Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate AO356_20660 AO356_20660 glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_20660 Length = 443 Score = 361 bits (927), Expect = e-104 Identities = 171/432 (39%), Positives = 261/432 (60%), Gaps = 12/432 (2%) Query: 6 PTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAYVAGQI 65 P+ R+ +L +L + T INY DR I+IA L KDLG+D + +G IFSAF W Y + Sbjct: 22 PSRRRWFMLSLLLIATIINYIDRVNISIAAPFLAKDLGLDKIEMGLIFSAFAWTYAIALV 81 Query: 66 PGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAEAPSFP 125 P G++ DRFGS+ Y +S+ +WS TV QG+ +T +LF LR VG EAP+FP Sbjct: 82 PAGFIADRFGSRFTYGVSLISWSTVTVCQGF------ATGFASLFGLRLAVGAMEAPAFP 135 Query: 126 GNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGVIGIIF 185 N+R V WFP ERG AS+I+ QY T LF + W+ ++ W+HVF G +GI+F Sbjct: 136 ANSRAVTVWFPARERGLASSIYVCGQYLGTALFTGALLWLATTYDWRHVFYSTGALGIVF 195 Query: 186 SLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQLLTNRM 245 + WL + P +++ E +I A G +V Q++ + W I +L + R Sbjct: 196 GVAWLFLYRDPMNCKKVSKEELKYIEAGGGLVKSSQERTRFN------WRQIAELFSYRQ 249 Query: 246 MLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLGGVISD 305 + + +G++ YFFLTWFP YL+++R +T++KAG A LP + +G +L G++SD Sbjct: 250 VWAICIGKFASTSALYFFLTWFPTYLIEERQLTMIKAGIFAVLPFVGATVGILLAGIVSD 309 Query: 306 YLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGALGWAVV 365 L+R+G+SL+FARK P++ G ++ SIV N+ D + + + +AFF +G+ + WA V Sbjct: 310 LLIRRGYSLSFARKLPLVVGSMLGMSIVLVNFTDSNVICIAVLTIAFFAQGIASSSWAAV 369 Query: 366 SDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVAVFSYL 425 S+ +PK++ GL+GG+ + N+ I TPIVIG I+ TGSF A F+G AL+ SY Sbjct: 370 SEVAPKELIGLTGGITSLAANIGGIVTPIVIGAIVHKTGSFALAFWFIGGVALIGTLSYS 429 Query: 426 VIVGPIKRVVLK 437 +++G + R+ LK Sbjct: 430 LLLGRLYRIELK 441 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: 596 Number of extensions: 34 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: 443 Length adjustment: 33 Effective length of query: 421 Effective length of database: 410 Effective search space: 172610 Effective search space used: 172610 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