Align D-galacturonate transporter (MFS superfamily) (characterized)
to candidate 17750 b3691 D-galactonate transport (VIMSS)
Query= reanno::WCS417:GFF828 (454 letters) >FitnessBrowser__Keio:17750 Length = 430 Score = 383 bits (984), Expect = e-111 Identities = 193/434 (44%), Positives = 276/434 (63%), Gaps = 9/434 (2%) Query: 1 MQATKPTHVRYLILLMLFLVTTINYADRATIAIAGSSLQKDLGIDAVTLGYIFSAFGWAY 60 + A KP RYL L+M+F+ I Y DRA +A+A + +Q++ GI +GY+FSAF W Y Sbjct: 5 VNAAKPGRRRYLTLVMIFITVVICYVDRANLAVASAHIQEEFGITKAEMGYVFSAFAWLY 64 Query: 61 VAGQIPGGWLLDRFGSKKVYALSIFTWSLFTVLQGYVGEFGVSTAVVALFMLRFMVGLAE 120 QIPGGW LDR GS+ Y ++IF WS+ T+ QG+ +T +++L LR + G+ E Sbjct: 65 TLCQIPGGWFLDRVGSRVTYFIAIFGWSVATLFQGF------ATGLMSLIGLRAITGIFE 118 Query: 121 APSFPGNARIVAAWFPTAERGTASAIFNSAQYFATVLFAPLMGWIVYSFGWQHVFIVMGV 180 AP+FP N R+V +WFP ER +A + S Q+ PL+ WI W VFIV G Sbjct: 119 APAFPTNNRMVTSWFPEHERASAVGFYTSGQFVGLAFLTPLLIWIQEMLSWHWVFIVTGG 178 Query: 181 IGIIFSLIWLKVIHSPRQHPMINEAEFNHIAANGAMVDMDQDKGKGKKTDGPKWDYIRQL 240 IGII+SLIW KV PR I++AE ++I G +VD D K + D+ +L Sbjct: 179 IGIIWSLIWFKVYQPPRLTKGISKAELDYIRDGGGLVDGDAPVKKEARQPLTAKDW--KL 236 Query: 241 LTNRMMLGVYLGQYCINGITYFFLTWFPVYLVQDRGMTILKAGFIASLPAICGFIGGVLG 300 + +R ++GVYLGQ+ + +FFLTWFP YL Q++G+T LKAGF+ ++P + F+G +L Sbjct: 237 VFHRKLIGVYLGQFAVASTLWFFLTWFPNYLTQEKGITALKAGFMTTVPFLAAFVGVLLS 296 Query: 301 GVISDYLLRKGHSLTFARKAPIIGGLLISSSIVACNYVDIEWMVVGFMALAFFGKGVGAL 360 G ++D L+RKG SL FARK PII GLLIS+ I+ NY + M++ MALAFFG G ++ Sbjct: 297 GWVADLLVRKGFSLGFARKTPIICGLLISTCIMGANYTNDPMMIMCLMALAFFGNGFASI 356 Query: 361 GWAVVSDTSPKQIAGLSGGLFNTFGNLASITTPIVIGYIISTTGSFKWALVFVGANALVA 420 W++VS +P ++ GL+GG+FN G L IT P+V+GY+ G F ALV++ A AL+ Sbjct: 357 TWSLVSSLAPMRLIGLTGGVFNFAGGLGGITVPLVVGYLAQGYG-FAPALVYISAVALIG 415 Query: 421 VFSYLVIVGPIKRV 434 SY+++VG +KRV Sbjct: 416 ALSYILLVGDVKRV 429 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: 683 Number of extensions: 41 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: 430 Length adjustment: 32 Effective length of query: 422 Effective length of database: 398 Effective search space: 167956 Effective search space used: 167956 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