Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate H281DRAFT_05318 H281DRAFT_05318 MFS transporter, ACS family, glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Burk376:H281DRAFT_05318 Length = 449 Score = 577 bits (1486), Expect = e-169 Identities = 268/434 (61%), Positives = 341/434 (78%), Gaps = 1/434 (0%) Query: 5 KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQ 64 K T VRY ILL++F++TT NYADRAT+++ GS+++ + G DA+ +GYIFSAF WAYV Q Sbjct: 14 KRTKVRYAILLLIFVITTFNYADRATLSVTGSAMRAEFGFDAIRMGYIFSAFSWAYVLSQ 73 Query: 65 IPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFG-VSTAVVALFMLRFMVGLAEAPS 123 +P GWLLDRFG+++VYA SIF WSLFT+LQ +G G + AV LF+LRF +G AE+P+ Sbjct: 74 LPAGWLLDRFGARRVYAASIFFWSLFTLLQSSIGLLGSAAAAVTGLFLLRFAMGAAESPA 133 Query: 124 FPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGI 183 FP NA++VA+WFPT ERGTASAIFNSAQYFA V+F PLM W+ ++FGW V++VMG G+ Sbjct: 134 FPANAKVVASWFPTKERGTASAIFNSAQYFAAVVFTPLMAWLTHAFGWHMVYVVMGFAGL 193 Query: 184 IFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTN 243 + +L WLKV+ P HP ++ AE +I G +V + + W +RQLL+N Sbjct: 194 LLALTWLKVMKHPADHPGVSAAELEYIEQGGGVVSGQHNARRENVEKAGGWSLVRQLLSN 253 Query: 244 RMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVI 303 RM++GVYL QYCIN +TYFFLTWFP+YLVQ RGMTIL+AG +ASLPAICGF GGVLGG++ Sbjct: 254 RMLVGVYLAQYCINVLTYFFLTWFPIYLVQARGMTILQAGLVASLPAICGFSGGVLGGIL 313 Query: 304 SDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWA 363 SD L+R+GHSLT ARK PI+GG+L+S SI+ CNYV +W+VV M+LAFFGKG+GALGWA Sbjct: 314 SDSLIRRGHSLTVARKVPIVGGMLLSVSIIGCNYVSTDWVVVALMSLAFFGKGIGALGWA 373 Query: 364 VVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFS 423 VV+DTSPK+ GLSG +FN FGN+A I TPIVIGY+++ +GSF ALVFVGANAL+ VFS Sbjct: 374 VVADTSPKEALGLSGAIFNMFGNVAGIVTPIVIGYLVAKSGSFNGALVFVGANALLTVFS 433 Query: 424 YLVIVGPIKRVVLK 437 YLVIV IKRV L+ Sbjct: 434 YLVIVKDIKRVELR 447 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: 746 Number of extensions: 38 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: 449 Length adjustment: 33 Effective length of query: 421 Effective length of database: 416 Effective search space: 175136 Effective search space used: 175136 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