YRC Public Data Repository - Protein Structure Prediction

Protein:	DUR1,2
Organism:	Saccharomyces cerevisiae
Length:	1835 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 DUR1,2.

Description	E-value	Query Range	Subject Range
gi\|25400722 - pir\|\|H87475 urea amidolyase-related protein [imported] - Caulobacter crescentus gi\|13423266, gi\|... - gi\|16126072\|ref\|NP_420636.1\| urea amidolyase-related protein [Caulobacter crescentus CB15], gi\|13423... gi\|220964014, gi... - gi\|221234842\|ref\|YP_002517278.1\| urea carboxylase [Caulobacter crescentus NA1000], gi\|220964014\|gb\|A...	0.0	[632..1835]	[1..1203]
gi\|173122 - gi\|173122\|gb\|AAC41643.1\| urea amidolyase [Saccharomyces cerevisiae]	0.0	[1..1835]	[1..1835]
gi\|447739 - gi\|447739\|prf\|\|1915304A nylB upstream ORF	0.0	[12..1832]	[4..1830]
gi\|5457424 - gi\|5457424\|emb\|CAB48407.1\| urea amidolyase homologue [Pseudomonas fluorescens]	0.0	[632..1834]	[1..1213]
gi\|7438130 - pir\|\|S74380 biotin carboxylase accC - Synechocystis sp. (strain PCC 6803) gi\|16331500, gi\|... - gi\|16331500\|ref\|NP_442228.1\| acetyl-CoA carboxylase biotin carboxylase subunit [Synechocystis sp. PC...	0.0	[633..1074]	[3..446]
gi\|18144735, gi\|... - gi\|18310056\|ref\|NP_561990.1\| biotin carboxylase [Clostridium perfringens str. 13], gi\|18144735\|dbj\|B...	0.0	[632..1074]	[1..445]
gi\|25293960 - pir\|\|AH1923 biotin carboxylase [imported] - Nostoc sp. (strain PCC 7120) gi\|289133, gi\|10... - gi\|289133\|gb\|AAB51770.1\| biotin carboxylase, pir\|\|A53311 biotin carboxylase (EC 6.3.4.14) - Anabaena... ACCC_NOSS1 - Biotin carboxylase OS=Nostoc sp. (strain PCC 7120 / UTEX 2576) GN=accC PE=3 SV=1	0.0	[633..1072]	[3..444]
gi\|56685145, gi\|... - gi\|56750186\|ref\|YP_170887.1\| acetyl-CoA carboxylase biotin carboxylase subunit [Synechococcus elonga... gi\|1399818, gi\|4... - gi\|81300188\|ref\|YP_400396.1\| acetyl-CoA carboxylase biotin carboxylase subunit [Synechococcus elonga...	0.0	[633..1072]	[3..444]
gi\|17937288, gi\|... - gi\|17937288\|ref\|NP_534077.1\| propionyl-coenzyme A carboxylase, alpha polypeptide [Agrobacterium tume... gi\|25293906 - pir\|\|AC2997 hypothetical protein pccA [imported] - Agrobacterium tumefaciens (strain C58, Dupont)	0.0	[622..1170]	[1..579]

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Predicted Domain #1

Region A:
Residues: [1-483]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTVSSDTTAE ISLGWSIQDW IDFHKSSSSQ ASLRLLESLL DSQNVAPVDN AWISLISKEN  60
   61 LLHQFQILKS RENKETLPLY GVPIAVKDNI DVRGLPTTAA CPSFAYEPSK DSKVVELLRN 120
  121 AGAIIVGKTN LDQFATGLVG TRSPYGKTPC AFSKEHVSGG SSAGSASVVA RGIVPIALGT 180
  181 DTAGSGRVPA ALNNLIGLKP TKGVFSCQGV VPACKSLDCV SIFALNLSDA ERCFRIMCQP 240
  241 DPDNDEYSRP YVSNPLKKFS SNVTIAIPKN IPWYGETKNP VLFSNAVENL SRTGANVIEI 300
  301 DFEPLLELAR CLYEGTWVAE RYQAIQSFLD SKPPKESLDP TVISIIEGAK KYSAVDCFSF 360
  361 EYKRQGILQK VRRLLESVDV LCVPTCPLNP TMQQVADEPV LVNSRQGTWT NFVNLADLAA 420
  421 LAVPAGFRDD GLPNGITLIG KKFTDYALLE LANRYFQNIF PNGSRTYGTF TSSSVKPAND 480
  481 QLV

