Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate RR42_RS29085 RR42_RS29085 glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Cup4G11:RR42_RS29085 Length = 451 Score = 632 bits (1630), Expect = 0.0 Identities = 295/440 (67%), Positives = 365/440 (82%), Gaps = 2/440 (0%) Query: 2 QATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYV 61 +AT+ +HVRY ILLM+F+VTT+NYADRAT++I G +++ + G DAV +G+IFSAF WAYV Sbjct: 12 EATRRSHVRYWILLMIFVVTTVNYADRATLSITGPAMRSEFGFDAVQMGFIFSAFSWAYV 71 Query: 62 AGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFG-VSTAVVALFMLRFMVGLAE 120 QIPGGWLLDRFG++++YA SIF WS FT+LQG++G F V AV LF+LRF VGLAE Sbjct: 72 MAQIPGGWLLDRFGARRIYACSIFLWSFFTLLQGFIGVFATVGAAVTTLFVLRFAVGLAE 131 Query: 121 APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGV 180 +P+FP NA++VA+WFPTAERGTASAIFNSAQYFA VLF PLM W+ ++ GW HV++ MG Sbjct: 132 SPAFPANAKVVASWFPTAERGTASAIFNSAQYFAAVLFTPLMAWLTHALGWHHVYLWMGA 191 Query: 181 IGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGK-GKKTDGPKWDYIRQ 239 +G++ + +WLKV+ SP HP +N AE ++I G +++M D GK K+ G +W Y+RQ Sbjct: 192 LGMVLAGLWLKVVRSPATHPGVNRAELDYIKQGGGLIEMSGDAGKKDKEASGTRWFYVRQ 251 Query: 240 LLTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVL 299 LL+NRM+LGVYLGQYCIN +TYFFLTWFPVYLVQ RGM+ILKAGF+ASLPAICGF+GGVL Sbjct: 252 LLSNRMLLGVYLGQYCINVLTYFFLTWFPVYLVQARGMSILKAGFVASLPAICGFLGGVL 311 Query: 300 GGVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGA 359 GGVISD LR+G+SLT ARK PI+ G+L+S S++ACNYVD EW+VVGFMALAFFGKG+GA Sbjct: 312 GGVISDGFLRRGYSLTVARKVPIVAGMLLSVSMIACNYVDSEWLVVGFMALAFFGKGIGA 371 Query: 360 LGWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALV 419 LGWAVV+DT+PK++ GL+G +FN FGN+A I TPIVIGYI+ TTGSF ALVFVGANALV Sbjct: 372 LGWAVVADTAPKEVIGLAGSIFNMFGNIAGIVTPIVIGYILGTTGSFNGALVFVGANALV 431 Query: 420 AVFSYLVIVGPIKRVVLKEP 439 V SYLVIV IKRV LK P Sbjct: 432 TVISYLVIVKEIKRVELKHP 451 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: 790 Number of extensions: 27 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: 451 Length adjustment: 33 Effective length of query: 421 Effective length of database: 418 Effective search space: 175978 Effective search space used: 175978 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