YRC Public Data Repository - Protein Structure Prediction

Protein:	SAM50
Organism:	Saccharomyces cerevisiae
Length:	484 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 SAM50.

Description	E-value	Query Range	Subject Range
BAMA_PHOLU - Outer membrane protein assembly factor BamA OS=Photorhabdus luminescens GN=bamA PE=3 SV=1	5.0E-89	[9..482]	[329..796]
gi\|45437431, gi\|... - gi\|45442566\|ref\|NP_994105.1\| outer membrane protein assembly factor YaeT [Yersinia pestis biovar Mic... gi\|167050489, gi... - gi\|167399781\|ref\|ZP_02305299.1\| surface antigen/outer membrane protein, OMP85 family [Yersinia pesti... gi\|21960049, gi\|... - gi\|22127003\|ref\|NP_670426.1\| outer membrane protein assembly factor YaeT [Yersinia pestis KIM], gi\|2... gi\|166211785, gi... - gi\|166211785\|ref\|ZP_02237820.1\| surface antigen/outer membrane protein, OMP85 family [Yersinia pesti... gi\|16121352, gi\|... - gi\|218928220\|ref\|YP_002346095.1\| outer membrane protein assembly factor YaeT [Yersinia pestis CO92],... gi\|167055752, gi... - gi\|167425352\|ref\|ZP_02317105.1\| surface antigen/outer membrane protein, OMP85 family [Yersinia pesti... BAMA_YERPS - Outer membrane protein assembly factor BamA OS=Yersinia pseudotuberculosis serotype I (strain IP3295... gi\|166962531, gi... - gi\|167419790\|ref\|ZP_02311543.1\| surface antigen/outer membrane protein, OMP85 family [Yersinia pesti... BAMA_YERPB - Outer membrane protein assembly factor BamA OS=Yersinia pseudotuberculosis serotype IB (strain PB1/+... BAMA_YERPY - Outer membrane protein assembly factor BamA OS=Yersinia pseudotuberculosis serotype O:3 (strain YPII... YAET_YERPS - Outer membrane protein assembly factor yaeT OS=Yersinia pseudotuberculosis GN=yaeT PE=3 SV=1 gi\|229837759, gi... - gi\|229837759\|ref\|ZP_04457919.1\| conserved protein [Yersinia pestis Pestoides A], gi\|229704136\|gb\|EEO... gi\|229840981, gi... - gi\|229840981\|ref\|ZP_04461140.1\| conserved protein [Yersinia pestis biovar Orientalis str. PEXU2], gi... gi\|229843082, gi... - gi\|229843082\|ref\|ZP_04463232.1\| conserved protein [Yersinia pestis biovar Orientalis str. India 195]... gi\|165912221, gi... - gi\|89105142\|ref\|ZP_01177667.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Yersinia pe... BAMA_YERPA - Outer membrane protein assembly factor BamA OS=Yersinia pestis bv. Antiqua (strain Antiqua) GN=bamA ... BAMA_YERPN - Outer membrane protein assembly factor BamA OS=Yersinia pestis bv. Antiqua (strain Nepal516) GN=bamA... gi\|165989161, gi... - gi\|166011895\|ref\|ZP_02232793.1\| surface antigen/outer membrane protein, OMP85 family [Yersinia pesti... gi\|165927078, gi... - gi\|165927078\|ref\|ZP_02222910.1\| surface antigen/outer membrane protein, OMP85 family [Yersinia pesti... gi\|149366947, gi... - gi\|149366947\|ref\|ZP_01888980.1\| putative surface antigen [Yersinia pestis CA88-4125], gi\|149290561\|g... BAMA_YERPG - Outer membrane protein assembly factor BamA OS=Yersinia pestis bv. Antiqua (strain Angola) GN=bamA P... BAMA_YERPP - Outer membrane protein assembly factor BamA OS=Yersinia pestis (strain Pestoides F) GN=bamA PE=3 SV=... BAMA_YERP3 - Outer membrane protein assembly factor BamA OS=Yersinia pseudotuberculosis serotype O:1b (strain IP ... BAMA_YERPE - Outer membrane protein assembly factor BamA OS=Yersinia pestis GN=bamA PE=3 SV=1	3.0E-86	[9..482]	[329..794]
