YRC Public Data Repository - Protein Structure Prediction

Protein:	DBPA_ECOLI
Organism:	Escherichia coli
Length:	457 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 DBPA_ECOLI.

Description	E-value	Query Range	Subject Range
gi\|81245612, gi\|... - gi\|82544201\|ref\|YP_408148.1\| ATP-dependent RNA helicase DbpA [Shigella boydii Sb227], gi\|81245612\|gb...	405.0	[0..1]	[457..1]
gi\|73855762, gi\|... - gi\|74312285\|ref\|YP_310704.1\| ATP-dependent RNA helicase DbpA [Shigella sonnei Ss046], gi\|73855762\|gb...	405.0	[0..1]	[457..1]
gi\|110641577, gi... - gi\|110641577\|ref\|YP_669307.1\| ATP-dependent RNA helicase DbpA [Escherichia coli 536], gi\|110343169\|g...	403.0	[0..1]	[457..1]
gi\|188016533, gi... - gi\|188016533\|gb\|EDU54655.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4113]... gi\|168756028, gi... - gi\|189356796\|gb\|EDU75215.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4401]... gi\|189361561, gi... - gi\|189361561\|gb\|EDU79980.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4486]... gi\|15831181, gi\|... - gi\|15831181\|ref\|NP_309954.1\| ATP-dependent RNA helicase DbpA [Escherichia coli O157:H7 str. Sakai], ... gi\|187769343, gi... - gi\|187769343\|gb\|EDU33187.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4196]... gi\|208815022, gi... - gi\|208815022\|ref\|ZP_03256201.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4... gi\|254592338, gi... - gi\|254792938\|ref\|YP_003077775.1\| ATP-dependent RNA helicase, specific for 23S rRNA [Escherichia coli... gi\|208740468, gi... - gi\|208820345\|ref\|ZP_03260665.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4... gi\|209160623, gi... - gi\|209399223\|ref\|YP_002270403.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC... gi\|217317836, gi... - gi\|217329397\|ref\|ZP_03445477.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. TW1... gi\|15831181, gi\|... - gi\|15831181\|ref\|NP_309954.1\| ATP-dependent RNA helicase [Escherichia coli O157:H7], gi\|13361392\|dbj\|... gi\|168782877, gi... - gi\|188999660\|gb\|EDU68646.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4076]... gi\|25385203, gi\|... - pir\|\|B85749 ATP-dependent RNA helicase [imported] - Escherichia coli (strain O157:H7, substrain EDL... gi\|168788327, gi... - gi\|189371812\|gb\|EDU90228.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC869],... gi\|189377976, gi... - gi\|189377976\|gb\|EDU96392.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC508],... gi\|12515409, gi\|... - gi\|15801822\|ref\|NP_287840.1\| ATP-dependent RNA helicase DbpA [Escherichia coli O157:H7 EDL933], gi\|1... gi\|208724673, gi... - gi\|208811167\|ref\|ZP_03253000.1\| ATP-independent RNA helicase DbpA [Escherichia coli O157:H7 str. EC4...	403.0	[0..1]	[457..1]
gi\|226900130, gi... - gi\|237705373\|ref\|ZP_04535854.1\| ATP-independent RNA helicase DbpA [Escherichia sp. 3_2_53FAA], gi\|22... gi\|218558330, gi... - gi\|218558330\|ref\|YP_002391243.1\| ATP-dependent RNA helicase DbpA [Escherichia coli S88], gi\|21836509... gi\|91210637, gi\|... - gi\|91210637\|ref\|YP_540623.1\| ATP-dependent RNA helicase DbpA [Escherichia coli UTI89], gi\|91072211\|g... gi\|115512719, gi... - gi\|117623595\|ref\|YP_852508.1\| ATP-dependent RNA helicase DbpA [Escherichia coli APEC O1], gi\|1155127...	403.0	[0..1]	[457..1]
gi\|26247679, gi\|... - gi\|26247679\|ref\|NP_753719.1\| ATP-dependent RNA helicase DbpA [Escherichia coli CFT073], gi\|26108081\|...	402.0	[0..1]	[457..1]
gi\|120597664, gi... - gi\|82743625\|ref\|ZP_00906260.1\| Helicase, C-terminal:DEAD/DEAH box helicase, N-terminal [Shewanella s... gi\|124508103, gi... - gi\|124549019\|ref\|ZP_01707446.1\| DEAD/DEAH box helicase-like [Shewanella putrefaciens 200], gi\|124508...	396.0	[0..3]	[457..2]
gi\|145565888, gi... - gi\|77814044\|ref\|ZP_00813313.1\| Helicase, C-terminal:DbpA, RNA-binding:DEAD/DEAH box helicase, N-term...	396.0	[0..3]	[457..2]
gi\|30041114, gi\|... - gi\|30062866\|ref\|NP_837037.1\| ATP-dependent RNA helicase DbpA [Shigella flexneri 2a str. 2457T], gi\|3... gi\|56479969, gi\|... - gi\|56479969\|ref\|NP_707684.2\| ATP-dependent RNA helicase DbpA [Shigella flexneri 2a str. 301], gi\|563... gi\|110805760, gi... - gi\|110805760\|ref\|YP_689280.1\| ATP-dependent RNA helicase DbpA [Shigella flexneri 5 str. 8401], gi\|11...	395.0	[0..1]	[457..1]
gi\|160874024, gi... - gi\|160874024\|ref\|YP_001553340.1\| ATP-dependent RNA helicase DbpA [Shewanella baltica OS195], gi\|1608... gi\|152999404, gi... - gi\|152999404\|ref\|YP_001365085.1\| ATP-dependent RNA helicase DbpA [Shewanella baltica OS185], gi\|1513... gi\|149116925, gi... - gi\|149116925\|ref\|ZP_01843637.1\| DEAD/DEAH box helicase domain protein [Shewanella baltica OS223], gi... gi\|68519047, gi\|... - gi\|68543263\|ref\|ZP_00582974.1\| Helicase, C-terminal:DbpA, RNA-binding:DEAD/DEAH box helicase, N-term...	395.0	[0..3]	[457..2]

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Predicted Domain #1

Region A:
Residues: [1-379]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MTAFSTLNVL PPAQLTNLNE LGYLTMTPVQ AAALPAILAG KDVRVQAKTG SGKTAAFGLG  60
   61 LLQQIDASLF QTQALVLCPT RELADQVAGE LRRLARFLPN TKILTLCGGQ PFGMQRDSLQ 120
  121 HAPHIIVATP GRLLDHLQKG TVSLDALNTL VMDEADRMLD MGFSDAIDDV IRFAPASRQT 180
  181 LLFSATWPEA IAAISGRVQR DPLAIEIDST DALPPIEQQF YETSSKGKIP LLQRLLSLHQ 240
  241 PSSCVVFCNT KKDCQAVCDA LNEVGQSALS LHGDLEQRDR DQTLVRFANG SARVLVATDV 300
  301 AARGLDIKSL ELVVNFELAW DPEVHVHRIG RTARAGNSGL AISFCAPEEA QRANIISDML 360
  361 QIKLNWQTPP ANSSIATLE

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	89.522879
Match:	1s2mA
Description:	Crystal Structure of the DEAD box protein Dhh1p
Matching Structure (courtesy of the PDB):

Predicted functions:

Term	Confidence	Notes
translation initiation factor activity	7.79457008386475	bayes_pls_golite062009
translation factor activity, nucleic acid binding	4.98637553020315	bayes_pls_golite062009
translation regulator activity	4.94658029227343	bayes_pls_golite062009
	4.704140727858	bayes_pls_golite062009
structural constituent of ribosome	3.070470376968	bayes_pls_golite062009
nucleoside-triphosphatase activity	2.95079405147356	bayes_pls_golite062009
pyrophosphatase activity	2.87427509025394	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides	2.85499564954033	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides	2.85178667290149	bayes_pls_golite062009
motor activity	2.79327761685782	bayes_pls_golite062009
microtubule motor activity	2.74365461017633	bayes_pls_golite062009
binding	2.64537357529343	bayes_pls_golite062009
transporter activity	2.58140740499725	bayes_pls_golite062009
nucleic acid binding	2.51683451033161	bayes_pls_golite062009
transmembrane transporter activity	2.39695871109024	bayes_pls_golite062009
ATPase activity	2.39535714892224	bayes_pls_golite062009
RNA binding	2.29590582680214	bayes_pls_golite062009
ATPase activity, coupled	2.18396165590908	bayes_pls_golite062009
RNA cap binding	2.17871969124431	bayes_pls_golite062009
structural molecule activity	2.08211451183607	bayes_pls_golite062009
DNA binding	1.94055378599526	bayes_pls_golite062009
transcription regulator activity	1.83584389083042	bayes_pls_golite062009
helicase activity	1.70242731830224	bayes_pls_golite062009
hydrolase activity	1.57549510726226	bayes_pls_golite062009
protein-DNA loading ATPase activity	1.54436515966471	bayes_pls_golite062009
DNA clamp loader activity	1.51134988628578	bayes_pls_golite062009
RNA helicase activity	1.42791449104435	bayes_pls_golite062009
cytoskeletal protein binding	1.40488517180956	bayes_pls_golite062009
RNA-dependent ATPase activity	1.39335733374328	bayes_pls_golite062009
ATP-dependent RNA helicase activity	1.36724390116598	bayes_pls_golite062009
substrate-specific transporter activity	1.29730375126024	bayes_pls_golite062009
DNA-dependent ATPase activity	1.2155186842031	bayes_pls_golite062009
purine NTP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
ATP-dependent helicase activity	1.19311444180077	bayes_pls_golite062009
catalytic activity	1.00104173493322	bayes_pls_golite062009
tubulin binding	0.979946830272106	bayes_pls_golite062009
DNA-directed DNA polymerase activity	0.971476020912368	bayes_pls_golite062009
transcription factor activity	0.959949409533517	bayes_pls_golite062009
purine nucleotide binding	0.929901285538132	bayes_pls_golite062009
DNA polymerase activity	0.928091843881235	bayes_pls_golite062009
nucleotide binding	0.922442819194247	bayes_pls_golite062009
purine ribonucleotide binding	0.920987930180051	bayes_pls_golite062009
ribonucleotide binding	0.920926158369519	bayes_pls_golite062009
microtubule binding	0.907162506177187	bayes_pls_golite062009
substrate-specific transmembrane transporter activity	0.906554174337376	bayes_pls_golite062009
actin binding	0.883285269827407	bayes_pls_golite062009
structure-specific DNA binding	0.782430219754236	bayes_pls_golite062009
mRNA binding	0.76699944561918	bayes_pls_golite062009
DNA helicase activity	0.72881469450553	bayes_pls_golite062009
general RNA polymerase II transcription factor activity	0.652333406433794	bayes_pls_golite062009
double-stranded DNA binding	0.6071273686445	bayes_pls_golite062009
ATP-dependent DNA helicase activity	0.5886142102548	bayes_pls_golite062009
GTPase activity	0.437665353870877	bayes_pls_golite062009
active transmembrane transporter activity	0.434775387083003	bayes_pls_golite062009
snRNA binding	0.418985924846052	bayes_pls_golite062009
ATP binding	0.41092997612902	bayes_pls_golite062009
adenyl ribonucleotide binding	0.385813421701492	bayes_pls_golite062009
adenyl nucleotide binding	0.377870145186619	bayes_pls_golite062009
ion transmembrane transporter activity	0.355466224802969	bayes_pls_golite062009
guanyl nucleotide binding	0.296406132096546	bayes_pls_golite062009
GTP binding	0.295705904888768	bayes_pls_golite062009
primary active transmembrane transporter activity	0.294474570607914	bayes_pls_golite062009
guanyl ribonucleotide binding	0.29028316917561	bayes_pls_golite062009
P-P-bond-hydrolysis-driven transmembrane transporter activity	0.282352478532746	bayes_pls_golite062009
hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances	0.220608508617331	bayes_pls_golite062009
ATPase activity, coupled to transmembrane movement of substances	0.219533217661421	bayes_pls_golite062009
ATPase activity, coupled to movement of substances	0.219157471322311	bayes_pls_golite062009
protein binding	0.170837278876362	bayes_pls_golite062009
microfilament motor activity	0.10236059675512	bayes_pls_golite062009
protein transporter activity	0.0397092337273124	bayes_pls_golite062009
cation transmembrane transporter activity	0.0254369227200564	bayes_pls_golite062009
signal sequence binding	6.53725193420218E-4	bayes_pls_golite062009

Predicted Domain #2

Region A:
Residues: [380-457]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 AEMATLCIDG GKKAKMRPGD VLGALTGDIG LDGADIGKIA VHPAHVYVAV RQAVAHKAWK  60
   61 QLQGGKIKGK TCRVRLLK

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	21.045757
Match:	2d7dA
Description:	No description for 2d7dA was found.

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: