YRC Public Data Repository - Protein Structure Prediction

Protein:	gi\|213857769
Organism:	Salmonella enterica subsp. enterica serovar Typhi str. M223
Length:	127 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

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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 gi|213857769.

Description	E-value	Query Range	Subject Range
gi\|237705089, gi... - gi\|237705089\|ref\|ZP_04535570.1\| yfiD [Escherichia sp. 3_2_53FAA], gi\|226901455\|gb\|EEH87714.1\| yfiD [... gi\|26109350, gi\|... - gi\|26248944\|ref\|NP_754984.1\| Protein yfiD [Escherichia coli CFT073], gi\|26109350\|gb\|AAN81552.1\|AE016... gi\|91211906, gi\|... - gi\|91211906\|ref\|YP_541892.1\| protein YfiD [Escherichia coli UTI89], gi\|91073480\|gb\|ABE08361.1\| prote...	9.0E-58	[1..127]	[7..133]
YFID_ECOLI, GRCA... - (P33633) Protein yfiD, Autonomous glycyl radical cofactor - Escherichia coli gi\|89109385, gi\|... - gi\|89109385\|ref\|AP_003165.1\| pyruvate formate lyase subunit [Escherichia coli str. K-12 substr. W311... gi\|13362916, gi\|... - gi\|15832699\|ref\|NP_311472.1\| autonomous glycyl radical cofactor GrcA [Escherichia coli O157:H7 str. ... gi\|187770653, gi... - gi\|187770653\|gb\|EDU34497.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC4196... gi\|189362269, gi... - gi\|189362269\|gb\|EDU80688.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC4486... gi\|189370144, gi... - gi\|189370144\|gb\|EDU88560.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC869]... gi\|168778558, gi... - gi\|189003388\|gb\|EDU72374.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC4076... GRCA_ECODH - Autonomous glycyl radical cofactor OS=Escherichia coli (strain K12 / DH10B) GN=grcA PE=3 SV=1 gi\|189376188, gi... - gi\|189376188\|gb\|EDU94604.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC508]... gi\|208805911, gi... - gi\|208805911\|ref\|ZP_03248248.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC... gi\|195936727 - gi\|195936727\|ref\|ZP_03082109.1\| autonomous glycyl radical cofactor GrcA [Escherichia coli O157:H7 st... gi\|189365093, gi... - gi\|189365093\|gb\|EDU83509.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC4501... gi\|189355275, gi... - gi\|189355275\|gb\|EDU73694.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC4401... GRCA_SHIBS - Autonomous glycyl radical cofactor OS=Shigella boydii serotype 4 (strain Sb227) GN=grcA PE=3 SV=1 gi\|188491291, gi... - gi\|75513189\|ref\|ZP_00735631.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli 53638],... GRCA_SHISS - Autonomous glycyl radical cofactor OS=Shigella sonnei (strain Ss046) GN=grcA PE=3 SV=1 GRCA_ECOLC - Autonomous glycyl radical cofactor OS=Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks) GN=grc... GRCA_ECO24 - Autonomous glycyl radical cofactor OS=Escherichia coli O139:H28 (strain E24377A / ETEC) GN=grcA PE=3... gi\|208738696, gi... - gi\|208818573\|ref\|ZP_03258893.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC... GRCA_ECOHS - Autonomous glycyl radical cofactor OS=Escherichia coli O9:H4 (strain HS) GN=grcA PE=3 SV=1 gi\|208734189, gi... - gi\|208812912\|ref\|ZP_03254241.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. EC... gi\|194423387, gi... - gi\|83586769\|ref\|ZP_00925400.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli 101-1],... GRCA_ECOSE - Autonomous glycyl radical cofactor OS=Escherichia coli (strain SE11) GN=grcA PE=3 SV=1 GRCA_SHIB3 - Autonomous glycyl radical cofactor OS=Shigella boydii serotype 18 (strain CDC 3083-94 / BS512) GN=gr... GRCA_ECO5E - Autonomous glycyl radical cofactor OS=Escherichia coli O157:H7 (strain EC4115 / EHEC) GN=grcA PE=3 S... gi\|192958376, gi... - gi\|75237675\|ref\|ZP_00721691.