Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_092483642.1 BM299_RS10185 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_900115975.1:WP_092483642.1 Length = 484 Score = 289 bits (739), Expect = 2e-82 Identities = 170/461 (36%), Positives = 262/461 (56%), Gaps = 20/461 (4%) Query: 15 ADKHYNQ-----VLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAG 69 ADK N+ L D ALGVG +I T IF L G AA +AGPGVVFS++L+ + A Sbjct: 14 ADKKKNKRGLVPTLGVADLTALGVGAVIGTGIFVLTGVAAANYAGPGVVFSFILSGIAAT 73 Query: 70 FVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQ 129 A+ YAE+ +P AGSAY++ V GE W+ GW L+ EY +A V G+S+ + Sbjct: 74 LAAMVYAELGAAIPSAGSAYTFSYVSLGEIIAWLVGWNLILEYLVAAGAVSIGWSSYMGD 133 Query: 130 LLAPLGFHLPKVL-ANPFGTDGGVVDIISLLVILLSAIIVFRGASDAGRISQILVVLKVA 188 LL +G LP ++PF DGG+V++ + L++L+ ++ G + ++I+VV K+A Sbjct: 134 LLQSVGITLPAAFTSSPF--DGGIVNLPAALIVLVITGLIITGTQHSTTANKIIVVAKLA 191 Query: 189 AVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIAANSAE 248 A+ FI +G+ I PAN+ P +P G SG++ G +++F AYIGFD++A S E Sbjct: 192 AIALFIALGVQHINPANWRPVLP--------YGISGVFHGAAIVFFAYIGFDAVATASEE 243 Query: 249 AKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGYSVLSE 308 KNPQ+ +PRGII +L+I+ +L+ V +L GM Y+ A+PV AL ++G S Sbjct: 244 VKNPQRDLPRGIIWTLVISTLLYIVVAGILTGMVKYT-NLNTASPVATALLRAGIPWASA 302 Query: 309 VVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGVWTLAIVAI 367 +V+ ALAG+ LL + SR+ +A RD LLP ++ R P + ++ Sbjct: 303 LVSVGALAGLTSVLLVAMYGQSRIFFAMARDDLLPPIFDWLHPRLRTPVWDSIIIGVLVA 362 Query: 368 VIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEATYKMPFYPVLPALGFI 427 +IGAF P +A+L + GTL AF+ V+ G L RR DL +++P+ P +P L I Sbjct: 363 LIGAFLPIGLVAELANIGTLTAFIAVSTGAIIL-RRTNPDL-RRPFRLPWMPAIPVLTII 420 Query: 428 GSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSEE 468 + ++ L + W IG+++Y+ YG R+S+ + E Sbjct: 421 SAGYLAINLPPLTWVRFIAWVAIGLVVYWLYGYRKSKLARE 461 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: 657 Number of extensions: 33 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: 484 Length adjustment: 33 Effective length of query: 436 Effective length of database: 451 Effective search space: 196636 Effective search space used: 196636 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 Apr 09 2024. 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