Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate PP_2837 PP_2837 putative uronate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Putida:PP_2837 Length = 436 Score = 194 bits (493), Expect = 5e-54 Identities = 125/423 (29%), Positives = 207/423 (48%), Gaps = 23/423 (5%) Query: 12 LILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQIPGGWLL 71 + ++ L L+ +NY DR+ ++IA +S+QKD+ I +G + SAF AY Q+P G ++ Sbjct: 10 ITVVFLLLIGIVNYLDRSALSIANTSIQKDMMISPSQMGILLSAFSIAYAFAQLPMGMII 69 Query: 72 DRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFM-LRFMVGLAEAPSFPGNARI 130 DR GSK S+ WS+ G V F A FM LR ++G+ EAP FP A+ Sbjct: 70 DRLGSKIALGASLLGWSVAQAAFGMVNSF-------AGFMGLRVLLGIGEAPMFPSAAKA 122 Query: 131 VAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIFSLIWL 190 ++ WF ERGT + + S+ L PL+ + +FGW+ +FI+ GVIG++ +L WL Sbjct: 123 LSEWFDANERGTPTGVVWSSTCLGPCLAPPLLTLFMVNFGWRGMFIITGVIGVVLALCWL 182 Query: 191 KVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIR---QLLTNRMML 247 S + +AA G + ++ + PK Y L +R Sbjct: 183 TFYKSKARF-------LAELAAEGKPLPSER---QAAAATAPKASYFAGWLDLFKHRSTW 232 Query: 248 GVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISDYL 307 G LG + + + LTW P Y ++ G+ + K ++ SL G G ++ G D+L Sbjct: 233 GAVLGFMGVIYMLWLHLTWLPGYFEREHGLDLYKTAWVVSLAYGFGAAGTIVAGRFCDWL 292 Query: 308 LRKGHSLTFARKAPIIGGLLISSSI-VACNYVDIEWMVVGFMALAFFGKGV-GALGWAVV 365 +R+G S+ +RK +I GL++++ + ++V + + LA F + A W +V Sbjct: 293 VRRGMSVLGSRKFSVITGLVLAALFTLPLSFVTGLTGCIMLLCLALFSINMASATAWMIV 352 Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425 + Q G + N G +A PIV G+ I +GSF A + AL + +Y Sbjct: 353 NTIVDSQRVASFGSIQNFGGYIAGSVAPIVTGFSIQYSGSFTTAFMISAVVALCSAVAYF 412 Query: 426 VIV 428 +++ Sbjct: 413 LLL 415 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: 597 Number of extensions: 34 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: 436 Length adjustment: 32 Effective length of query: 422 Effective length of database: 404 Effective search space: 170488 Effective search space used: 170488 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