YRC Public Data Repository - Protein Structure Prediction

Protein:	SRP54
Organism:	Saccharomyces cerevisiae
Length:	541 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 SRP54.

Description	E-value	Query Range	Subject Range
gi\|199605327, gi... - gi\|200388229\|ref\|ZP_03214841.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|197937627, gi... - gi\|198243111\|ref\|YP_002216687.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|197241849, gi... - gi\|197263594\|ref\|ZP_03163668.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|197247718, gi... - gi\|197247718\|ref\|YP_002147614.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|213424862 - gi\|213424862\|ref\|ZP_03357612.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|213161442 - gi\|213161442\|ref\|ZP_03347152.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|206709828, gi... - gi\|207858025\|ref\|YP_002244676.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|204929456, gi... - gi\|204929456\|ref\|ZP_03220530.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|168823045, gi... - gi\|205340654\|gb\|EDZ27418.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|195633364, gi... - gi\|195633364\|gb\|EDX51778.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|168262150, gi... - gi\|205349192\|gb\|EDZ35823.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|168244700, gi... - gi\|205336482\|gb\|EDZ23246.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|194736625, gi... - gi\|194736625\|ref\|YP_002115688.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|194456913, gi... - gi\|194470549\|ref\|ZP_03076533.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|194405923, gi... - gi\|194447619\|ref\|YP_002046682.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|194402560, gi... - gi\|194443897\|ref\|YP_002041940.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|62128881, gi\|... - gi\|62181248\|ref\|YP_217665.1\| signal recognition particle protein [Salmonella enterica subsp. enteric... gi\|213999735 - gi\|213999735\|ref\|ZP_03410470.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|213647495 - gi\|213647495\|ref\|ZP_03377548.1\| signal recognition particle protein [Salmonella enterica subsp. ente... gi\|213622617 - gi\|213622617\|ref\|ZP_03375400.1\| signal recognition particle protein [Salmonella enterica subsp. ente... lcl\|NC_016856.1_... - [gene=ffh] [protein=signal recognition particle protein] [protein_id=YP_005238801.1] [location=compl... gi\|161615610, gi... - gi\|161615610\|ref\|YP_001589575.1\| signal recognition particle protein [Salmonella enterica subsp. ent... gi\|168239447, gi... - gi\|197287864\|gb\|EDY27252.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|168234200, gi... - gi\|205331826\|gb\|EDZ18590.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|167992457, gi... - gi\|205329303\|gb\|EDZ16067.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|167553522, gi... - gi\|205322062\|gb\|EDZ09901.1\| signal recognition particle protein [Salmonella enterica subsp. enterica... gi\|29143001, gi\|... - gi\|29143001\|ref\|NP_806343.1\| signal recognition particle protein [Salmonella enterica subsp. enteric... gi\|16761530 - gi\|16761530\|ref\|NP_457147.1\| signal recognition particle protein [Salmonella enterica subsp. enteric... gi\|25294415, gi\|... - gi\|25294415\|pir\|\|AI0833 signal recognition particle protein [imported] - Salmonella enterica subsp. ... gi\|16765992, gi\|... - gi\|16765992\|ref\|NP_461607.1\| signal recognition particle protein [Salmonella typhimurium LT2], gi\|16...	0.0	[2..462]	[1..452]
gi\|189367273, gi... - gi\|189367273\|gb\|EDU85689.1\| signal recognition particle protein [Escherichia coli O157:H7 str. EC450... gi\|189362137, gi... - gi\|189362137\|gb\|EDU80556.1\| signal recognition particle protein [Escherichia coli O157:H7 str. EC448... gi\|187770557, gi... - gi\|187770557\|gb\|EDU34401.1\| signal recognition particle protein [Escherichia coli O157:H7 str. EC419... gi\|189003543, gi... - gi\|189003543\|gb\|EDU72529.1\| signal recognition particle protein [Escherichia coli O157:H7 str. EC407... gi\|189370881, gi... - gi\|189370881\|gb\|EDU89297.1\| signal recognition particle protein [Escherichia coli O157:H7 str. EC869... gi\|168801727, gi... - gi\|189376173\|gb\|EDU94589.1\| signal recognition particle protein [Escherichia coli O157:H7 str. EC508... gi\|169754041, gi... - gi\|170019113\|ref\|YP_001724067.1\| signal recognition particle protein [Escherichia coli ATCC 8739], g... gi\|218355412, gi... - gi\|218547871\|ref\|YP_002381662.1\| signal recognition particle protein [Escherichia fergusonii ATCC 35... gi\|218366299, gi... - gi\|218559530\|ref\|YP_002392443.1\| signal recognition particle protein [Escherichia coli S88], gi\|2183... gi\|218690728, gi... - gi\|218690728\|ref\|YP_002398940.1\| signal recognition particle protein [Escherichia coli ED1a], gi\|218... gi\|218696234, gi... - gi\|218696234\|ref\|YP_002403901.1\| signal recognition particle protein [Escherichia coli 55989], gi\|21... gi\|254794556, gi... - gi\|254794556\|ref\|YP_003079393.