Align ABC-type sugar transport system, permease component protein (characterized, see rationale)
to candidate GFF2276 PGA1_c23080 ribose transport system permease protein RbsC
Query= uniprot:D8J112 (347 letters) >FitnessBrowser__Phaeo:GFF2276 Length = 324 Score = 191 bits (486), Expect = 2e-53 Identities = 120/312 (38%), Positives = 180/312 (57%), Gaps = 18/312 (5%) Query: 37 LLAFASLLLMILFFSFASPNFMEVDNLVSILQSTAVNGVLAIACTYVIITSGIDLSVGTM 96 L+AFA L I+ F+ A+P F+ +DN ++++S+A+ GV+A+ T+V+I+ +DLSVG+M Sbjct: 19 LIAFA---LFIIGFTIANPKFLTLDNFENVVRSSAILGVMALGVTFVVISGNLDLSVGSM 75 Query: 97 MTFCAVMAGVVLTNWG--MPLPLGIAAAIFFGALSGWISGMVIAKLKVPPFIATLGMMML 154 M+F ++ + G + +P A + GAL G++ G LK+ I TLGM+ Sbjct: 76 MSFSTIVVLDLHDKLGPTLAIPAMFAMTLCLGALIGFLVGY----LKLNSLIVTLGMLSA 131 Query: 155 LKGLSLVISGTRPIYFNDTEG--FSAIAQDSLIGDLIPSLPIPNAVLILFLVAIGASIIL 212 + GL+L SG + + D EG F+ Q +++G I +LI +A IIL Sbjct: 132 IHGLTLTYSGGKNMDIADKEGTWFAIFGQGNILG-------IQTPILIFIALAALLGIIL 184 Query: 213 NKTVFGRYTFALGSNEEALRLSGVKVDFWKVAVYTFSGAICGIAGLIIASRLNSAQPALG 272 KT FGR +A+G N A SG++ Y S AGLI ASR +Q +G Sbjct: 185 AKTPFGRKVYAVGGNGTAATFSGIRRARVVFLCYIMSALCVATAGLIQASRSMGSQNTVG 244 Query: 273 QGYELDAIAAVVIGGTSLSGGTGTILGTIIGAFIMSVLVNGLRIMSVAQEWQTVVTGVII 332 QG EL+ +AAV++GG SL GG+GTI T+IG I+ + NGL ++ + Q VVT +II Sbjct: 245 QGLELEVLAAVILGGASLLGGSGTIFKTVIGVLILGFIQNGLLLVGLDFSVQYVVTWIII 304 Query: 333 ILAVYLDILRRR 344 ILAV+LDI +R Sbjct: 305 ILAVWLDIAAKR 316 Lambda K H 0.326 0.139 0.398 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 221 Number of extensions: 12 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 347 Length of database: 324 Length adjustment: 28 Effective length of query: 319 Effective length of database: 296 Effective search space: 94424 Effective search space used: 94424 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory