Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate PP_3600 PP_3600 glucarate transporter
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Putida:PP_3600 Length = 454 Score = 754 bits (1946), Expect = 0.0 Identities = 368/451 (81%), Positives = 407/451 (90%), Gaps = 12/451 (2%) Query: 1 MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY 60 MQATK THVRYLIL MLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY Sbjct: 1 MQATKKTHVRYLILFMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY 60 Query: 61 VAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAE 120 VAGQIPGGWLLDRFGSK VYA SIFTWSLFT+LQG+VG V+ AVV LF LRF+VG AE Sbjct: 61 VAGQIPGGWLLDRFGSKNVYAFSIFTWSLFTLLQGFVGGLPVAWAVVTLFTLRFLVGFAE 120 Query: 121 APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGV 180 APSFPGNARIVAAWFPT ERGTASAIFNSAQYFAT LFAP+MGWIV+SFGW+HVF+VMGV Sbjct: 121 APSFPGNARIVAAWFPTQERGTASAIFNSAQYFATALFAPIMGWIVFSFGWEHVFVVMGV 180 Query: 181 IGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQL 240 +GIIFS++WLK I++PRQHP I+++E HI NG +VDMDQ +G +DGPKW YI+QL Sbjct: 181 LGIIFSMVWLKTIYNPRQHPRISQSELEHIEQNGGLVDMDQKRG----SDGPKWGYIKQL 236 Query: 241 LTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLG 300 LT+RM+LGVYLGQYCIN ITYFFLTWFPVYLVQ+RGMTILKAGFIASLPA+CGFIGGVLG Sbjct: 237 LTSRMLLGVYLGQYCINAITYFFLTWFPVYLVQERGMTILKAGFIASLPAVCGFIGGVLG 296 Query: 301 GVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGAL 360 GVISD+LLR+G+SLTF+RK PI+ GLL+S+++V CNYVD EWMVVGFM LAFFGKG+GAL Sbjct: 297 GVISDWLLRRGNSLTFSRKLPIVCGLLLSTTMVFCNYVDAEWMVVGFMTLAFFGKGIGAL 356 Query: 361 GWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVA 420 GWAVV+DTSPKQIAGLSGGLFNTFGN+ASITTPIVIGYIIS TGSFKWALV+VGANALVA Sbjct: 357 GWAVVADTSPKQIAGLSGGLFNTFGNIASITTPIVIGYIISATGSFKWALVYVGANALVA 416 Query: 421 VFSYLVIVGPIKRVVLK--------EPPTQG 443 VFSYLVIVGPIKR+ L+ EP T G Sbjct: 417 VFSYLVIVGPIKRIELRDAAPKPHAEPATDG 447 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: 915 Number of extensions: 50 Number of successful extensions: 6 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: 454 Length adjustment: 33 Effective length of query: 421 Effective length of database: 421 Effective search space: 177241 Effective search space used: 177241 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