YRC Public Data Repository - Protein Structure Prediction

Protein:	PUS9
Organism:	Saccharomyces cerevisiae
Length:	462 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

[What does the above image mean?]

[Show Ginzu Version Information]

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 PUS9.

Description	E-value	Query Range	Subject Range
PUS9_YEAST - tRNA pseudouridine(32) synthase, mitochondrial OS=Saccharomyces cerevisiae (strain ATCC 204508 / S28... PUS9 - Mitochondrial tRNA:pseudouridine synthase, catalyzes the formation of pseudouridine at position 32 i...	0.0	[1..462]	[1..462]
gi\|15615105, gi\|... - gi\|15615105\|ref\|NP_243408.1\| hypothetical protein BH2542 [Bacillus halodurans C-125], gi\|10175162\|db... gi\|25322336 - pir\|\|F83967 hypothetical protein BH2542 [imported] - Bacillus halodurans (strain C-125)	2.0E-76	[116..419]	[6..300]
YBC5_CHLVI - Uncharacterized RNA pseudouridine synthase in bchI 5'region - Chlorobium vibrioforme Y723_CHLP8 - Uncharacterized RNA pseudouridine synthase Cpar_0723 OS=Chlorobaculum parvum (strain NCIB 8327) GN=C...	3.0E-75	[115..419]	[1..317]
EG12098 - 23S rRNA pseudouridine(1911,1915,1917) synthase / 23S rRNA pseudouridine(1911,1915,1917) synthase; m... gi\|238901755, gi... - gi\|238901755\|ref\|YP_002927551.1\| 23S rRNA pseudouridine synthase [Escherichia coli BW2952], gi\|23885... RLUD_ECOLI - Ribosomal large subunit pseudouridine synthase D (EC 5.4.99.-) (rRNA-uridine isomerase D) (rRNA pseu... gi\|251785917, gi... - gi\|251785917\|ref\|YP_003000221.1\| hypothetical protein B21_02448 [Escherichia coli BL21], gi\|24237819... gi\|124500887, gi... - gi\|124527995\|ref\|ZP_01699348.1\| pseudouridine synthase, RluA family [Escherichia coli B], gi\|1245008... gi\|254289326, gi... - gi\|254289326\|ref\|YP_003055074.1\| 23S rRNA pseudouridine synthase [Escherichia coli BL21(DE3)], gi\|25... EG12098 - 23S rRNA pseudouridine(1911,1915,1917) synthase / 23S rRNA pseudouridine(1911,1915,1917) synthase; m... gi\|226839295, gi... - gi\|254037671\|ref\|ZP_04871729.1\| 23S rRNA pseudouridine synthase D [Escherichia sp. 1_1_43], gi\|22683... gi\|253974466, gi... - gi\|254162565\|ref\|YP_003045673.1\| 23S rRNA pseudouridine synthase [Escherichia coli B str. REL606], g... gi\|194439337, gi... - gi\|83585274\|ref\|ZP_00923923.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|157162070, gi... - gi\|75196609\|ref\|ZP_00706679.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|188493998, gi... - gi\|75513200\|ref\|ZP_00735642.1\| COG0564: Pseudouridylate synthases, 23S RNA-specific [Escherichia col... gi\|89109396, gi\|... - gi\|89109396\|ref\|AP_003176.1\| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr. W31... gi\|169890034, gi... - gi\|170082199\|ref\|YP_001731519.1\| 23S rRNA pseudouridine synthase [Escherichia coli str. K-12 substr.... gi\|169754055, gi... - gi\|170019127\|ref\|YP_001724081.1\| 23S rRNA pseudouridine synthase D [Escherichia coli ATCC 8739], gi\|...	1.0E-74	[116..430]	[8..326]
gi\|32468746, gi\|... - gi\|50812225\|ref\|NP_389429.2\| hypothetical protein BSU15460 [Bacillus subtilis subsp. subtilis str. 1... YLYB_BACSU - Uncharacterized RNA pseudouridine synthase ylyB OS=Bacillus subtilis GN=ylyB PE=3 SV=2	3.0E-74	[118..418]	[7..297]
gi\|209762680, gi... - pir\|\|A91061 suppressor of ftsH mutation [imported] - Escherichia coli (strain O157:H7, substrain RI... gi\|13362928, gi\|... - gi\|15832711\|ref\|NP_311484.1\| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. Sakai]... gi\|168801712, gi... - gi\|189376176\|gb\|EDU94592.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... RLUD_ECO57 - Ribosomal large subunit pseudouridine synthase D OS=Escherichia coli O157:H7 GN=rluD PE=3 SV=3 gi\|168789497, gi... - gi\|189370886\|gb\|EDU89302.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|189003176, gi... - gi\|189003176\|gb\|EDU72162.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|187770638, gi... - gi\|187770638\|gb\|EDU34482.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|208821085, gi... - gi\|208821085\|ref\|ZP_03261405.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|208734055, gi... - gi\|208812778\|ref\|ZP_03254107.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|208728533, gi... - gi\|208808732\|ref\|ZP_03251069.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|195940189 - gi\|195940189\|ref\|ZP_03085571.1\| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 str. EC4... gi\|254794542, gi... - gi\|254794542\|ref\|YP_003079379.1\| 23S rRNA pseudouridine synthase [Escherichia coli O157:H7 str. TW14... gi\|168771700, gi... - gi\|189359603\|gb\|EDU78022.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|168762387, gi... - gi\|189367297\|gb\|EDU85713.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|189354550, gi... - gi\|189354550\|gb\|EDU72969.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|188014009, gi... - gi\|188014009\|gb\|EDU52131.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O157:... gi\|217326855, gi... - gi\|217326855\|ref\|ZP_03442938.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli O... gi\|209158035, gi... - gi\|209396635\|ref\|YP_002272067.1\| ribosomal large subunit pseudouridine synthase D [Escherichia coli ...	3.0E-74	[116..430]	[8..326]
RLUD_NEIMA - Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup A GN=rluD PE=3 ... gi\|11279836 - pir\|\|D81937 probable ribosomal large subunit pseudouridine synthase D NMA0908 [imported] - Neisseria... RLUD_NEIMA - Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup A / serotype 4A...	4.0E-74	[118..452]	[31..351]
RLUD_NEIMB - Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup B GN=rluD PE=3 ... gi\|11279837 - pir\|\|A81168 ribosomal large chain pseudouridine synthase D NMB0704 [imported] - Neisseria meningitid... RLUD_NEIMB - Ribosomal large subunit pseudouridine synthase D OS=Neisseria meningitidis serogroup B (strain MC58)...	1.0E-73	[118..452]	[31..351]
gi\|25322380 - gi\|25322380\|pir\|\|G85905 suppressor of ftsH mutation [imported] - Escherichia coli (strain O157:H7, ... gi\|12517018, gi\|... - gi\|15803118\|ref\|NP_289149.1\| 23S rRNA pseudouridine synthase D [Escherichia coli O157:H7 EDL933], gi...	1.0E-73	[116..430]	[8..326]