gi\|254791310, gi... - gi\|254791310\|ref\|YP_003076147.1\| hypothetical protein ECSP_0176 [Escherichia coli O157:H7 str. TW143... gi\|253972197, gi... - gi\|254160296\|ref\|YP_003043404.1\| hypothetical protein ECB_00175 [Escherichia coli B str. REL606], gi... gi\|226840702, gi... - gi\|254037596\|ref\|ZP_04871673.1\| outer membrane protein assembly factor yaeT [Escherichia sp. 1_1_43]... gi\|253976406, gi... - gi\|254287099\|ref\|YP_003052847.1\| hypothetical protein ECD_00175 [Escherichia coli BL21(DE3)], gi\|253... gi\|251783735, gi... - gi\|251783735\|ref\|YP_002998039.1\| hypothetical protein B21_00174 [Escherichia coli BL21], gi\|24237600... BAMA_ECOBW - Outer membrane protein assembly factor BamA OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=ba... gi\|226902248, gi... - gi\|237704336\|ref\|ZP_04534817.1\| outer membrane protein assembly factor yaeT [Escherichia sp. 3_2_53F... gi\|227884910, gi... - gi\|227884910\|ref\|ZP_04002715.1\| outer membrane protein assembly factor YaeT [Escherichia coli 83972]... gi\|192959168, gi... - gi\|75238880\|ref\|ZP_00722862.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Escherichia... gi\|191172808, gi... - gi\|75240234\|ref\|ZP_00724181.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Escherichia... BAMA_ECO24 - Outer membrane protein assembly factor BamA OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=... BAMA_ECOHS - Outer membrane protein assembly factor BamA OS=Escherichia coli O9:H4 (strain HS) GN=bamA PE=3 SV=1 gi\|124499755, gi... - gi\|124529599\|ref\|ZP_01700543.1\| surface antigen (D15) [Escherichia coli B], gi\|124499755\|gb\|EAY47238... BAMA_SHIBS - Outer membrane protein assembly factor BamA OS=Shigella boydii serotype 4 (strain Sb227) GN=bamA PE=... gi\|85674369, gi\|... - gi\|89107057\|ref\|AP_000837.1\| hypothetical protein [Escherichia coli str. K-12 substr. W3110], gi\|856... gi\|193063191, gi... - gi\|75258832\|ref\|ZP_00730222.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Escherichia... gi\|188495809, gi... - gi\|75512189\|ref\|ZP_00734761.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Escherichia... YAET_ECOL6 - Outer membrane protein assembly factor yaeT OS=Escherichia coli O6 GN=yaeT PE=3 SV=1 BAMA_SHIB3 - Outer membrane protein assembly factor BamA OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS5... BAMA_SHISS - Outer membrane protein assembly factor BamA OS=Shigella sonnei (strain Ss046) GN=bamA PE=3 SV=1 BAMA_ECOLC - Outer membrane protein assembly factor BamA OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crook... sp\|B7UIM2\|YAET_ECO27 - Outer membrane protein assembly factor yaeT OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=... EG12676 - BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor / Outer membrane protein ... BAMA_SHIFL - Outer membrane protein assembly factor BamA OS=Shigella flexneri GN=bamA PE=2 SV=1 BAMA_ECOL6 - Outer membrane protein assembly factor BamA OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 /... gi\|24111612, gi\|... - gi\|24111612\|ref\|NP_706122.1\| outer membrane protein assembly factor YaeT [Shigella flexneri 2a str. ... BAMA_ECO57 - Outer membrane protein assembly factor BamA OS=Escherichia coli O157:H7 GN=bamA PE=3 SV=1 gi\|30039976, gi\|... - gi\|30061734\|ref\|NP_835905.1\| outer membrane protein assembly factor YaeT [Shigella flexneri 2a str. ... gi\|12512902, gi\|... - gi\|15799859\|ref\|NP_285871.1\| outer membrane protein assembly factor YaeT [Escherichia coli O157:H7 E... EG12676 - BamABCDE complex OM biogenesis outer membrane pore-forming assembly factor / Outer membrane protein ... BAMA_SHIF8 - Outer membrane protein assembly factor BamA OS=Shigella flexneri serotype 5b (strain 8401) GN=bamA P... BAMA_ECOUT - Outer membrane protein assembly factor BamA OS=Escherichia coli (strain UTI89 / UPEC) GN=bamA PE=3 S... gi\|189357088, gi... - gi\|189357088\|gb\|EDU75507.1\| outer membrane protein assembly complex, YaeT protein [Escherichia coli ... gi\|13359635, gi\|... - gi\|15829433\|ref\|NP_308206.1\| outer membrane protein assembly factor YaeT [Escherichia coli O157:H7 s... gi\|189360697, gi... - gi\|189360697\|gb\|EDU79116.1\| outer membrane protein assembly complex, YaeT protein [Escherichia coli ... BAMA_ECOL5 - Outer membrane protein assembly factor BamA OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=ba... gi\|189000478, gi... - gi\|189000478\|gb\|EDU69464.1\| outer membrane protein assembly complex, YaeT protein [Escherichia coli ... YAET_ECOLI, UP05... - Outer membrane protein assembly factor yaeT precursor (Omp85) - Escherichia coli, (P39170) Unknown p... BAMA_ECO8A - Outer membrane protein assembly factor BamA OS=Escherichia coli O8 (strain IAI1) GN=bamA PE=3 SV=1 BAMA_ECO45 - Outer membrane protein assembly factor BamA OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=bamA ... BAMA_ECO55 - Outer membrane protein assembly factor BamA OS=Escherichia coli (strain 55989 / EAEC) GN=bamA PE=3 S... BAMA_ECO7I - Outer membrane protein assembly factor BamA OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=bamA... BAMA_ECOLU - Outer membrane protein assembly factor BamA OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) ... gi\|168789286, gi... - gi\|189371106\|gb\|EDU89522.1\| outer membrane protein assembly complex, YaeT protein [Escherichia coli ... BAMA_ECODH - Outer membrane protein assembly factor BamA OS=Escherichia coli (strain K12 / DH10B) GN=bamA PE=3 SV... gi\|208728121, gi... - gi\|208808320\|ref\|ZP_03250657.1\| outer membrane protein assembly complex, YaeT protein [Escherichia c... gi\|208734522, gi... - gi\|208813245\|ref\|ZP_03254574.1\| outer membrane protein assembly complex, YaeT protein [Escherichia c... BAMA_ECO5E - Outer membrane protein assembly factor BamA OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=ba... BAMA_ECOSE - Outer membrane protein assembly factor BamA OS=Escherichia coli (strain SE11) GN=bamA PE=3 SV=1 BAMA_ECO27 - Outer membrane protein assembly factor BamA OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=... gi\|217320784, gi... - gi\|217324563\|ref\|ZP_03440647.1\| outer membrane protein assembly complex, YaeT protein [Escherichia c...	4.0E-86	[9..482]	[329..809]
gi\|168823253, gi... - gi\|205340481\|gb\|EDZ27245.1\| outer membrane protein assembly complex, YaeT protein [Salmonella enteri... gi\|214000833 - gi\|214000833\|ref\|ZP_03411568.1\| outer membrane protein assembly factor YaeT [Salmonella enterica sub... BAMA_SALTI - Outer membrane protein assembly factor BamA OS=Salmonella typhi GN=bamA PE=3 SV=1 gi\|213646661 - gi\|213646661\|ref\|ZP_03376714.1\| outer membrane protein assembly factor YaeT [Salmonella enterica sub... gi\|213425950 - gi\|213425950\|ref\|ZP_03358700.1\| outer membrane protein assembly factor YaeT [Salmonella enterica sub... gi\|213163131 - gi\|213163131\|ref\|ZP_03348841.1\| outer membrane protein assembly factor YaeT [Salmonella enterica sub... gi\|29136388, gi\|... - gi\|29140764\|ref\|NP_804106.1\| outer membrane protein assembly factor YaeT [Salmonella enterica subsp.... gi\|16759214 - gi\|16759214\|ref\|NP_454831.1\| outer membrane protein assembly factor YaeT [Salmonella enterica subsp.... YAET_SALTI - Outer membrane protein assembly factor yaeT OS=Salmonella typhi GN=yaeT PE=3 SV=1	2.0E-85	[9..482]	[329..802]
gi\|4902918 - dbj\|BAA77852.1\| Unknown protein from 2D-page (spots m62/m63/o3/t35) . [Escherichia coli]	3.0E-85	[9..482]	[304..784]
