YRC Public Data Repository - Protein Structure Prediction

Protein:	RRP5
Organism:	Saccharomyces cerevisiae
Length:	1729 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 RRP5.

Description	E-value	Query Range	Subject Range
RRP5_YEAST - rRNA biogenesis protein RRP5 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=RRP5 PE=1 S... RRP5 - RNA binding protein with preference for single stranded tracts of U's involved in synthesis of both ...	0.0	[1..1729]	[1..1729]
RRP5_SCHPO - rRNA biogenesis protein rrp5 OS=Schizosaccharomyces pombe (strain 972 / ATCC 24843) GN=rrp5 PE=1 SV=... SPCC1183.07 - U3 snoRNP-associated protein Rrp5	0.0	[2..1725]	[1..1689]
gi\|15229915 - gi\|15229915\|ref\|NP_187803.1\| S1 RNA-binding domain-containing protein [Arabidopsis thaliana]	0.0	[4..1718]	[16..1832]
gi\|168272922 - gi\|168272922\|dbj\|BAG10300.1\| RRP5 protein homolog [synthetic construct] PDCD11 - programmed cell death 11	0.0	[35..1723]	[18..1772]
gi\|13363518, gi\|... - gi\|15833299\|ref\|NP_312072.1\| polynucleotide phosphorylase [Escherichia coli O157:H7], gi\|13363518\|db... gi\|74313701, gi\|... - gi\|74313701\|ref\|YP_312120.1\| polynucleotide phosphorylase/polyadenylase [Shigella sonnei Ss046], gi\|... gi\|209920641, gi... - gi\|209920641\|ref\|YP_002294725.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli SE11],... gi\|209758380, gi... - pir\|\|H85979 polynucleotide phosphorylase [imported] - Escherichia coli (strain O157:H7, substrain E... gi\|218353603, gi... - gi\|218696871\|ref\|YP_002404538.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli 55989]... gi\|218701935, gi... - gi\|218701935\|ref\|YP_002409564.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli IAI39]... gi\|12517775, gi\|... - gi\|15803706\|ref\|NP_289740.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7 ED... gi\|13363518, gi\|... - gi\|15833299\|ref\|NP_312072.1\| polynucleotide phosphorylase/polyadenylase [Escherichia coli O157:H7 st...	0.0	[700..1331]	[88..709]
EG10743 - polynucleotide phosphorylase /polyadenylase / Polynucleotide phosphorylase; exoribonuclease; PNPase c... EG10743 - polynucleotide phosphorylase /polyadenylase / Polynucleotide phosphorylase; exoribonuclease; PNPase c... gi\|194422295, gi... - gi\|83585805\|ref\|ZP_00924446.1\| COG1185: Polyribonucleotide nucleotidyltransferase (polynucleotide ph... PNP_ECOBW - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=pnp ... PNP_ECOHS - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli O9:H4 (strain HS) GN=pnp PE=3 SV=1 gi\|253323044, gi... - gi\|253772000\|ref\|YP_003034831.1\| Polyribonucleotide nucleotidyltransferase [Escherichia coli BL21(DE... gi\|254038330, gi... - gi\|254038330\|ref\|ZP_04872388.1\| polynucleotide phosphorylase/polyadenylase [Escherichia sp. 1_1_43],... PNP_ECOLI - Polyribonucleotide nucleotidyltransferase (EC 2.7.7.8) (Polynucleotide phosphorylase) (PNPase) - Esc... PNP_ECODH - Polyribonucleotide nucleotidyltransferase OS=Escherichia coli (strain K12 / DH10B) GN=pnp PE=3 SV=2	0.0	[700..1331]	[65..686]
gi\|7507776 - gi\|7507776\|pir\|\|T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans	0.0	[700..1331]	[88..709]

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Predicted Domain #1

Region A:
Residues: [1-69]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVASTKRKRD EDFPLSREDS TKQPSTSSLV RNTEEVSFPR GGASALTPLE LKQVANEAAS  60
   61 DVLFGNESV

[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 constituent of ribosome	5.1118741250402	bayes_pls_golite062009
structural molecule activity	4.51553901145182	bayes_pls_golite062009
nuclease activity	3.11657409772275	bayes_pls_golite062009
	3.02322635335914	bayes_pls_golite062009
ribonuclease activity	2.66669472409706	bayes_pls_golite062009
exoribonuclease activity	2.4082195258205	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	2.3619669410791	bayes_pls_golite062009
RNA binding	2.33019817554364	bayes_pls_golite062009
3'-5'-exoribonuclease activity	2.12039058720352	bayes_pls_golite062009
exonuclease activity	1.87925169250843	bayes_pls_golite062009
endoribonuclease activity, producing 5'-phosphomonoesters	1.74431545836806	bayes_pls_golite062009
translation regulator activity	1.66546288751201	bayes_pls_golite062009
translation factor activity, nucleic acid binding	1.61238850131825	bayes_pls_golite062009
endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	1.59628511603826	bayes_pls_golite062009
3'-5' exonuclease activity	1.44123900197846	bayes_pls_golite062009
translation initiation factor activity	1.27539679024898	bayes_pls_golite062009
catalytic activity	1.25233849524628	bayes_pls_golite062009
hydrolase activity, acting on ester bonds	1.19753926150484	bayes_pls_golite062009
nucleic acid binding	1.12235348738959	bayes_pls_golite062009
transcription regulator activity	1.10433412699603	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	1.07288786419238	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	1.07285050275461	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	1.07285050275461	bayes_pls_golite062009
excinuclease ABC activity	1.05238432657007	bayes_pls_golite062009
endonuclease activity	0.991569665925888	bayes_pls_golite062009
damaged DNA binding	0.95191912850966	bayes_pls_golite062009
binding	0.762139256580538	bayes_pls_golite062009
DNA binding	0.710663468386339	bayes_pls_golite062009
translation elongation factor activity	0.55678032558705	bayes_pls_golite062009
exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters	0.52627345520111	bayes_pls_golite062009
DNA-directed RNA polymerase activity	0.39251242706379	bayes_pls_golite062009
RNA polymerase activity	0.39251242706379	bayes_pls_golite062009
transcription factor activity	0.332903382446869	bayes_pls_golite062009
sequence-specific DNA binding	0.21650406007586	bayes_pls_golite062009
ligase activity	0.148928528645156	bayes_pls_golite062009
mRNA binding	0.10617671731447	bayes_pls_golite062009
deoxyribonuclease activity	0.07404631453071	bayes_pls_golite062009
endoribonuclease activity	0.016619833072142	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [70-231]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KASEPASRPL KKKKTTKKST SKDSEASSAN SDEARAGLIE HVNFKTLKNG SSLLGQISAI  60
   61 TKQDLCITFT DGISGYVNLT HISEEFTSIL EDLDEDMDSD TDAADEKKSK VEDAEYESSD 120
  121 DEDEKLDKSN ELPNLRRYFH IGQWLRCSVI KNTSLEPSTK KS

[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 functions:

Term	Confidence	Notes
structural constituent of ribosome	5.22538452462352	bayes_pls_golite062009
structural molecule activity	4.65301390020308	bayes_pls_golite062009
RNA binding	3.36396086314433	bayes_pls_golite062009
transcription regulator activity	3.24341202600661	bayes_pls_golite062009
3'-5'-exoribonuclease activity	2.16830676862423	bayes_pls_golite062009
exoribonuclease activity, producing 5'-phosphomonoesters	1.94887328847363	bayes_pls_golite062009
exoribonuclease activity	1.90081280972069	bayes_pls_golite062009
nucleic acid binding	1.53286219413126	bayes_pls_golite062009
	1.49823328757628	bayes_pls_golite062009
binding	1.38311294671926	bayes_pls_golite062009
ribonuclease activity	1.31550811238109	bayes_pls_golite062009
translation initiation factor activity	1.27539679024898	bayes_pls_golite062009
aminoacyl-tRNA ligase activity	1.07288786419238	bayes_pls_golite062009
ligase activity, forming aminoacyl-tRNA and related compounds	1.07285050275461	bayes_pls_golite062009
ligase activity, forming carbon-oxygen bonds	1.07285050275461	bayes_pls_golite062009
transcription termination factor activity	1.01993495617192	bayes_pls_golite062009
DNA binding	0.86484629764139	bayes_pls_golite062009
mRNA binding	0.650019633484614	bayes_pls_golite062009
3'-5' exonuclease activity	0.477960254167	bayes_pls_golite062009
RNA polymerase activity	0.39251242706379	bayes_pls_golite062009
DNA-directed RNA polymerase activity	0.39251242706379	bayes_pls_golite062009
tRNA-specific ribonuclease activity	0.383567539949931	bayes_pls_golite062009
transcription factor activity	0.298729064067577	bayes_pls_golite062009
protein binding	0.292595239533272	bayes_pls_golite062009
transferase activity, transferring phosphorus-containing groups	0.1757578095579	bayes_pls_golite062009
ligase activity	0.148928528645156	bayes_pls_golite062009
catalytic activity	0.10089766806364	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [232-295]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KKKRIELTIE PSSVNIYADE DLVKSTSIQC AVKSIEDHGA TLDVGLPGFT GFIAKKDFGN  60
   61 FEKL

[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	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.816	0.658	nucleolus	b.34.2	SH3-domain

Predicted functions:

Term	Confidence	Notes
binding	2.12690485191789	bayes_pls_golite062009
RNA binding	2.0770703064779	bayes_pls_golite062009
protein binding	1.39668540998298	bayes_pls_golite062009
transcription regulator activity	1.26149030245805	bayes_pls_golite062009
nucleic acid binding	1.01193875360949	bayes_pls_golite062009
DNA binding	0.80346414607277	bayes_pls_golite062009
transcription factor activity	0.374364600772076	bayes_pls_golite062009
signal sequence binding	0.0529781042891342	bayes_pls_golite062009

Predicted Domain #4

Region A:
Residues: [296-454]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LPGAVFLGNI TKKSDRSIVV NTDFSDKKNK ITQISSIDAI IPGQIVDLLC ESITKNGIAG  60
   61 KVFGLVSGVV NVSHLRTFSE EDLKHKFVIG SSIRCRIIAC LENKSGDKVL ILSNLPHILK 120
  121 LEDALRSTEG LDAFPIGYTF ESCSIKGRDS EYLYLALDD

[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 #5

Region A:
Residues: [455-550]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DRLGKVHSSR VGEIENSENL SSRVLGYSPV DDIYQLSTDP KYLKLKYLRT NDIPIGELLP  60
   61 SCEITSVSSS GIELKIFNGQ FKASVPPLHI SDTRLV

[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 #6

Region A:
Residues: [551-689]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YPERKFKIGS KVKGRVISVN SRGNVHVTLK KSLVNIEDNE LPLVSTYENA KNIKEKNEKT  60
   61 LATIQVFKPN GCIISFFGGL SGFLPNSEIS EVFVKRPEEH LRLGQTVIVK LLDVDADRRR 120
  121 IIATCKVSNE QAAQQKDTI

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	56.522879
Match:	1sro__
Description:	S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase
Matching Structure (courtesy of the PDB):

Predicted Domain #7

Region A:
Residues: [690-785]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ENIVPGRTII TVHVIEKTKD SVIVEIPDVG LRGVIYVGHL SDSRIEQNRA QLKKLRIGTE  60
   61 LTGLVIDKDT RTRVFNMSLK SSLIKDAKKE TLPLTY

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [858-880]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 FLLSLKAPKV KEEKKKVESN IED

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.30103
Match:	1e3pA_
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted Domain #8

Region A:
Residues: [786-857]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDVKDLNKDV PMHAYIKSIS DKGLFVAFNG KFIGLVLPSY AVDSRDIDIS KAFYINQSVT  60
   61 VYLLRTDDKN QK

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [881-943]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PVDSSIKSWD DLSIGSIVKA KIKSVKKNQL NVILAANLHG RVDIAEVFDT YEEITDKKQP  60
   61 LSN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.30103
Match:	1e3pA_
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted Domain #9

Region A:
Residues: [944-966]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 YKKDDVIKVK IIGNHDVKSH KFL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [1097-1175]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KIAEKYVLLD LGNKVTGISF ITDALNDFSL TLKEAFEDKI NNVIPTTVLS VDEQNKKIEL  60
   61 SLRPATAKTR SIKSHEDLK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.30103
Match:	1e3pA_
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted Domain #10

Region A:
Residues: [967-1096]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PITHKISKAS VLELSMKPSE LKSKEVHTKS LEEINIGQEL TGFVNNSSGN HLWLTISPVL  60
   61 KARISLLDLA DNDSNFSENI ESVFPLGSAL QVKVASIDRE HGFVNAIGKS HVDINMSTIK 120
  121 VGDELPGRVL

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [1176-1369]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 QGEIVDGIVK NVNDKGIFVY LSRKVEAFVP VSKLSDSYLK EWKKFYKPMQ YVLGKVVTCD  60
   61 EDSRISLTLR ESEINGDLKV LKTYSDIKAG DVFEGTIKSV TDFGVFVKLD NTVNVTGLAH 120
  121 ITEIADKKPE DLSALFGVGD RVKAIVLKTN PEKKQISLSL KASHFSKEAE LASTTTTTTT 180
  181 VDQLEKEDED EVMA

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	75.30103
Match:	1e3pA_
Description:	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3; S1 RNA-binding domain of polyribonucleotide phosphorylase, PNPase; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 1 and 4; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 6; Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domains 2 and 5
Matching Structure (courtesy of the PDB):

Predicted Domain #11

Region A:
Residues: [1370-1528]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DAGFNDSDSE SDIGDQNTEV ADRKPETSSD GLSLSAGFDW TASILDQAQE EEESDQDQED  60
   61 FTENKKHKHK RRKENVVQDK TIDINTRAPE SVADFERLLI GNPNSSVVWM NYMAFQLQLS 120
  121 EIEKARELAE RALKTINFRE EAEKLNIWIA MLNLENTFG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	23.69897
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
Matching Structure (courtesy of the PDB):

Predicted Domain #12

Region A:
Residues: [1529-1596]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 TEETLEEVFS RACQYMDSYT IHTKLLGIYE ISEKFDKAAE LFKATAKKFG GEKVSIWVSW  60
   61 GDFLISHN

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	23.69897
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
Matching Structure (courtesy of the PDB):

Predicted Domain #13

Region A:
Residues: [1597-1729]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EEQEARTILG NALKALPKRN HIEVVRKFAQ LEFAKGDPER GRSLFEGLVA DAPKRIDLWN  60
   61 VYVDQEVKAK DKKKVEDLFE RIITKKITRK QAKFFFNKWL QFEESEGDEK TIEYVKAKAT 120
  121 EYVASHESQK ADE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	23.69897
Match:	1fchA_
Description:	Peroxin pex5 (peroxisomal targeting signal 1 (PTS1) receptor)
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: