Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate CA265_RS15000 CA265_RS15000 amino acid permease
Query= TCDB::S6EX81 (469 letters) >FitnessBrowser__Pedo557:CA265_RS15000 Length = 491 Score = 263 bits (673), Expect = 7e-75 Identities = 158/477 (33%), Positives = 251/477 (52%), Gaps = 24/477 (5%) Query: 14 DADKHYNQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVAL 73 D+ K + L+ +ALGVG II +F AAQ AGP V +++AA+ L Sbjct: 18 DSGKGLKRTLSAGALVALGVGAIIGAGLFVRTAAAAAQNAGPSVTIGFIIAAIGCALAGL 77 Query: 74 AYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLL-- 131 YAE+S+ +P +GSAY++ GE W+ GW L+ EY + A VG +S L +LL Sbjct: 78 CYAELSSSIPISGSAYTYTYATMGELMAWVIGWDLVLEYAVGAATVGIAWSEYLNKLLVE 137 Query: 132 ----APLGF---HLPKVLANPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVV 184 +P+ + H P ++P GT G++++ +L ++ L ++++ +G S++ ++ ++V+ Sbjct: 138 VLHTSPIPYEWCHSP-FQSHPDGTVNGIMNLPALFIVGLLSLLLIKGTSESAFVNGLIVI 196 Query: 185 LKVAAVIAFIIVGITVIKPANYHPFIPPHNP-------KTGFGGFSGIWSGVSMIFLAYI 237 KV VI I++G I +N+HP+IP FGGF G+ +F A+I Sbjct: 197 TKVGIVILIIVLGWGFINESNHHPYIPAATTYVDHAGISHSFGGFWGVIGAAGTVFFAFI 256 Query: 238 GFDSIAANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAY--AGNAAPVG 295 GFD+++ + E KNP+ MP GI+GSL + VL+ VL G+ P + G A V Sbjct: 257 GFDAVSTAAQETKNPKTAMPIGILGSLAVCTVLYILFAHVLTGIAPVEFFRTKGGEASVV 316 Query: 296 WALQQ--SGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR- 352 A+ + +GYS LS++VT LAG +L M+L SR+ Y+ +DGLLPK ++ + Sbjct: 317 AAISEYMTGYSWLSKLVTVAILAGFSSVILVMLLGQSRVFYSMSKDGLLPKMFSDLHPKF 376 Query: 353 NLPANGVWTLAIVAIVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEAT 412 P + I+ + AF P + + S GTL AFM V + + LR+ DLP Sbjct: 377 KTPYKANLVILIIVGLFAAFIPGDVVGDMTSIGTLFAFMLVCVAVIILRKTD-PDLPR-Q 434 Query: 413 YKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSEEK 469 +K P+ P++P LG + + GL L W +G +IYF Y + S + K Sbjct: 435 FKTPWVPLIPILGVVACGLMILGLGWTNWLRLFGWLALGFIIYFGYSKKNSHLKDVK 491 Lambda K H 0.328 0.143 0.433 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: 653 Number of extensions: 39 Number of successful extensions: 7 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: 469 Length of database: 491 Length adjustment: 34 Effective length of query: 435 Effective length of database: 457 Effective search space: 198795 Effective search space used: 198795 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