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	194.980454
Match:	1gr8A_
Description:	No description for 1gr8A_ was found.

Predicted functions:

Term	Confidence	Notes
ligase activity	7.63077869457441	bayes_pls_golite062009
glutaminyl-tRNA synthase (glutamine-hydrolyzing) activity	7.42914157198604	bayes_pls_golite062009
binding	1.24905380693412	bayes_pls_golite062009
hydrolase activity	1.16287375250451	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	1.02750000262516	bayes_pls_golite062009
ligase activity, forming carbon-nitrogen bonds	0.977723384067654	bayes_pls_golite062009
catalytic activity	0.906509857495572	bayes_pls_golite062009
carbon-nitrogen ligase activity, with glutamine as amido-N-donor	0.461750895886233	bayes_pls_golite062009
protein binding	0.276132955069873	bayes_pls_golite062009
hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	0.0166505316914077	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [484-604]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GPDYDPSTSI KLAVVGAHLK GLPLHWQLEK VNATYLCTTK TSKAYQLFAL PKNGPVLKPG  60
   61 LRRVQDSNGS QIELEVYSVP KELFGAFISM VPEPLGIGSV ELESGEWIKS FICEESGYKA 120
  121 K

[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 functions:

Term	Confidence	Notes
structural molecule activity	1.24470630176758	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [605-735]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 GTVDITKYGG FRAYFEMLKK KESQKKKLFD TVLIANRGEI AVRIIKTLKK LGIRSVAVYS  60
   61 DPDKYSQHVT DADVSVPLHG TTAAQTYLDM NKIIDAAKQT NAQAIIPGYG FLSENADFSD 120
  121 ACTSAGITFV G

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1882.218487
Match:	1bncA_
Description:	Biotin carboxylase subunit of acetyl-CoA carboxylase (BC), C-domain; Biotin carboxylase subunit of acetyl-CoA carboxylase, (BC), N-domain; Biotin carboxylase subunit of acetyl-CoA carboxylase (BC), domain 2
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [736-762]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PSGDIIRGLG LKHSARQIAQ KAGVPLV

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [833-858]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 IENARHVEVQ LMGDGFGKAI ALGERD

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [872-963]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TPAPNLPEKT RLALRKAAES LGSLLNYKCA GTVEFIYDEK KDEFYFLEVN TRLQVEHPIT  60
   61 EMVTGLDLVE WMIRIAANDA PDFDSTKVEV NG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1882.218487
Match:	1bncA_
Description:	Biotin carboxylase subunit of acetyl-CoA carboxylase (BC), C-domain; Biotin carboxylase subunit of acetyl-CoA carboxylase, (BC), N-domain; Biotin carboxylase subunit of acetyl-CoA carboxylase (BC), domain 2
Matching Structure (courtesy of the PDB):

Predicted Domain #5

Region A:
Residues: [763-832]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGSLLITSVE EAKKVAAELE YPVMVKSTAG GGGIGLQKVD SEEDIEHIFE TVKHQGETFF  60
   61 GDAGVFLERF

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [859-871]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 CSLQRRNQKV IEE

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [964-1094]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VSMEARLYAE NPLKNFRPSP GLLVDVKFPD WARVDTWVKK GTNISPEYDP TLAKIIVHGK  60
   61 DRDDAISKLN QALEETKVYG CITNIDYLKS IITSDFFAKA KVSTNILNSY QYEPTAIEIT 120
  121 LPGAHTSIQD Y

