Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate PP_1710 PP_1710 MFS transporter, phthalate permease family
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Putida:PP_1710 Length = 446 Score = 358 bits (920), Expect = e-103 Identities = 171/432 (39%), Positives = 258/432 (59%), Gaps = 12/432 (2%) Query: 6 PTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQI 65 PT R+ +L +L + T INY DR I+IA + KDLG+D V +G IFSAF W Y + Sbjct: 24 PTRRRWFMLSLLLVATIINYVDRVNISIAAPFMAKDLGLDKVEMGLIFSAFAWTYALALV 83 Query: 66 PGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFP 125 P G++ DRFGS+ Y +S+ +WS TV QG F +LF LR VG EAP+FP Sbjct: 84 PAGFIADRFGSRLTYGVSLISWSAVTVAQGLASGFA------SLFGLRLAVGAMEAPAFP 137 Query: 126 GNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIF 185 N+R V WFP ERG AS+I+ QY T LF + W+ ++ W+HVF G++GI+F Sbjct: 138 ANSRAVTVWFPARERGMASSIYVCGQYLGTALFTGALLWLATTYDWRHVFYSTGLVGILF 197 Query: 186 SLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRM 245 ++WL + P +++ E +I G +V Q++ + W + +L R Sbjct: 198 GVVWLVLYRDPLNCKKVSKEELAYIENGGGLVKSSQERTRFD------WRQVAELFRYRQ 251 Query: 246 MLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISD 305 + + LG++ YFFLTWFP YL+++R +T++K G A +P I +G +L G++SD Sbjct: 252 VWAICLGKFASTSALYFFLTWFPTYLIEERQLTLIKVGIFAVMPFIGATVGILLAGIVSD 311 Query: 306 YLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVV 365 L+RKG+SL+FARK P++ G ++ SIV N+ D + + + LAFF +G+ + WA V Sbjct: 312 LLIRKGYSLSFARKLPLVVGSMLGMSIVLVNFTDSNVLCIAVLTLAFFAQGIASSSWAAV 371 Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425 S+ +PK++ GL+GG+ + N+ I TPIVIG I+ +GSF A F+G AL+ SY Sbjct: 372 SEVAPKELIGLTGGITSLAANIGGIVTPIVIGAIVHASGSFAMAFWFIGGVALMGTLSYS 431 Query: 426 VIVGPIKRVVLK 437 +++G + R+ LK Sbjct: 432 LLLGKLYRIELK 443 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: 595 Number of extensions: 29 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: 454 Length of database: 446 Length adjustment: 33 Effective length of query: 421 Effective length of database: 413 Effective search space: 173873 Effective search space used: 173873 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