gi\|205331366, gi... - gi\|205331366\|gb\|EDZ18130.1\| outer membrane protein assembly complex, YaeT protein [Salmonella enteri... gi\|168263908, gi... - gi\|205347521\|gb\|EDZ34152.1\| outer membrane protein assembly complex, YaeT protein [Salmonella enteri... lcl\|NC_016856.1_... - [gene=yaeT] [protein=outer membrane protein assembly factor YaeT] [protein_id=YP_005235896.1] [locat... BAMA_SALTY - Outer membrane protein assembly factor BamA OS=Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC ... YAET_SALTY - Outer membrane protein assembly factor yaeT OS=Salmonella typhimurium GN=yaeT PE=3 SV=1 gi\|197265202, gi... - gi\|197265202\|ref\|ZP_03165276.1\| outer membrane protein assembly complex, YaeT protein [Salmonella en... YAET_SALTY - Outer membrane protein assembly factor yaeT OS=Salmonella typhimurium GN=yaeT PE=3 SV=1	6.0E-85	[9..482]	[329..803]
gi\|15603857, gi\|... - gi\|15603857\|ref\|NP_246931.1\| hypothetical protein PM1992 [Pasteurella multocida subsp. multocida str...	7.0E-83	[9..483]	[325..791]
gi\|1401350 - gi\|1401350\|gb\|AAC44600.1\| outer membrane antigen Oma87	9.0E-82	[9..483]	[323..789]
gi\|14586745 - gi\|14586745\|gb\|AAK70345.1\|AF329831_1 integral outer membrane protein [Haemophilus ducreyi] gi\|33152299, gi\|... - gi\|33152299\|ref\|NP_873652.1\| outer membrane protein D-15 [Haemophilus ducreyi 35000HP], gi\|33148522\|...	9.0E-82	[9..483]	[326..793]
gi\|75831249, gi\|... - gi\|75831249\|ref\|ZP_00760514.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Vibrio chol... gi\|15642250, gi\|... - gi\|9656813\|gb\|AAF95396.1\| surface antigen [Vibrio cholerae O1 biovar El Tor str. N16961], gi\|1564225... gi\|75827541, gi\|... - gi\|75827541\|ref\|ZP_00756976.1\| COG4775: Outer membrane protein/protective antigen OMA87 [Vibrio chol... gi\|11279712 - pir\|\|B82099 surface antigen VC2252 [imported] - Vibrio cholerae (strain N16961 serogroup O1) gi\|124119769, gi... - gi\|153221240\|ref\|ZP_01952255.1\| surface antigen [Vibrio cholerae MAK 757], gi\|124119769\|gb\|EAY38512.... gi\|126509288, gi... - gi\|153820170\|ref\|ZP_01972837.1\| surface antigen [Vibrio cholerae NCTC 8457], gi\|126509288\|gb\|EAZ7188... gi\|229352096, gi... - gi\|229512131\|ref\|ZP_04401610.1\| outer membrane protein assembly factor YaeT precursor [Vibrio choler... gi\|227010264, gi... - gi\|227082376\|ref\|YP_002810927.1\| surface antigen [Vibrio cholerae M66-2], gi\|227010264\|gb\|ACP06476.1... gi\|229507674, gi... - gi\|229507674\|ref\|ZP_04397179.1\| outer membrane protein assembly factor YaeT precursor [Vibrio choler... gi\|229519266, gi... - gi\|229519266\|ref\|ZP_04408709.1\| outer membrane protein assembly factor YaeT precursor [Vibrio choler... gi\|229369833, gi... - gi\|229607178\|ref\|YP_002877826.1\| outer membrane protein assembly factor YaeT precursor [Vibrio chole...	1.0E-79	[9..483]	[329..803]

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Predicted Domain #1

Region A:
Residues: [1-100]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTSSSGVDNE ISLDSPMPIF NESSTLKPIR VAGVVTTGTD HIDPSVLQAY LDDTIMKSIT  60
   61 LGQLVKNADV LNKRLCQHHI ALNAKQSFHF QGNTYISDEK

[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	0.775	a.118.1	ARM repeat
View	Download	0.524	a.133.1	Phospholipase A2, PLA2
View	Download	0.534	a.130.1	Chorismate mutase II
View	Download	0.651	a.46.1	Methionine synthase domain
View	Download	0.587	a.39.3	Cloroperoxidase
View	Download	0.491	a.118.9	ENTH/VHS domain
View	Download	0.459	a.4.6	C-terminal effector domain of the bipartite response regulators
View	Download	0.445	a.23.4	Mitochondrial import receptor subunit Tom20