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	1882.218487
Match:	1bncA_
Description:	Biotin carboxylase subunit of acetyl-CoA carboxylase (BC), C-domain; Biotin carboxylase subunit of acetyl-CoA carboxylase, (BC), N-domain; Biotin carboxylase subunit of acetyl-CoA carboxylase (BC), domain 2
Matching Structure (courtesy of the PDB):

Predicted Domain #6

Region A:
Residues: [1095-1417]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PGRVGYWRIG VPPSGPMDAY SFRLANRIVG NDYRTPAIEV TLTGPSIVFH CETVIAITGG  60
   61 TALCTLDGQE IPQHKPVEVK RGSTLSIGKL TSGCRAYLGI RGGIDVPKYL GSYSTFTLGN 120
  121 VGGYNGRVLK LGDVLFLPSN EENKSVECLP QNIPQSLIPQ ISETKEWRIG VTCGPHGSPD 180
  181 FFKPESIEEF FSEKWKVHYN SNRFGVRLIG PKPKWARSNG GEGGMHPSNT HDYVYSLGAI 240
  241 NFTGDEPVII TCDGPSLGGF VCQAVVPEAE LWKVGQVKPG DSIQFVPLSY ESSRSLKESQ 300
  301 DVAIKSLDGT KLRRLDSVSI LPS

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	190.244125
Match:	PF02626
Description:	Allophanate hydrolase subunit 2

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 functions:

Term	Confidence	Notes
ligase activity	6.81588178611521	bayes_pls_golite062009
peptidyl-prolyl cis-trans isomerase activity	1.05326644345172	bayes_pls_golite062009
binding	1.03084911722464	bayes_pls_golite062009
cis-trans isomerase activity	0.985752998974367	bayes_pls_golite062009
catalytic activity	0.748655649755714	bayes_pls_golite062009
nucleic acid binding	0.438324825951616	bayes_pls_golite062009
protein binding	0.130251391659493	bayes_pls_golite062009

Predicted Domain #7

Region A:
Residues: [1418-1655]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FETPILAQME KVNELSPKVV YRQAGDRYVL VEYGDNEMNF NISYRIECLI SLVKKNKTIG  60
   61 IVEMSQGVRS VLIEFDGYKV TQKELLKVLV AYETEIQFDE NWKITSNIIR LPMAFEDSKT 120
  121 LACVQRYQET IRSSAPWLPN NVDFIANVNG ISRNEVYDML YSARFMVLGL GDVFLGSPCA 180
  181 VPLDPRHRFL GSKYNPSRTY TERGAVGIGG MYMCIYAANS PGGYQLVGRT IPIWDKLC

[Run NCBI BLAST on this sequence.]

Detection Method:	Pfam
Confidence:	3.008774
Match:	PF02682
Description:	Allophanate hydrolase subunit 1

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 #8

Region A:
Residues: [1656-1751]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LAASSEVPWL MNPFDQVEFY PVSEEDLDKM TEDCDNGVYK VNIEKSVFDH QEYLRWINAN  60
   61 KDSITAFQEG QLGERAEEFA KLIQNANSEL KESVTV

[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.

		MCM Score	SCOP Match	SCOP Description
View	Download	0.810	c.58.1	Aminoacid dehydrogenase-like, N-terminal domain

Predicted Domain #9

Region A:
Residues: [1752-1835]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KPDEEEDFPE GAEIVYSEYS GRFWKSIASV GDVIEAGQGL LIIEAMKAEM IISAPKSGKI  60
   61 IKICHGNGDM VDSGDIVAVI ETLA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	46.09691
Match:	1dczA_
Description:	Biotin carboxyl carrier domain of transcarboxylase (TC 1.3S)
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

Predicted functions:

Predicted functions:

Predicted functions: