Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate HSERO_RS15805 HSERO_RS15805 glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__HerbieS:HSERO_RS15805 Length = 447 Score = 632 bits (1629), Expect = 0.0 Identities = 303/437 (69%), Positives = 361/437 (82%), Gaps = 2/437 (0%) Query: 2 QATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYV 61 + KPTHVRYLIL +LF+VTT+NYADRAT++IAGS+++ +L +D V +GYIFSAF WAYV Sbjct: 12 EVAKPTHVRYLILFLLFVVTTVNYADRATLSIAGSAMKTELSLDPVMMGYIFSAFSWAYV 71 Query: 62 AGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEA 121 Q+PGGWLLDRFGSKK+Y SI WS+FT LQ V + AV +LF+LRFMVGLAEA Sbjct: 72 LAQLPGGWLLDRFGSKKIYMWSIALWSVFTFLQAGVTWMSTAAAVASLFLLRFMVGLAEA 131 Query: 122 PSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVI 181 PSFP N RIVAAWFPT ERGTASAIFNSAQYFA VLF PLM WIV+++ W HVF VMGV+ Sbjct: 132 PSFPANGRIVAAWFPTKERGTASAIFNSAQYFAAVLFTPLMAWIVHTYSWHHVFTVMGVV 191 Query: 182 GIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLL 241 GI +LIW ++I+SP+ HP IN+AE HI + G +VDMD K T G YIRQLL Sbjct: 192 GIALALIWGRIIYSPKDHPRINQAELAHIESGGGLVDMDNRKVAAPSTKGR--GYIRQLL 249 Query: 242 TNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGG 301 +NRM+LGVY+GQYCIN ITYFFLTWFPVYLVQ+RGM+ILKAGF+AS+PA+CGFIGGV+GG Sbjct: 250 SNRMLLGVYIGQYCINVITYFFLTWFPVYLVQERGMSILKAGFVASIPAVCGFIGGVVGG 309 Query: 302 VISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALG 361 +ISD L+++G S+T+ARK PI+GG+L+S +++ CNYV+ +WMVVG MALAFFGKGVGALG Sbjct: 310 LISDRLIKRGLSVTWARKIPIVGGMLLSMTMILCNYVEAQWMVVGIMALAFFGKGVGALG 369 Query: 362 WAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAV 421 WAVV+DT+PKQI GLSGGLFN FGN+A ITTPIVIGYI+ TGSF ALVFVG NALV V Sbjct: 370 WAVVADTAPKQIVGLSGGLFNMFGNVAGITTPIVIGYIVKETGSFSGALVFVGINALVTV 429 Query: 422 FSYLVIVGPIKRVVLKE 438 SYLVIV IKRV LK+ Sbjct: 430 ISYLVIVKEIKRVELKD 446 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: 820 Number of extensions: 32 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: 447 Length adjustment: 33 Effective length of query: 421 Effective length of database: 414 Effective search space: 174294 Effective search space used: 174294 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