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View Structure Prediction Details

Protein: RTR1
Organism: Saccharomyces cerevisiae
Length: 226 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 RTR1.

Description E-value Query
Range
Subject
Range
RTR1_YEAST - RNA polymerase II subunit B1 CTD phosphatase RTR1 OS=Saccharomyces cerevisiae (strain ATCC 204508 / ...
gi|151944857 - gi|151944857|gb|EDN63116.1| conserved protein [Saccharomyces cerevisiae YJM789]
RTR1 - CTD phosphatase; dephosphorylates S5-P in the C-terminal domain of Rpo21p; has a cysteine-rich motif...
gi|207345837 - gi|207345837|gb|EDZ72529.1| YER139Cp-like protein [Saccharomyces cerevisiae AWRI1631]
gi|190405698 - gi|190405698|gb|EDV08965.1| conserved hypothetical protein [Saccharomyces cerevisiae RM11-1a]
4.0E-90 [1..226] [1..226]
CE00290 - status:Confirmed UniProt:P30641 protein_id:CAA78048.1
3.0E-58 [26..215] [14..215]
gi|18257341, gi|... - gi|21450301|ref|NP_659160.1| RNA polymerase II associated protein 2 [Mus musculus], gi|18257341|gb|A...
4.0E-38 [24..136] [52..160]
gi|13376202, gi|... - gi|13376202|ref|NP_079089.1| RNA polymerase II associated protein 2 [Homo sapiens], gi|10435038|dbj|...
5.0E-36 [24..136] [52..160]
SPAC23A1.16c - DUF408 family protein
RPAP2_SCHPO - Putative RNA polymerase II subunit B1 CTD phosphatase rtr1 OS=Schizosaccharomyces pombe (strain 972 ...
2.0E-31 [22..148] [34..155]
gi|60471883, gi|... - gi|60471883|gb|EAL69837.1| hypothetical protein DDB0167475 [Dictyostelium discoideum], gi|19569876|g...
gi|60471883, gi|... - gi|66820244|ref|XP_643755.1| hypothetical protein [Dictyostelium discoideum AX4], gi|60471883|gb|EAL...
4.0E-25 [24..135] [91..200]

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Predicted Domain #1
Region A:
Residues: [1-142]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MATIEDIKET ALIPFQKHRQ LSMHEAEVIT LEIIGLLCDS ECKDEKTLKY LGRFLTPDMY  60
   61 QDLVDERNLN KRCGYPLCGK SPERIRDPFS MNDTTKKFLL ENNPYAYLSH YCSKFHFRCS 120
  121 QFYQVQLSDE ALFARTGVHL FE

[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.

    MCM
Score
GO
Score
GO
Term
SCOP
Match
SCOP Description
View Download 0.293 0.170 cytoplasm a.47.2 t-snare proteins
View Download 0.227 0.132 cytoplasm a.73.1 Retrovirus capsid protein, N-terminal core domain
View Download 0.524 0.000 cytoplasm a.24.4 Hemerythrin
View Download 0.200 0.000 cytoplasm a.23.3 Methane monooxygenase hydrolase, gamma subunit
View Download 0.524 N/A N/A a.24.4 Hemerythrin
View Download 0.293 N/A N/A a.47.2 t-snare proteins
View Download 0.227 N/A N/A a.73.1 Retrovirus capsid protein, N-terminal core domain
View Download 0.200 N/A N/A a.23.3 Methane monooxygenase hydrolase, gamma subunit

Predicted Domain #2
Region A:
Residues: [143-226]
      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 DPEQDKHDID FKVTLFEELL REKASEEDIK SLISGLKKLG LNPDSGTTEK DDTELEDDLS  60
   61 KWLAQIKIVE NDNPSILGDF TRED

[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 0.769 a.4.5 "Winged helix" DNA-binding domain
View Download 0.731 a.64.1 Saposin
View Download 0.630 a.13.1 alpha-2-Macroglobulin receptor associated protein (RAP) domain 1
View Download 0.577 a.112.1 Description not found.
View Download 0.577 a.4.1 Homeodomain-like
View Download 0.566 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.554 a.59.1 PAH2 domain
View Download 0.549 a.3.1 Cytochrome c
View Download 0.493 a.61.1 Retroviral matrix proteins
View Download 0.460 a.77.1 DEATH domain
View Download 0.453 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.453 f.1.5 Exotoxin A, middle domain
View Download 0.450 a.112.1 Description not found.
View Download 0.422 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.410 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.406 a.3.1 Cytochrome c
View Download 0.395 a.3.1 Cytochrome c
View Download 0.392 d.50.3 PI-Pfui intein middle domain
View Download 0.387 a.112.1 Description not found.
View Download 0.363 a.4.5 "Winged helix" DNA-binding domain
View Download 0.357 a.100.1 6-phosphogluconate dehydrogenase C-terminal domain-like
View Download 0.356 a.83.1 Guanido kinase N-terminal domain
View Download 0.346 a.144.1 PABC (PABP) domain
View Download 0.343 d.58.36 Sulfite reductase, domains 1 and 3
View Download 0.343 a.112.1 Description not found.
View Download 0.341 a.2.3 Chaperone J-domain
View Download 0.339 a.61.1 Retroviral matrix proteins
View Download 0.338 a.24.7 FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP)
View Download 0.338 a.61.1 Retroviral matrix proteins
View Download 0.337 a.4.5 "Winged helix" DNA-binding domain
View Download 0.335 a.39.1 EF-hand
View Download 0.332 a.64.1 Saposin
View Download 0.332 a.23.5 Hemolysin expression modulating protein HHA
View Download 0.329 a.48.3 Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View Download 0.326 a.3.1 Cytochrome c
View Download 0.322 a.4.1 Homeodomain-like
View Download 0.319 a.48.3 Conserved domain common to transcription factors TFIIS, elongin A, CRSP70
View Download 0.310 a.112.1 Description not found.
View Download 0.308 a.112.1 Description not found.
View Download 0.307 a.135.1 Tetraspanin
View Download 0.300 d.134.1 Sulfite reductase hemoprotein (SiRHP), domains 2 and 4
View Download 0.292 a.28.3 Retrovirus capsid protein C-terminal domain
View Download 0.292 a.4.5 "Winged helix" DNA-binding domain
View Download 0.291 a.144.1 PABC (PABP) domain
View Download 0.289 d.49.1 Signal recognition particle alu RNA binding heterodimer, SRP9/14
View Download 0.289 a.4.5 "Winged helix" DNA-binding domain
View Download 0.289 a.159.1 Protein serine/threonine phosphatase 2C, C-terminal domain
View Download 0.278 d.58.18 Regulatory domain in the aminoacid metabolism
View Download 0.276 a.64.1 Saposin
View Download 0.276 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.274 a.4.5 "Winged helix" DNA-binding domain
View Download 0.269 a.69.3 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain
View Download 0.262 g.53.1 TAZ domain
View Download 0.261 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.260 a.29.4 RecG, N-terminal domain
View Download 0.254 a.80.1 DNA polymerase III clamp loader subunits, C-terminal domain
View Download 0.252 a.144.1 PABC (PABP) domain
View Download 0.252 a.64.1 Saposin
View Download 0.250 a.61.1 Retroviral matrix proteins
View Download 0.247 a.60.9 lambda integrase-like, N-terminal domain
View Download 0.246 a.61.1 Retroviral matrix proteins
View Download 0.241 d.58.23 Probable ACP-binding domain of malonyl-CoA ACP transacylase
View Download 0.240 a.57.1 Protein HNS-dependent expression A; HdeA
View Download 0.239 a.24.13 Domain of the SRP/SRP receptor G-proteins
View Download 0.233 a.64.1 Saposin
View Download 0.231 a.4.9 Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3
View Download 0.230 a.77.1 DEATH domain
View Download 0.230 d.58.17 Metal-binding domain
View Download 0.229 a.121.1 Tetracyclin repressor-like, C-terminal domain
View Download 0.228 d.204.1 Ribosome binding protein Y (YfiA homologue)
View Download 0.227 a.74.1 Cyclin-like
View Download 0.225 a.112.1 Description not found.
View Download 0.223 a.2.3 Chaperone J-domain
View Download 0.222 a.74.1 Cyclin-like
View Download 0.222 a.126.1 Serum albumin-like
View Download 0.221 a.126.1 Serum albumin-like
View Download 0.220 a.2.5 Prefoldin
View Download 0.218 a.77.1 DEATH domain
View Download 0.217 a.144.2 Ribosomal protein L20
View Download 0.216 a.39.1 EF-hand
View Download 0.214 a.1.1 Globin-like
View Download 0.213 a.77.1 DEATH domain
View Download 0.213 d.58.17 Metal-binding domain
View Download 0.211 a.144.1 PABC (PABP) domain
View Download 0.210 a.144.1 PABC (PABP) domain
View Download 0.208 a.144.1 PABC (PABP) domain
View Download 0.208 d.58.11 EF-G/eEF-2 domains III and V
View Download 0.204 a.118.1 ARM repeat
View Download 0.204 d.50.3 PI-Pfui intein middle domain
View Download 0.202 d.58.19 Bacterial exopeptidase dimerisation domain


YRC Informatics Platform - Version 3.0
Created and Maintained by: Michael Riffle