Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate BPHYT_RS24150 BPHYT_RS24150 glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__BFirm:BPHYT_RS24150 Length = 450 Score = 579 bits (1492), Expect = e-170 Identities = 272/437 (62%), Positives = 348/437 (79%), Gaps = 6/437 (1%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 K T VRY ILL++FL+TT NYADRAT+++ GS+++ + G DA+ +GYIFSAF WAYV Q Sbjct: 14 KRTRVRYGILLLIFLITTFNYADRATLSVTGSAMRAEFGFDAIRMGYIFSAFSWAYVLSQ 73 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFG-VSTAVVALFMLRFMVGLAEAPS 123 +P GWLLDRFG+++VYA SIF WSLFT+LQ +G G + AV ALF+LRF +G AE+P+ Sbjct: 74 LPAGWLLDRFGARRVYAASIFFWSLFTLLQSSIGLLGSAAAAVTALFVLRFAMGAAESPA 133 Query: 124 FPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGI 183 FP NA++VA+WFPT ERGTASAIFNSAQYFA V+F PLM W+ ++FGW V++VMGV+G+ Sbjct: 134 FPANAKVVASWFPTNERGTASAIFNSAQYFAAVVFTPLMAWLTHAFGWHMVYVVMGVMGL 193 Query: 184 IFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQ---DKGKGKKTDGPKWDYIRQL 240 + +L WLKV+ +P HP ++ +E +I G +++ + GK + T G W +RQL Sbjct: 194 LLALTWLKVMKNPADHPRVSRSELEYIEQGGGVINGQKKAPSAGKIENTGG--WSLVRQL 251 Query: 241 LTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLG 300 L+NRM+LGVYL QYCIN +TYFFLTWFP+YLVQ RGMTIL+AG +ASLPAICGF GGVLG Sbjct: 252 LSNRMLLGVYLAQYCINVLTYFFLTWFPIYLVQARGMTILQAGLVASLPAICGFSGGVLG 311 Query: 301 GVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGAL 360 G++SD L+R+GHSLT ARK PI+GG+L+S I+ CNYV +W+VV M+LAFFGKG+GAL Sbjct: 312 GILSDGLIRRGHSLTVARKVPIVGGMLLSVCIIGCNYVSTDWVVVALMSLAFFGKGIGAL 371 Query: 361 GWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVA 420 GWAVV+DTSP++ GLSG +FN FGN+A I TPIVIGY+++ TGSF ALVFVG NAL+ Sbjct: 372 GWAVVADTSPREALGLSGAIFNMFGNVAGIVTPIVIGYLVAKTGSFNGALVFVGINALLT 431 Query: 421 VFSYLVIVGPIKRVVLK 437 VFSYLVIV IKRV L+ Sbjct: 432 VFSYLVIVKDIKRVELR 448 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: 749 Number of extensions: 38 Number of successful extensions: 5 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: 450 Length adjustment: 33 Effective length of query: 421 Effective length of database: 417 Effective search space: 175557 Effective search space used: 175557 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