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View Structure Prediction Details

Protein: MTR4
Organism: Saccharomyces cerevisiae
Length: 1073 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 MTR4.

Description E-value Query
Range		 Subject
Range
MTR4 - ATP-dependent 3'-5' RNA helicase, involved in nuclear RNA processing and degredation both as a compo...
MTR4_YEAST - ATP-dependent RNA helicase DOB1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=MTR4 PE=...
 0.0 [1..1073] [1..1073]
gi|6633995, gi|2... - gi|6633995|dbj|BAA06124.2| KIAA0052 protein [Homo sapiens], sp|P42285|K052_HUMAN Protein KIAA0052
 0.0 [5..1073] [12..1046]
SK2L2_MOUSE - Superkiller viralicidic activity 2-like 2 OS=Mus musculus GN=Skiv2l2 PE=1 SV=1
gi|71681012 - gi|71681012|gb|AAH99802.1| RGD1305984 protein [Rattus norvegicus]
 0.0 [5..1073] [8..1040]
gi|7507776 - gi|7507776|pir||T16867 probable cytochrome P450 T13C5.1 [similarity] - Caenorhabditis elegans
 0.0 [2..1072] [172..1244]
l(2)35Df-PA - The gene lethal (2) 35Df is referred to in FlyBase by the symbol Dmel\l(2)35Df (CG4152, FBgn0001986)...
gi|220943740 - gi|220943740|gb|ACL84413.1| l(2)35Df-PA [synthetic construct]
 0.0 [1..1073] [1..1055]

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Predicted Domain #1
Region A:
Residues: [1-109] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDSTDLFDVF EETPVELPTD SNGEKNADTN VGDTPDHTQD KKHGLEEEKE EHEENNSENK  60
   61 KIKSNKSKTE DKNKKVVVPV LADSFEQEAS REVDASKGLT NSETLQVEQ

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #2
Region A:
Residues: [110-321] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DGKVRLSHQV RHQVALPPNY DYTPIAEHKR VNEARTYPFT LDPFQDTAIS CIDRGESVLV  60
   61 SAHTSAGKTV VAEYAIAQSL KNKQRVIYTS PIKALSNQKY RELLAEFGDV GLMTGDITIN 120
  121 PDAGCLVMTT EILRSMLYRG SEVMREVAWV IFDEVHYMRD KERGVVWEET IILLPDKVRY 180
  181 VFLSATIPNA MEFAEWICKI HSQPCHIVYT NF

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 89.522879
Match: 1hv8A_
Description: Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted functions:

Term Confidence Notes
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
binding 2.64537357529343 bayes_pls_golite062009
transporter activity 2.58140740499725 bayes_pls_golite062009
hydrolase activity 2.55157966585974 bayes_pls_golite062009
transmembrane transporter activity 2.39695871109024 bayes_pls_golite062009
ATPase activity 2.39535714892224 bayes_pls_golite062009
ATPase activity, coupled 2.18396165590908 bayes_pls_golite062009
RNA helicase activity 1.42791449104435 bayes_pls_golite062009
nucleic acid binding 1.41477043612798 bayes_pls_golite062009
RNA-dependent ATPase activity 1.39335733374328 bayes_pls_golite062009
ATP-dependent RNA helicase activity 1.36724390116598 bayes_pls_golite062009
motor activity 1.34881124154297 bayes_pls_golite062009
substrate-specific transporter activity 1.29730375126024 bayes_pls_golite062009
protein binding 1.22129154759482 bayes_pls_golite062009
DNA binding 1.11699929651302 bayes_pls_golite062009
catalytic activity 1.00104173493322 bayes_pls_golite062009
transcription regulator activity 0.989226939888218 bayes_pls_golite062009
purine nucleotide binding 0.929901285538132 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
substrate-specific transmembrane transporter activity 0.906554174337376 bayes_pls_golite062009
ribonuclease activity 0.712344060953362 bayes_pls_golite062009
helicase activity 0.6191010101321 bayes_pls_golite062009
ligase activity 0.491120745447751 bayes_pls_golite062009
0.442119153778711 bayes_pls_golite062009
active transmembrane transporter activity 0.434775387083003 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
microtubule motor activity 0.32730260506261 bayes_pls_golite062009
purine NTP-dependent helicase activity 0.29664013896754 bayes_pls_golite062009
ATP-dependent helicase activity 0.29664013896754 bayes_pls_golite062009
primary active transmembrane transporter activity 0.294474570607914 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
GTPase activity 0.105546189348878 bayes_pls_golite062009
microfilament motor activity 0.10236059675512 bayes_pls_golite062009
transcription factor activity 0.0434163635422169 bayes_pls_golite062009
protein transporter activity 0.0397092337273124 bayes_pls_golite062009
guanyl nucleotide binding 0.0289841199143713 bayes_pls_golite062009
RNA binding 0.0261282189186349 bayes_pls_golite062009
cation transmembrane transporter activity 0.0254369227200564 bayes_pls_golite062009
guanyl ribonucleotide binding 0.0187537754688351 bayes_pls_golite062009
GTP binding 0.0171298013679982 bayes_pls_golite062009

Predicted Domain #3
Region A:
Residues: [322-455] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RPTPLQHYLF PAHGDGIYLV VDEKSTFREE NFQKAMASIS NQIGDDPNST DSRGKKGQTY  60
   61 KGGSAKGDAK GDIYKIVKMI WKKKYNPVIV FSFSKRDCEE LALKMSKLDF NSDDEKEALT 120
  121 KIFNNAIALL PETD

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 89.522879
Match: 1hv8A_
Description: Putative DEAD box RNA helicase
Matching Structure (courtesy of the PDB):

Predicted Domain #4
Region A:
Residues: [456-636] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 RELPQIKHIL PLLRRGIGIH HSGLLPILKE VIEILFQEGF LKVLFATETF SIGLNMPAKT  60
   61 VVFTSVRKWD GQQFRWVSGG EYIQMSGRAG RRGLDDRGIV IMMIDEKMEP QVAKGMVKGQ 120
  121 ADRLDSAFHL GYNMILNLMR VEGISPEFML EHSFFQFQNV ISVPVMEKKL AELKKDFDGI 180
  181 E

[Run NCBI BLAST on this sequence.]

Detection Method: PSI-BLAST
Confidence: 25.39794
Match: 1fukA_
Description: Initiation factor 4a
Matching Structure (courtesy of the PDB):

Predicted Domain #5
Region A:
Residues: [637-752] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 VEDEENVKEY HEIEQAIKGY REDVRQVVTH PANALSFLQP GRLVEISVNG KDNYGWGAVV  60
   61 DFAKRINKRN PSAVYTDHES YIVNVVVNTM YIDSPVNLLK PFNPTLPEGI RPAEEG

[Run NCBI BLAST on this sequence.]

Detection Method: deduced

Shown below is our most confident de novo (Rosetta) prediction for this domain.
Click here to view all matches.

Found no confident structure predictions for this domain.

Predicted Domain #6
Region A:
Residues: [753-838] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 EKSICAVIPI TLDSIKSIGN LRLYMPKDIR ASGQKETVGK SLREVNRRFP DGIPVLDPVK  60
   61 NMKIEDEDFL KLMKKIDVLN TKLSSN

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [852-859] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 KYSRKHDL

[Run NCBI BLAST on this sequence.]

Region C:
Residues: [940-1073] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 LSCFAFQERC KEAPRLKPEL AEPLKAMREI AAKIAKIMKD SKIEVVEKDY VESFRHELME  60
   61 VVYEWCRGAT FTQICKMTDV YEGSLIRMFK RLEELVKELV DVANTIGNSS LKEKMEAVLK 120
  121 LIHRDIVSAG SLYL

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 8.05
Match: 1n1bA
Description: (+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):

Predicted Domain #7
Region A:
Residues: [839-851] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 PLTNSMRLEE LYG

[Run NCBI BLAST on this sequence.]

Region B:
Residues: [860-939] 
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 HEDMKQLKRK ISESQAVIQL DDLRRRKRVL RRLGFCTPND IIELKGRVAC EISSGDELLL  60
   61 TELIFNGNFN ELKPEQAAAL

[Run NCBI BLAST on this sequence.]

Detection Method: ORFEUS
Confidence: 8.05
Match: 1n1bA
Description: (+)-bornyl diphosphate synthase
Matching Structure (courtesy of the PDB):
YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle