domain #4

Region A:
Residues: [462-830]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SSGNDSRRQS FFNSTSDTTL SRDETSLKER ELEVRMKELE LQERELELQR KALQQQQQYQ  60
   61 QRPPKQVYSG PSGTPTSGNN NNKSYNPNRK SSYSQPQHVA MMTSRGLHGP SAASSSPVIS 120
  121 ANNFVDPVSS GTPYSSNSSR FSQQIPSQQY MHTVKPTSRK NRSSVMPNIG YVPGLTNNEY 180
  181 GRKFNGNGMN GTQSRLNSLS NQSTFRSQQG PPITQQKSFQ NNGGSMRTNR IPSANYNISN 240
  241 QQSGFVNSIS SPNLSNLENR NTVQNSRNAD SAPCVNQLNS DSPPQLQSLS QNGTSKVPQI 300
  301 NITQPSPIQT NFATSDNPAA VIKLGTPSED TVSAAATANN ISTMGDESRK EDVKEKKKKK 360
  361 FSFFGKRKK

[Run NCBI BLAST on this sequence.]

Detection Method:	ORFEUS
Confidence:	7.06
Match:	1i3qA
Description:	RBP1
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