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli E110019... GRCA_ECO8A - Autonomous glycyl radical cofactor OS=Escherichia coli O8 (strain IAI1) GN=grcA PE=3 SV=1 EG11784 - autonomous glycyl radical cofactor / Autonomous glycine radical cofactor; can reactivate pyruvate fo... gi\|193064113, gi... - gi\|75258004\|ref\|ZP_00729478.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli E22], g... gi\|124499838, gi... - gi\|124529531\|ref\|ZP_01700501.1\| formate C-acetyltransferase glycine radical [Escherichia coli B], gi... gi\|217319577, gi... - gi\|217327210\|ref\|ZP_03443293.1\| autonomous glycyl radical cofactor [Escherichia coli O157:H7 str. TW... gi\|75209512, gi\|... - gi\|75209512\|ref\|ZP_00709737.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli B171], ... GRCA_ECO55 - Autonomous glycyl radical cofactor OS=Escherichia coli (strain 55989 / EAEC) GN=grcA PE=3 SV=1 gi\|75228846, gi\|... - gi\|75228846\|ref\|ZP_00715447.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli B7A], g... GRCA_ECO81 - Autonomous glycyl radical cofactor OS=Escherichia coli O81 (strain ED1a) GN=grcA PE=3 SV=1 GRCA_ECO57 - Autonomous glycyl radical cofactor OS=Escherichia coli O157:H7 GN=grcA PE=3 SV=1 gi\|83570816, gi\|... - gi\|83570816\|ref\|ZP_00922259.1\| COG3445: Acid-induced glycyl radical enzyme [Shigella dysenteriae 101... GRCA_ECOBW - Autonomous glycyl radical cofactor OS=Escherichia coli (strain K12 / MC4100 / BW2952) GN=grcA PE=3 S... EG11784 - autonomous glycyl radical cofactor / Autonomous glycine radical cofactor; can reactivate pyruvate fo... gi\|251785906, gi... - gi\|251785906\|ref\|YP_003000210.1\| hypothetical protein B21_02437 [Escherichia coli BL21], gi\|24237817... gi\|254289315, gi... - gi\|254289315\|ref\|YP_003055063.1\| pyruvate formate lyase subunit [Escherichia coli BL21(DE3)], gi\|253... gi\|253974455, gi... - gi\|254162554\|ref\|YP_003045662.1\| pyruvate formate lyase subunit [Escherichia coli B str. REL606], gi... gi\|254794530, gi... - gi\|254794530\|ref\|YP_003079367.1\| pyruvate formate lyase subunit [Escherichia coli O157:H7 str. TW143...	2.0E-57	[1..127]	[1..127]
GRCA_ECOL6 - Autonomous glycyl radical cofactor OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) GN... gi\|162138388 - gi\|162138388\|ref\|YP_541892.2\| autonomous glycyl radical cofactor GrcA [Escherichia coli UTI89] GRCA_ECO27 - Autonomous glycyl radical cofactor OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=grcA PE=3... GRCA_ESCF3 - Autonomous glycyl radical cofactor OS=Escherichia fergusonii (strain ATCC 35469 / DSM 13698 / CDC 05... GRCA_ECOSM - Autonomous glycyl radical cofactor OS=Escherichia coli (strain SMS-3-5 / SECEC) GN=grcA PE=3 SV=1 gi\|170767612, gi... - gi\|170767612\|ref\|ZP_02902065.1\| autonomous glycyl radical cofactor [Escherichia albertii TW07627], g... GRCA_ECOL6 - Autonomous glycyl radical cofactor OS=Escherichia coli O6 GN=grcA PE=3 SV=2 GRCA_ECOL5 - Autonomous glycyl radical cofactor OS=Escherichia coli O6:K15:H31 (strain 536 / UPEC) GN=grcA PE=3 S... gi\|227835965, gi... - gi\|227887615\|ref\|ZP_04005420.1\| autonomous glycyl radical cofactor GrcA [Escherichia coli 83972], gi... GRCA_ECOK1 - Autonomous glycyl radical cofactor OS=Escherichia coli O1:K1 / APEC GN=grcA PE=3 SV=1 sp\|B7UH18\|GRCA_ECO27 - Autonomous glycyl radical cofactor OS=Escherichia coli O127:H6 (strain E2348/69 / EPEC) GN=grcA PE=3... gi\|191174033, gi... - gi\|75237402\|ref\|ZP_00721437.1\| COG3445: Acid-induced glycyl radical enzyme [Escherichia coli F11], g... GRCA_ECOLU - Autonomous glycyl radical cofactor OS=Escherichia coli O17:K52:H18 (strain UMN026 / ExPEC) GN=grcA P... GRCA_ECO45 - Autonomous glycyl radical cofactor OS=Escherichia coli O45:K1 (strain S88 / ExPEC) GN=grcA PE=3 SV=1 GRCA_ECO7I - Autonomous glycyl radical cofactor OS=Escherichia coli O7:K1 (strain IAI39 / ExPEC) GN=grcA PE=3 SV=...	2.0E-57	[1..127]	[1..127]
GRCA_SHIFL - Autonomous glycyl radical cofactor OS=Shigella flexneri GN=grcA PE=3 SV=2 gi\|56383695, gi\|... - gi\|56480144\|ref\|NP_708430.2\| autonomous glycyl radical cofactor GrcA [Shigella flexneri 2a str. 301]... gi\|30063980, gi\|... - gi\|30063980\|ref\|NP_838151.1\| autonomous glycyl radical cofactor GrcA [Shigella flexneri 2a str. 2457...	1.0E-56	[1..127]	[1..127]
GRCA_SHIF8 - Autonomous glycyl radical cofactor OS=Shigella flexneri serotype 5b (strain 8401) GN=grcA PE=3 SV=1	1.0E-56	[1..127]	[1..127]
GRCA_SHIDS - Autonomous glycyl radical cofactor OS=Shigella dysenteriae serotype 1 (strain Sd197) GN=grcA PE=3 SV...	1.0E-56	[1..127]	[1..127]
gi\|144983818 - gi\|144983818\|gb\|EDJ91268.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae R3021] GRCA_HAEIG - Autonomous glycyl radical cofactor OS=Haemophilus influenzae (strain PittGG) GN=grcA PE=3 SV=1 gi\|145271251, gi... - gi\|145639694\|ref\|ZP_01795297.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae Pitt... GRCA_HAEIN, YFID... - (P44455) Protein HI0017, Autonomous glycyl radical cofactor OS=Haemophilus influenzae GN=grcA PE=1 S... gi\|42629200 - gi\|42629200\|ref\|ZP_00154748.1\| COG3445: Acid-induced glycyl radical enzyme [Haemophilus influenzae R... gi\|145636779, gi... - gi\|145636779\|ref\|ZP_01792445.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae Pitt... gi\|42631986 - gi\|42631986\|ref\|ZP_00157524.1\| COG3445: Acid-induced glycyl radical enzyme [Haemophilus influenzae R... gi\|145267486, gi... - gi\|145635207\|ref\|ZP_01790911.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae Pitt... GRCA_HAEIN - Autonomous glycyl radical cofactor OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 /... gi\|145633426, gi... - gi\|145633426\|ref\|ZP_01789156.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae 3655... gi\|145630692 - gi\|145630692\|ref\|ZP_01786471.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae 22.4... gi\|229811671, gi... - gi\|229845363\|ref\|ZP_04465494.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae 6P18...	5.0E-56	[1..127]	[1..127]
gi\|25285925 - gi\|25285925\|pir\|\|C85904 probable formate acetyltransferase yfiD [imported] - Escherichia coli (strai... gi\|15803106, gi\|... - gi\|15803106\|ref\|NP_289137.1\| autonomous glycyl radical cofactor GrcA [Escherichia coli O157:H7 EDL93...	6.0E-56	[1..127]	[1..127]
GRCA_PASMU - Autonomous glycyl radical cofactor OS=Pasteurella multocida GN=grcA PE=3 SV=1 tr\|J8PQE3\|J8PQE3... - Autonomous glycyl radical cofactor OS=Pasteurella multocida subsp. multocida str. Anand1_cattle GN=g... GRCA_PASMU - Autonomous glycyl radical cofactor OS=Pasteurella multocida (strain Pm70) GN=grcA PE=3 SV=1	8.0E-56	[1..127]	[1..127]
gi\|229846936, gi... - gi\|229846936\|ref\|ZP_04467042.1\| autonomous glycyl radical cofactor GrcA [Haemophilus influenzae 7P49... GRCA_HAEIE - Autonomous glycyl radical cofactor OS=Haemophilus influenzae (strain PittEE) GN=grcA PE=3 SV=1 GRCA_HAEI8 - Autonomous glycyl radical cofactor OS=Haemophilus influenzae (strain 86-028NP) GN=grcA PE=3 SV=1	3.0E-55	[1..127]	[1..127]

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Predicted Domain #1

Region A:
Residues: [1-127]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MITGIQITKA ANDDLLNSFW LLDSEKGEAR CIVAKSGFAE DEVVAVSKLG EIEYREIPME  60
   61 VKPEVRVEGG QHLNVNVLRR ETLEDAVKHP EKYPQLTIRV SGYAVRFNSL TPEQQRDVIA 120
  121 RTFTESL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	31.69897
Match:	1h16A
Description:	Pyruvate formate-lyase, PFL
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