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Es... gi\|218706111, gi... - gi\|218706111\|ref\|YP_002413630.1\| signal recognition particle protein [Escherichia coli UMN026], gi\|2... gi\|254162580, gi... - gi\|254162580\|ref\|YP_003045688.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Es... gi\|226839310, gi... - gi\|254037686\|ref\|ZP_04871744.1\| signal recognition particle protein [Escherichia sp. 1_1_43], gi\|226... gi\|253323540, gi... - gi\|254289341\|ref\|YP_003055089.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Es... gi\|251785932, gi... - gi\|251785932\|ref\|YP_003000236.1\| hypothetical protein B21_02463 [Escherichia coli BL21], gi\|24237820... gi\|170082214, gi... - gi\|170082214\|ref\|YP_001731534.1\| Signal recognition particle (SRP) component with 4.5S RNA (ffs) [Es... gi\|238901770, gi... - gi\|238901770\|ref\|YP_002927566.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Es... gi\|208806160, gi... - gi\|208806160\|ref\|ZP_03248497.1\| signal recognition particle protein [Escherichia coli O157:H7 str. E... gi\|226899842, gi... - gi\|237706802\|ref\|ZP_04537283.1\| signal recognition particle protein [Escherichia sp. 3_2_53FAA], gi\|... EG10300 - Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) / Signal Recognition Particle (SRP) ... gi\|208735091, gi... - gi\|208813814\|ref\|ZP_03255143.1\| signal recognition particle protein [Escherichia coli O157:H7 str. E... gi\|227888176, gi... - gi\|227888176\|ref\|ZP_04005981.1\| signal recognition particle protein [Escherichia coli 83972], gi\|227... gi\|208819384, gi... - gi\|208819384\|ref\|ZP_03259704.1\| signal recognition particle protein [Escherichia coli O157:H7 str. E... gi\|209398002, gi... - gi\|209398002\|ref\|YP_002272081.1\| signal recognition particle protein [Escherichia coli O157:H7 str. ... gi\|209913344, gi... - gi\|209920085\|ref\|YP_002294169.1\| signal recognition particle protein [Escherichia coli SE11], gi\|209... gi\|215266032, gi... - gi\|215487960\|ref\|YP_002330391.1\| signal recognition particle protein [Escherichia coli O127:H6 str. ... gi\|217327115, gi... - gi\|217327115\|ref\|ZP_03443198.1\| signal recognition particle protein [Escherichia coli O157:H7 str. T... SRP54_ECOLI, SR5... - Signal recognition particle protein (Fifty-four homolog) (p48) - Escherichia coli, (P07019) Signal r... SRP54_ECOL6 - Signal recognition particle protein OS=Escherichia coli O6 GN=ffh PE=3 SV=1 gi\|115513956, gi... - gi\|117624832\|ref\|YP_853745.1\| signal recognition particle protein [Escherichia coli APEC O1], gi\|115... gi\|124500901, gi... - gi\|124528009\|ref\|ZP_01699362.1\| signal recognition particle protein [Escherichia coli B], gi\|1245009... gi\|91211944, gi\|... - gi\|91211944\|ref\|YP_541930.1\| signal recognition particle protein [Escherichia coli UTI89], gi\|910735... gi\|15832727, gi\|... - gi\|15832727\|ref\|NP_311500.1\| signal recognition particle protein [Escherichia coli O157:H7 str. Saka... gi\|110344363, gi... - gi\|110642771\|ref\|YP_670501.1\| signal recognition particle protein [Escherichia coli 536], gi\|1103443... gi\|191169064, gi... - gi\|75227659\|ref\|ZP_00714400.1\| COG0541: Signal recognition particle GTPase [Escherichia coli B7A], g... gi\|75258029, gi\|... - gi\|75258029\|ref\|ZP_00729503.1\| COG0541: Signal recognition particle GTPase [Escherichia coli E22], g... gi\|75196624, gi\|... - gi\|75196624\|ref\|ZP_00706694.1\| COG0541: Signal recognition particle GTPase [Escherichia coli HS], gi... gi\|75208556, gi\|... - gi\|75208556\|ref\|ZP_00708869.1\| COG0541: Signal recognition particle GTPase [Escherichia coli B171], ... gi\|82545154, gi\|... - gi\|82545154\|ref\|YP_409101.1\| signal recognition particle protein [Shigella boydii Sb227], gi\|8124656... gi\|85675481, gi\|... - gi\|89109411\|ref\|AP_003191.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Escher... gi\|188489634, gi... - gi\|75513216\|ref\|ZP_00735658.1\| COG0541: Signal recognition particle GTPase [Escherichia coli 53638],... gi\|73856677, gi\|... - gi\|74313200\|ref\|YP_311619.1\| signal recognition particle protein [Shigella sonnei Ss046], gi\|7385667... SRP54_ECOL6 - Signal recognition particle protein OS=Escherichia coli O6:H1 (strain CFT073 / ATCC 700928 / UPEC) G... EG10300 - Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) / Signal Recognition Particle (SRP) ... SRP54_ECO57 - Signal recognition particle protein OS=Escherichia coli O157:H7 GN=ffh PE=3 SV=1 gi\|187730941, gi... - gi\|75178222\|ref\|ZP_00698281.1\| COG0541: Signal recognition particle GTPase [Shigella boydii BS512], ... gi\|12517035, gi\|... - gi\|15803132\|ref\|NP_289163.1\| signal recognition particle protein [Escherichia coli O157:H7 EDL933], ... gi\|157081263, gi... - gi\|75187357\|ref\|ZP_00700624.1\| COG0541: Signal recognition particle GTPase [Escherichia coli E24377A... gi\|83585222, gi\|... - gi\|83585222\|ref\|ZP_00923871.1\| COG0541: Signal recognition particle GTPase [Escherichia coli 101-1],...	0.0	[2..462]	[1..452]
gi\|24113948, gi\|... - gi\|24113948\|ref\|NP_708458.1\| signal recognition particle protein [Shigella flexneri 2a str. 301], gi... gi\|30042265, gi\|... - gi\|30064009\|ref\|NP_838180.1\| signal recognition particle protein [Shigella flexneri 2a str. 2457T], ...	0.0	[2..462]	[1..452]
gi\|20807909 - gi\|20807909\|ref\|NP_623080.1\| Signal recognition particle GTPase [Thermoanaerobacter tengcongensis MB... gi\|20807909, gi\|... - gi\|20807909\|ref\|NP_623080.1\| Signal recognition particle GTPase [Thermoanaerobacter tengcongensis MB...	0.0	[1..458]	[2..447]
SRP54_HAEIN, SR5... - Signal recognition particle protein OS=Haemophilus influenzae GN=ffh PE=3 SV=1, (P44518) Signal reco... SRP54_HAEIN - Signal recognition particle protein OS=Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 ...	0.0	[2..447]	[1..437]
gi\|15603048, gi\|... - gi\|15603048\|ref\|NP_246120.1\| hypothetical protein PM1183 [Pasteurella multocida subsp. multocida str...	0.0	[2..447]	[1..437]
gi\|22124802, gi\|... - gi\|22124802\|ref\|NP_668225.1\| signal recognition particle protein [Yersinia pestis KIM], gi\|21957627\|... gi\|166212941, gi... - gi\|166212941\|ref\|ZP_02238976.1\| signal recognition particle protein [Yersinia pestis biovar Antiqua ... gi\|25294421 - pir\|\|AD0400 signal recognition particle protein [imported] - Yersinia pestis (strain CO92) gi\|77635597, gi\|... - gi\|77635597\|ref\|ZP_00797679.1\| COG0541: Signal recognition particle GTPase [Yersinia pestis Angola],... gi\|167399424, gi... - gi\|167399424\|ref\|ZP_02304948.1\| signal recognition particle protein [Yersinia pestis biovar Antiqua ... gi\|218930317, gi... - gi\|218930317\|ref\|YP_002348192.1\| signal recognition particle protein [Yersinia pestis CO92], gi\|1612... gi\|152960549, gi... - gi\|77631805\|ref\|ZP_00794391.1\| COG0541: Signal recognition particle GTPase [Yersinia pseudotuberculo... gi\|166960399, gi... - gi\|167421480\|ref\|ZP_02313233.1\| signal recognition particle protein [Yersinia pestis biovar Oriental... gi\|45440246, gi\|... - gi\|45440246\|ref\|NP_991785.1\| signal recognition particle protein [Yersinia pestis biovar Microtus st... gi\|167057452, gi... - gi\|167423282\|ref\|ZP_02315035.1\| signal recognition particle protein [Yersinia pestis biovar Mediaeva... gi\|145600319, gi... - gi\|145600319\|ref\|YP_001164395.1\| signal recognition particle protein [Yersinia pestis Pestoides F], ... gi\|149289295, gi... - gi\|153997658\|ref\|ZP_02022758.1\| signal recognition particle protein [Yersinia pestis CA88-4125], gi\|... gi\|165915323, gi... - gi\|89103038\|ref\|ZP_01175634.1\| COG0541: Signal recognition particle GTPase [Yersinia pestis biovar O... gi\|108780752, gi... - gi\|108808839\|ref\|YP_652755.1\| signal recognition particle protein [Yersinia pestis Antiqua], gi\|1087... gi\|108810966, gi... - gi\|229901181\|ref\|ZP_04516304.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Yer... gi\|165925805, gi... - gi\|165925805\|ref\|ZP_02221637.1\| signal recognition particle protein [Yersinia pestis biovar Oriental... gi\|165991009, gi... - gi\|166010102\|ref\|ZP_02231000.1\| signal recognition particle protein [Yersinia pestis biovar Antiqua ... gi\|229899481, gi... - gi\|229899481\|ref\|ZP_04514623.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Yer... gi\|229896398, gi... - gi\|229896398\|ref\|ZP_04511566.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Yer... gi\|229838915, gi... - gi\|229838915\|ref\|ZP_04459074.1\| Signal Recognition Particle (SRP) component with 4.5S RNA (ffs) [Yer...	0.0	[2..462]	[1..452]
gi\|170718344, gi... - gi\|32030377\|ref\|ZP_00133238.1\| COG0541: Signal recognition particle GTPase [Haemophilus somnus 2336]...	0.0	[2..446]	[1..436]
gi\|33152972, gi\|... - gi\|33152972\|ref\|NP_874325.1\| signal recognition particle protein [Haemophilus ducreyi 35000HP], gi\|3...	0.0	[2..459]	[1..449]
gi\|15644313, gi\|... - gi\|4982134\|gb\|AAD36632.1\|AE001802_1 signal recognition particle protein [Thermotoga maritima MSB8], ... gi\|7440083 - pir\|\|F72236 signal recognition particle protein - Thermotoga maritima (strain MSB8) gi\|170289017, gi... - gi\|170289017\|ref\|YP_001739255.1\| signal recognition particle protein [Thermotoga sp. RQ2], gi\|170176...	0.0	[2..451]	[1..433]

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Predicted Domain #1

Region A:
Residues: [1-89]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVLADLGKRI NSAVNNAISN TQDDFTTSVD VMLKGIVTAL LESDVNIALV SKLRNNIRSQ  60
   61 LLSENRSEKS TTNAQTKKLI QKTVFDELC

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	655.228787
Match:	1j8mF_
Description:	Signal sequence recognition protein Ffh; GTPase domain of the signal sequence recognition protein Ffh
Matching Structure (courtesy of the PDB):

Predicted Domain #2

Region A:
Residues: [90-319]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KLVTCEGSEE KAFVPKKRKT NIIMFVGLQG SGKTTSCTKL AVYYSKRGFK VGLVCADTFR  60
   61 AGAFDQLKQN AIRARIPFYG SYTETDPAKV AEEGINKFKK EKFDIIIVDT SGRHHQEEEL 120
  121 FQEMIEISNV IKPNQTIMVL DASIGQAAEQ QSKAFKESSD FGAIILTKMD GHARGGGAIS 180
  181 AVAATNTPII FIGTGEHIHD LEKFSPKSFI SKLLGIGDIE SLFEQLQTVS

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	655.228787
Match:	1j8mF_
Description:	Signal sequence recognition protein Ffh; GTPase domain of the signal sequence recognition protein Ffh
Matching Structure (courtesy of the PDB):

Predicted Domain #3

Region A:
Residues: [320-408]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 NKEDAKATME NIQKGKFTLL DFKKQMQTIM KMGPLSNIAQ MIPGMSNMMN QVGEEETSQK  60
   61 MKKMVYVLDS MTKEELESDG RMFIEEPTR

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	165.10721
Match:	1mfqC_
Description:	SRP54M
Matching Structure (courtesy of the PDB):

Predicted Domain #4

Region A:
Residues: [409-541]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MVRVAKGSGT SVFEVEMILM QQQMMARMAQ TATQQQPGAP GANARMPGMP NMPGMPNMPG  60
   61 MPNMPGMPKV TPQMMQQAQQ KLKQNPGLMQ NMMNMFGGGM GGGMGGGMPD MNEMMKMMQD 120
  121 PQMQQMAKQF GMG

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	2.522879
Match:	1m2vB_
Description:	Sec24
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