Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BPHYT_RS20950 BPHYT_RS20950 D-galactonate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__BFirm:BPHYT_RS20950 Length = 438 Score = 344 bits (883), Expect = 3e-99 Identities = 174/433 (40%), Positives = 255/433 (58%), Gaps = 14/433 (3%) Query: 4 TKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAG 63 TK + VRY++L ML T +NY DR+ + I L K L +D + +G +F+AFG AY G Sbjct: 20 TKRSKVRYVVLSMLLAATILNYVDRSALGIVAPGLSKGLALDKMQMGELFAAFGLAYSIG 79 Query: 64 QIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPS 123 +PGG L D GS+ YALS+ WS T+ QG ++T L R +G EAP+ Sbjct: 80 LVPGGVLTDVLGSRVAYALSLLGWSFATLTQG------LATGYHMLLGSRLAIGALEAPA 133 Query: 124 FPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGI 183 FP NAR V WFP ERG A++++ QY T LF L+ WI ++GW+ VF V G +GI Sbjct: 134 FPSNARAVTLWFPARERGFATSVYVMGQYIGTPLFTGLLLWISAAYGWRMVFYVTGGVGI 193 Query: 184 IFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTN 243 +FSL W +V P QH +N AE +I D K + W +LL+ Sbjct: 194 LFSLFWYRVYRDPHQHASVNAAELQYIN--------DGSTAARKPREKFDWRMALKLLSY 245 Query: 244 RMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVI 303 R +L + +G++C N + FF TWF YL++ R M+++K G +LP I G +L G + Sbjct: 246 RQILAICVGKFCNNTLLVFFTTWFMTYLIEARHMSMIKVGIFQALPFIGATAGILLAGSL 305 Query: 304 SDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWA 363 SD+ +R+G S++ ARK P+I G L+ +SIV N+V+ V+ + +AFF +GVG++ WA Sbjct: 306 SDFFIRRGVSISTARKTPLIVGTLLGASIVLVNFVESNEAVIAILTIAFFAQGVGSMSWA 365 Query: 364 VVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFS 423 VS+ +P+Q GL+ + + N+A +TTP++IGYI TG F WAL +GA L+ FS Sbjct: 366 AVSEIAPRQYVGLTSSITSLAANIAGVTTPLMIGYITHHTGHFYWALNLMGAICLLGAFS 425 Query: 424 YLVIVGPIKRVVL 436 Y V++G + R+ L Sbjct: 426 YSVLLGKLSRIEL 438 Lambda K H 0.327 0.142 0.444 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: 564 Number of extensions: 24 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: 454 Length of database: 438 Length adjustment: 32 Effective length of query: 422 Effective length of database: 406 Effective search space: 171332 Effective search space used: 171332 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: 51 (24.3 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