Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate PfGW456L13_5043 D-galactarate permease
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5043 Length = 480 Score = 843 bits (2178), Expect = 0.0 Identities = 418/456 (91%), Positives = 440/456 (96%), Gaps = 5/456 (1%) Query: 1 MQAT-KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWA 59 MQ+T KPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWA Sbjct: 28 MQSTQKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWA 87 Query: 60 YVAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLA 119 YVAGQIPGGWLLDRFGSKK+YALSIFTWSLFTVLQG+VGEFG+STAVVALFMLRF+VGLA Sbjct: 88 YVAGQIPGGWLLDRFGSKKIYALSIFTWSLFTVLQGFVGEFGMSTAVVALFMLRFLVGLA 147 Query: 120 EAPSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMG 179 EAPSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGW+HVFIVMG Sbjct: 148 EAPSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWEHVFIVMG 207 Query: 180 VIGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQ 239 ++GIIFSL+WLKVI+SPR+HP IN+AEF HI+ NG MVDMDQ KGKK+DGPKWDYIRQ Sbjct: 208 ILGIIFSLVWLKVIYSPREHPRINDAEFKHISENGGMVDMDQ---KGKKSDGPKWDYIRQ 264 Query: 240 LLTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVL 299 LLTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQ+RGMTILKAGFIASLPAICGFIGGVL Sbjct: 265 LLTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQERGMTILKAGFIASLPAICGFIGGVL 324 Query: 300 GGVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGA 359 GGVISDYLLRKGHSLTFARKAPII GLL+SSSIVACNYVD+EWMVVGFMALAFFGKGVGA Sbjct: 325 GGVISDYLLRKGHSLTFARKAPIIAGLLVSSSIVACNYVDVEWMVVGFMALAFFGKGVGA 384 Query: 360 LGWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALV 419 LGWAVVSDTSPKQIAGLSGGLFNTFGN+ASITTPIVIGYIIS+TGSFKWALVFVG NALV Sbjct: 385 LGWAVVSDTSPKQIAGLSGGLFNTFGNIASITTPIVIGYIISSTGSFKWALVFVGCNALV 444 Query: 420 AVFSYLVIVGPIKRVVLKEPPTQGPELT-RLTEAHS 454 AVFSYLVIVGPIKRVVLKEPP G E +L++AHS Sbjct: 445 AVFSYLVIVGPIKRVVLKEPPANGTEAPGKLSQAHS 480 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: 961 Number of extensions: 34 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: 480 Length adjustment: 33 Effective length of query: 421 Effective length of database: 447 Effective search space: 188187 Effective search space used: 188187 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