View	Download	0.406	a.118.9	ENTH/VHS domain
View	Download	0.398	a.181.1	Antibiotic binding domain of TipA-like multidrug resistance regulators
View	Download	0.393	c.55.7	Methylated DNA-protein cysteine methyltransferase domain
View	Download	0.392	c.9.1	Barstar (barnase inhibitor)
View	Download	0.380	a.156.1	S13-like H2TH domain
View	Download	0.377	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.358	d.15.1	Ubiquitin-like
View	Download	0.346	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.344	a.81.1	N-terminal domain of DnaB helicase
View	Download	0.340	a.7.6	Ribosomal protein S20
View	Download	0.338	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.334	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.331	a.39.1	EF-hand
View	Download	0.324	g.53.1	TAZ domain
View	Download	0.321	d.44.1	Fe,Mn superoxide dismutase (SOD), C-terminal domain
View	Download	0.318	a.74.1	Cyclin-like
View	Download	0.317	a.4.8	Ribosomal protein S18
View	Download	0.316	a.142.1	PTS-regulatory domain, PRD
View	Download	0.312	a.7.1	Spectrin repeat
View	Download	0.307	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.287	a.61.1	Retroviral matrix proteins
View	Download	0.284	a.24.13	Domain of the SRP/SRP receptor G-proteins
View	Download	0.282	d.54.1	Enolase N-terminal domain-like
View	Download	0.274	a.2.3	Chaperone J-domain
View	Download	0.273	a.19.1	Fertilization protein
View	Download	0.272	i.1.1	Ribosome and ribosomal fragments
View	Download	0.268	d.15.2	CAD & PB1 domains
View	Download	0.257	d.110.4	SNARE-like
View	Download	0.255	a.40.1	Calponin-homology domain, CH-domain
View	Download	0.255	a.2.11	Fe,Mn superoxide dismutase (SOD), N-terminal domain
View	Download	0.254	c.55.7	Methylated DNA-protein cysteine methyltransferase domain
View	Download	0.248	d.58.1	4Fe-4S ferredoxins
View	Download	0.242	a.36.1	Signal peptide-binding domain
View	Download	0.240	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.240	a.45.1	Glutathione S-transferase (GST), C-terminal domain
View	Download	0.238	a.23.5	Hemolysin expression modulating protein HHA
View	Download	0.238	a.69.1	C-terminal domain of alpha and beta subunits of F1 ATP synthase
View	Download	0.238	a.77.1	DEATH domain
View	Download	0.236	d.222.1	YbaB-like
View	Download	0.234	c.97.1	Cytidine deaminase-like
View	Download	0.231	a.118.13	Arp2/3 complex 16 kDa subunit ARPC5
View	Download	0.230	a.100.1	6-phosphogluconate dehydrogenase C-terminal domain-like
View	Download	0.229	a.3.1	Cytochrome c
View	Download	0.224	a.4.1	Homeodomain-like
View	Download	0.223	d.15.1	Ubiquitin-like
View	Download	0.213	a.39.2	Insect pheromon/odorant-binding proteins
View	Download	0.213	a.4.9	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View	Download	0.211	d.19.1	MHC antigen-recognition domain
View	Download	0.203	a.35.1	lambda repressor-like DNA-binding domains
View	Download	0.203	a.4.5	"Winged helix" DNA-binding domain
View	Download	0.201	d.12.1	Ribosomal proteins L23 and L15e

Predicted Domain #2

Region A:
Residues: [101-484]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 ETHDVVPLME VVSQLDILPP KTFTAKTGTN FGNDNDAEAY LQFEKLIDKK YLKLPTRVNL  60
   61 EILRGTKIHS SFLFNSYSSL SPQSILNLKV FSQFYNWNTN KGLDIGQRGA RLSLRYEPLF 120
  121 LHKLLHNPHS NESPTLFHEW FLETCWRSTK ICSQGTSAPY MYSGTMLSQA GDQLRTILGH 180
  181 TFVLDKRDHI MCPTKGSMLK WSNELSPGKH LKTQLELNSV KSWMNDDFIT FSTTIKTGYL 240
  241 KNLSSQQSLP VHICDKFQSG GPSDIRGFQT FGLGPRDLYD AVGGDAFVSY GLSVFSRLPW 300
  301 KKVEKSNFRL HWFFNGGKLV NHDNTSLGNC IGQLSKEHST STGIGLVLRH PMARFELNFT 360
  361 LPITAHENDL IRKGFQFGLG LAFL

[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