Back

Predicted Domain #1

Region A:
Residues: [1-127]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MQRNNRLRNL FTVPVIMARQ LKRNALSAGL AFAGNATSNE FDEHLQNEVE REREIQKKKK  60
   61 IKRTQSKKSP DLINKSTFQS RTIGSKKEKH RQLDPEYEIV IDGPLRKIKP YHFTYRTFCK 120
  121 ERWRDKK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	22.522879
Match:	1fjgD_
Description:	Ribosomal protein S4
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [128-193]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LVDVFISEFR DRESEYYKRT IENGDVHIND ETADLSTVIR NGDLITHQVH RHEPPVTSRP  60
   61 IKVIFE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.69897
Match:	1kskA_
Description:	Ribosomal small subunit pseudouridine 516 synthase RsuA; Pseudouridine synthase RsuA N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
pseudouridine synthase activity	5.19957135839682	bayes_pls_golite062009
intramolecular transferase activity	3.78688422405974	bayes_pls_golite062009
isomerase activity	2.91720316078381	bayes_pls_golite062009
catalytic activity	2.02180970970004	bayes_pls_golite062009
transcription regulator activity	1.21173188039059	bayes_pls_golite062009
DNA binding	0.950713703876672	bayes_pls_golite062009
nucleic acid binding	0.909704702595901	bayes_pls_golite062009
binding	0.730744558777463	bayes_pls_golite062009
RNA binding	0.706879359688019	bayes_pls_golite062009
transferase activity	0.237728328252954	bayes_pls_golite062009

Predicted Domain #3

Region A:
Residues: [194-380]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DDNIMVIDKP SGIPVHPTGR YRFNTITKML QNNLGFVVNP CNRLDRLTSG LMFLAKTPKG  60
   61 ADNIGDQLKA REVTKEYVAK VVGEFPETEV IVEKPLKLIE PRLALNAVCQ MDEKGAKHAK 120
  121 TVFNRISYDG KTSIVKCKPL TGRSHQIRVH LQYLGHPIAN DPIYSNDEVW GNNLGKGGQA 180
  181 DFDIVIT

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	36.69897
Match:	1kskA_
Description:	Ribosomal small subunit pseudouridine 516 synthase RsuA; Pseudouridine synthase RsuA N-terminal domain
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [381-462]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KLDEIGKRKP AKSWFHSNGG YGEVLRQEKC SICESDLYTD PGPNDLDLWL HAYLYESTET  60
   61 EEGTEKKKWC YKTEYPEWAL RR

[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.

		MCM Score	GO Score	GO Term	SCOP Match	SCOP Description
View	Download	0.262	0.134	nucleus	a.12.1	Kix domain of CBP (creb binding protein)
View	Download	0.298	0.115	cytoplasm	a.64.1	Saposin
View	Download	0.278	0.071	cytoplasm	d.141.1	Ribosomal protein L6
View	Download	0.390	0.000	nucleus	d.68.4	YhbY-like
View	Download	0.262	0.000	nucleus	d.58.49	YajQ-like
View	Download	0.259	N/A	N/A	a.28.1	ACP-like
View	Download	0.253	N/A	N/A	a.144.1	PABC (PABP) domain
View	Download	0.251	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.231	N/A	N/A	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.228	N/A	N/A	a.61.1	Retroviral matrix proteins
View	Download	0.222	N/A	N/A	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.216	N/A	N/A	a.77.1	DEATH domain
View	Download	0.215	N/A	N/A	a.74.1	Cyclin-like
View	Download	0.210	N/A	N/A	a.61.1	Retroviral matrix proteins

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: