Align Fructose import permease protein FrcC (characterized)
to candidate GFF2365 PS417_12060 sugar ABC transporter permease
Query= SwissProt::Q9F9B1 (360 letters) >FitnessBrowser__WCS417:GFF2365 Length = 325 Score = 195 bits (495), Expect = 2e-54 Identities = 117/310 (37%), Positives = 179/310 (57%), Gaps = 15/310 (4%) Query: 50 VPLIVLVLSLIAFGVILGGKFFSAFTMTL-ILQQVAIVGIVGAAQTLVILTAGIDLSVGA 108 +PL+ ++L ++ + ++F + + IL+Q +I GI+ T VILT GIDLSVG+ Sbjct: 27 LPLVFILLCVV---MAFSSEYFMTWRNWMDILRQTSINGILAVGMTYVILTKGIDLSVGS 83 Query: 109 IMVLSSVIMGQF-TFRYGFPPALSVICGLGVGALCGYINGTLVARMKLPPFIVTLGMWQI 167 I+ + + T YG A+S G+ GA+ G +NG +VA + +PPF+ TLGM I Sbjct: 84 ILAFAGLCSAMVATQGYGLLAAVSA--GMFAGAMLGVVNGFMVANLSIPPFVATLGMLSI 141 Query: 168 VLASNFLYSANETIRAQDISANASILQFFGQNFRIGNAVFTYGVVVMVLLVCLLWYVLNR 227 F+ + I D+ +A + G+ IG + + VV ++ W VL Sbjct: 142 ARGMTFILNDGSPIT--DLP-DAYLALGIGKIGPIGVPIIIFAVVALIF-----WMVLRY 193 Query: 228 TAWGRYVYAVGDDPEAAKLAGVNVTRMLISIYTLSGLICALAGWALIGRIGSVSPTAGQF 287 T +GRYVYAVG + ++A+ +G+ V +++ S+Y +SGL+ LAG L R S P AG Sbjct: 194 TTYGRYVYAVGGNEKSARTSGIGVRKVMFSVYVVSGLLAGLAGVVLSARTTSALPQAGVS 253 Query: 288 ANIESITAVVIGGISLFGGRGSIMGMLFGALIVGVFSLGLRLMGTDPQWTYLLIGLLIII 347 +++I AVVIGG SL GG GSI+G LFGAL++GV + GL L+G + + GL+I+ Sbjct: 254 YELDAIAAVVIGGTSLSGGTGSIVGTLFGALLIGVINNGLNLLGVSSYYQQVAKGLIIVF 313 Query: 348 AVAIDQWIRK 357 AV ID W +K Sbjct: 314 AVLIDVWRKK 323 Lambda K H 0.327 0.141 0.420 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: 333 Number of extensions: 24 Number of successful extensions: 3 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: 360 Length of database: 325 Length adjustment: 29 Effective length of query: 331 Effective length of database: 296 Effective search space: 97976 Effective search space used: 97976 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