YRC Public Data Repository - Protein Structure Prediction

Protein:	NEW1
Organism:	Saccharomyces cerevisiae
Length:	1196 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 NEW1.

Description	E-value	Query Range	Subject Range
NEW1 - ATP binding cassette protein that cosediments with polysomes and is required for biogenesis of the s... NEW1_YEAST - [NU+] prion formation protein 1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=NEW1 PE=...	0.0	[1..1196]	[1..1196]
gi\|2707897 - gi\|2707897\|gb\|AAC35391.1\| elongation-like factor [Candida albicans]	0.0	[28..1196]	[30..1191]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[126..1116]	[1..985]
EF3_CANGA - Elongation factor 3 OS=Candida glabrata (strain ATCC 2001 / CBS 138 / JCM 3761 / NBRC 0622 / NRRL Y-... EF3_CANGA - Elongation factor 3 OS=Candida glabrata GN=TEF3 PE=3 SV=2	0.0	[134..1131]	[4..995]
EF3_SCHPO - Elongation factor 3 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=tef3 PE=1 SV=1 tef3 - translation elongation factor eEF3	0.0	[126..1165]	[1..1040]
gi\|32416300, gi\|... - gi\|32416300\|ref\|XP_328628.1\| hypothetical protein [Neurospora crassa], gi\|28924044\|gb\|EAA33202.1\| el... gi\|85107753 - gi\|85107753\|ref\|XP_962438.1\| elongation factor 3 [Neurospora crassa OR74A]	0.0	[128..1196]	[2..1055]

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Predicted Domain #1

Region A:
Residues: [1-172]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MPPKKFKDLN SFLDDQPKDP NLVASPFGGY FKNPAADAGS NNASKKSSYQ QQRNWKQGGN  60
   61 YQQGGYQSYN SNYNNYNNYN NYNNYNNYNN YNKYNGQGYQ KSTYKQSAVT PNQSGTPTPS 120
  121 ASTTSLTSLN EKLSNLELTP ISQFLSKIPE CQSITDCKNQ IKLIIEEFGK EG

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this domain.

Predicted Domain #2

Region A:
Residues: [173-280]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NSTGEKIEEW KIVDVLSKFI KPKNPSLVRE SAMLIISNIA QFFSGKPPQE AYLLPFFNVA  60
   61 LDCISDKENT VKRAAQHAID SLLNCFPMEA LTCFVLPTIL DYLSSGAK

[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	0.851	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.1	ARM repeat
View	Download	0.965	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.9	ENTH/VHS domain
View	Download	0.869	0.004	ATPase activity, coupled to transmembrane movement of substances	a.46.1	Methionine synthase domain
View	Download	0.784	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.9	ENTH/VHS domain
View	Download	0.732	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.11	Cytochrome c oxidase subunit E
View	Download	0.637	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.17	Group V grass pollen allergen
View	Download	0.637	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.8	TPR-like
View	Download	0.629	0.004	ATPase activity, coupled to transmembrane movement of substances	a.74.1	Cyclin-like
View	Download	0.608	0.004	ATPase activity, coupled to transmembrane movement of substances	a.61.1	Retroviral matrix proteins
View	Download	0.581	0.004	ATPase activity, coupled to transmembrane movement of substances	a.85.1	Hemocyanin, N-terminal domain
View	Download	0.551	0.004	ATPase activity, coupled to transmembrane movement of substances	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.537	0.004	ATPase activity, coupled to transmembrane movement of substances	a.80.1	DNA polymerase III clamp loader subunits, C-terminal domain
View	Download	0.527	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.503	0.004	ATPase activity, coupled to transmembrane movement of substances	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.496	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.492	0.004	ATPase activity, coupled to transmembrane movement of substances	a.11.1	Acyl-CoA binding protein
View	Download	0.455	0.004	ATPase activity, coupled to transmembrane movement of substances	a.7.6	Ribosomal protein S20
View	Download	0.453	0.004	ATPase activity, coupled to transmembrane movement of substances	a.126.1	Serum albumin-like
View	Download	0.452	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.1	ARM repeat
View	Download	0.449	0.004	ATPase activity, coupled to transmembrane movement of substances	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.447	0.004	ATPase activity, coupled to transmembrane movement of substances	a.74.1	Cyclin-like
View	Download	0.434	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.434	0.004	ATPase activity, coupled to transmembrane movement of substances	a.74.1	Cyclin-like
View	Download	0.429	0.004	ATPase activity, coupled to transmembrane movement of substances	a.74.1	Cyclin-like
View	Download	0.421	0.004	ATPase activity, coupled to transmembrane movement of substances	a.27.1	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
View	Download	0.417	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.8	TPR-like
View	Download	0.409	0.004	ATPase activity, coupled to transmembrane movement of substances	c.78.2	Aspartate/glutamate racemase
View	Download	0.405	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.398	0.004	ATPase activity, coupled to transmembrane movement of substances	e.37.1	Bifunctional dehydrogenase/ferrochelatase Met8p, dimerisation and C-terminal domains
View	Download	0.380	0.004	ATPase activity, coupled to transmembrane movement of substances	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.380	0.004	ATPase activity, coupled to transmembrane movement of substances	a.142.1	PTS-regulatory domain, PRD
View	Download	0.378	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.2	alpha-helical ferredoxin
View	Download	0.370	0.004	ATPase activity, coupled to transmembrane movement of substances	d.52.3	Prokaryotic type KH domain (KH-domain type II)
View	Download	0.361	0.004	ATPase activity, coupled to transmembrane movement of substances	d.122.1	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
View	Download	0.360	0.004	ATPase activity, coupled to transmembrane movement of substances	a.56.1	CO dehydrogenase ISP C-domain like
View	Download	0.358	0.004	ATPase activity, coupled to transmembrane movement of substances	a.39.1	EF-hand
View	Download	0.355	0.004	ATPase activity, coupled to transmembrane movement of substances	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.352	0.004	ATPase activity, coupled to transmembrane movement of substances	f.14.1	Voltage-gated potassium channels
View	Download	0.349	0.004	ATPase activity, coupled to transmembrane movement of substances	d.56.1	GroEL-intermediate domain like
View	Download	0.342	0.004	ATPase activity, coupled to transmembrane movement of substances	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.339	0.004	ATPase activity, coupled to transmembrane movement of substances	a.3.1	Cytochrome c
View	Download	0.337	0.004	ATPase activity, coupled to transmembrane movement of substances	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.335	0.004	ATPase activity, coupled to transmembrane movement of substances	a.60.9	lambda integrase-like, N-terminal domain
View	Download	0.335	0.004	ATPase activity, coupled to transmembrane movement of substances	a.13.1	alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View	Download	0.333	0.004	ATPase activity, coupled to transmembrane movement of substances	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.332	0.004	ATPase activity, coupled to transmembrane movement of substances	a.165.1	Myosin phosphatase inhibitor 17kDa protein, CPI-17
View	Download	0.330	0.004	ATPase activity, coupled to transmembrane movement of substances	d.95.2	Homing endonucleases
View	Download	0.329	0.004	ATPase activity, coupled to transmembrane movement of substances	a.4.1	Homeodomain-like
View	Download	0.329	0.004	ATPase activity, coupled to transmembrane movement of substances	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.321	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.319	0.004	ATPase activity, coupled to transmembrane movement of substances	a.149.1	RNase III endonuclease catalytic domain
View	Download	0.317	0.004	ATPase activity, coupled to transmembrane movement of substances	a.48.3	Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View	Download	0.314	0.004	ATPase activity, coupled to transmembrane movement of substances	a.29.2	Bromodomain
View	Download	0.313	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.12	Ran-GTPase activating protein 1 (RanGAP1), C-terminal domain
View	Download	0.312	0.004	ATPase activity, coupled to transmembrane movement of substances	a.71.1	Endoplasmic reticulum protein ERP29, C-domain
View	Download	0.311	0.004	ATPase activity, coupled to transmembrane movement of substances	d.14.1	Ribosomal protein S5 domain 2-like
View	Download	0.307	0.004	ATPase activity, coupled to transmembrane movement of substances	d.110.2	GAF domain-like
View	Download	0.299	0.004	ATPase activity, coupled to transmembrane movement of substances	a.60.5	Barrier-to-autointegration factor, BAF
View	Download	0.299	0.004	ATPase activity, coupled to transmembrane movement of substances	d.150.1	4'-phosphopantetheinyl transferase
View	Download	0.296	0.004	ATPase activity, coupled to transmembrane movement of substances	d.110.4	SNARE-like
View	Download	0.294	0.004	ATPase activity, coupled to transmembrane movement of substances	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain
View	Download	0.292	0.004	ATPase activity, coupled to transmembrane movement of substances	a.156.1	S13-like H2TH domain
View	Download	0.287	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.284	0.004	ATPase activity, coupled to transmembrane movement of substances	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.284	0.004	ATPase activity, coupled to transmembrane movement of substances	a.26.1	4-helical cytokines
View	Download	0.281	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.13	Arp2/3 complex 16 kDa subunit ARPC5
View	Download	0.274	0.004	ATPase activity, coupled to transmembrane movement of substances	f.1.4	Bcl-2 inhibitors of programmed cell death
View	Download	0.273	0.004	ATPase activity, coupled to transmembrane movement of substances	a.52.1	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin
View	Download	0.272	0.004	ATPase activity, coupled to transmembrane movement of substances	f.32.1	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)
View	Download	0.270	0.004	ATPase activity, coupled to transmembrane movement of substances	c.102.1	Cell-division inhibitor MinC, N-terminal domain
View	Download	0.268	0.004	ATPase activity, coupled to transmembrane movement of substances	a.133.1	Phospholipase A2, PLA2
View	Download	0.266	0.004	ATPase activity, coupled to transmembrane movement of substances	e.40.1	Cullin homology domain
View	Download	0.264	0.004	ATPase activity, coupled to transmembrane movement of substances	d.8.1	Urease, gamma-subunit
View	Download	0.264	0.004	ATPase activity, coupled to transmembrane movement of substances	a.7.1	Spectrin repeat
View	Download	0.264	0.004	ATPase activity, coupled to transmembrane movement of substances	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.263	0.004	ATPase activity, coupled to transmembrane movement of substances	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.259	0.004	ATPase activity, coupled to transmembrane movement of substances	a.61.1	Retroviral matrix proteins
View	Download	0.254	0.004	ATPase activity, coupled to transmembrane movement of substances	a.74.1	Cyclin-like
View	Download	0.253	0.004	ATPase activity, coupled to transmembrane movement of substances	d.58.4	Dimeric alpha+beta barrel
View	Download	0.252	0.004	ATPase activity, coupled to transmembrane movement of substances	a.118.1	ARM repeat
View	Download	0.250	0.004	ATPase activity, coupled to transmembrane movement of substances	a.3.1	Cytochrome c
View	Download	0.248	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.248	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.11	Bacterial GAP domain
View	Download	0.245	0.004	ATPase activity, coupled to transmembrane movement of substances	a.26.1	4-helical cytokines
View	Download	0.242	0.004	ATPase activity, coupled to transmembrane movement of substances	d.58.26	GHMP Kinase, C-terminal domain
View	Download	0.236	0.004	ATPase activity, coupled to transmembrane movement of substances	d.224.1	SufE-like
View	Download	0.231	0.004	ATPase activity, coupled to transmembrane movement of substances	d.52.2	GMP synthetase C-terminal dimerisation domain
View	Download	0.229	0.004	ATPase activity, coupled to transmembrane movement of substances	d.202.1	Transcription factor NusA, N-terminal domain
View	Download	0.226	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.17	Group V grass pollen allergen
View	Download	0.226	0.004	ATPase activity, coupled to transmembrane movement of substances	a.39.1	EF-hand
View	Download	0.226	0.004	ATPase activity, coupled to transmembrane movement of substances	b.40.1	Staphylococcal nuclease
View	Download	0.220	0.004	ATPase activity, coupled to transmembrane movement of substances	a.69.3	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View	Download	0.217	0.004	ATPase activity, coupled to transmembrane movement of substances	d.58.41	SEA domain
View	Download	0.216	0.004	ATPase activity, coupled to transmembrane movement of substances	a.61.1	Retroviral matrix proteins
View	Download	0.211	0.004	ATPase activity, coupled to transmembrane movement of substances	a.51.1	Cytochrome c oxidase subunit h
View	Download	0.209	0.004	ATPase activity, coupled to transmembrane movement of substances	a.39.1	EF-hand
View	Download	0.207	0.004	ATPase activity, coupled to transmembrane movement of substances	a.75.1	Ribosomal protein S7
View	Download	0.207	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.9	alpha-catenin/vinculin
View	Download	0.207	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.206	0.004	ATPase activity, coupled to transmembrane movement of substances	a.1.1	Globin-like
View	Download	0.205	0.004	ATPase activity, coupled to transmembrane movement of substances	a.79.1	Antitermination factor NusB
View	Download	0.205	0.004	ATPase activity, coupled to transmembrane movement of substances	a.71.2	Helical domain of Sec23/24
View	Download	0.204	0.004	ATPase activity, coupled to transmembrane movement of substances	c.8.5	GroEL apical domain-like
View	Download	0.203	0.004	ATPase activity, coupled to transmembrane movement of substances	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.203	0.004	ATPase activity, coupled to transmembrane movement of substances	a.24.16	Nucleotidyltransferase substrate binding subunit/domain
View	Download	0.201	0.004	ATPase activity, coupled to transmembrane movement of substances	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators

Predicted Domain #3

Region A:
Residues: [281-427]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 WQAKMAALSV VDRIREDSAN DLLELTFKDA VPVLTDVATD FKPELAKQGY KTLLDYVSIL  60
   61 DNLDLSPRYK LIVDTLQDPS KVPESVKSLS SVTFVAEVTE PSLSLLVPIL NRSLNLSSSS 120
  121 QEQLRQTVIV VENLTRLVNN RNEIESF

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.09691
Match:	1ii8B_
Description:	Crystal structure of the P. furiosus Rad50 ATPase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [428-498]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IPLLLPGIQK VVDTASLPEV RELAEKALNV LKEDDEADKE NKFSGRLTLE EGRDFLLDHL  60
   61 KDIKADDSCF V

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	6.09691
Match:	1ii8B_
Description:	Crystal structure of the P. furiosus Rad50 ATPase domain
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [499-564]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPYMNDETVI KYMSKILTVD SNVNDWKRLE DFLTAVFGGS DSQREFVKQD FIHNLRALFY  60
   61 QEKERA

[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.

Found no structure predictions for this domain.

Predicted Domain #6

Region A:
Residues: [565-767]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DEDEGIEIVN TDFSLAYGSR MLLNKTNLRL LKGHRYGLCG RNGAGKSTLM RAIANGQLDG  60
   61 FPDKDTLRTC FVEHKLQGEE GDLDLVSFIA LDEELQSTSR EEIAAALESV GFDEERRAQT 120
  121 VGSLSGGWKM KLELARAMLQ KADILLLDEP TNHLDVSNVK WLEEYLLEHT DITSLIVSHD 180
  181 SGFLDTVCTD IIHYENKKLA YYK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	118.045757
Match:	1oxsC_
Description:	Glucose transport protein GlcV, N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [768-1033]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GNLAAFVEQK PEAKSYYTLT DSNAQMRFPP PGILTGVKSN TRAVAKMTDV TFSYPGAQKP  60
   61 SLSHVSCSLS LSSRVACLGP NGAGKSTLIK LLTGELVPNE GKVEKHPNLR IGYIAQHALQ 120
  121 HVNEHKEKTA NQYLQWRYQF GDDREVLLKE SRKISEDEKE MMTKEIDIDD GRGKRAIEAI 180
  181 VGRQKLKKSF QYEVKWKYWK PKYNSWVPKD VLVEHGFEKL VQKFDDHEAS REGLGYRELI 240
  241 PSVITKHFED VGLDSEIANH TPLGSL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	93.679424
Match:	1jsqA_
Description:	MsbA
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [1034-1196]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 SGGQLVKVVI AGAMWNNPHL LVLDEPTNYL DRDSLGALAV AIRDWSGGVV MISHNNEFVG  60
   61 ALCPEQWIVE NGKMVQKGSA QVDQSKFEDG GNADAVGLKA SNLAKPSVDD DDSPANIKVK 120
  121 QRKKRLTRNE KKLQAERRRL RYIEWLSSPK GTPKPVDTDD EED

[Run NCBI BLAST on this sequence.]

Detection Method:

MSA

Shown below are all of our structure predictions for this domain.
Click here to view only most confident match.

Found no structure predictions for this 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