Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_057508922.1 ABB28_RS12355 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_001431535.1:WP_057508922.1 Length = 491 Score = 264 bits (675), Expect = 4e-75 Identities = 161/468 (34%), Positives = 253/468 (54%), Gaps = 26/468 (5%) Query: 14 DADKHYNQVLTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVFSYLLAALVAGFVAL 73 D + + LT + + LG+G +I IF + GQ AA AGP V S++LA L L Sbjct: 28 DGEATLKRTLTAKHLILLGIGAVIGAGIFVMTGQAAAFHAGPAVTLSFVLAGLACALAGL 87 Query: 74 AYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFVGSGFSANLQQLLAP 133 YAE + +MP +GSAYS+ GEG W GW L+ EY A A V +SA L + Sbjct: 88 CYAEFAAMMPVSGSAYSYSYATLGEGMAWFIGWCLVLEYLFASASVAVAWSAYLLSFVTT 147 Query: 134 LGFHLP---KVLANPFGTDGG-------VVDIISLLVILLSAIIVFRGASDAGRISQILV 183 HLP + + P +GG + ++ ++L++ +++ G S + ++ I+V Sbjct: 148 T-LHLPFPDALSSAPIAWEGGQFIASGQLFNLPAVLIVAAVTGLLYVGISQSTFVNGIIV 206 Query: 184 VLKVAAVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGVSMIFLAYIGFDSIA 243 +KV+ + FI G + I AN+ PFIP + G G+SG+ S++F A+IGFD+++ Sbjct: 207 AIKVSVICLFIGFGASHIDTANWQPFIPENTGTFGEFGWSGVLRAGSIVFFAFIGFDAVS 266 Query: 244 ANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAGNAAPVGWALQQSGY 303 + E K+PQ+ MP G++GSL I +++ V LVL G+ PY G A PV AL+ Y Sbjct: 267 TAAGETKDPQRNMPIGLLGSLAICTIIYVIVCLVLTGLLPYQ-QLGTAKPVATALE--AY 323 Query: 304 SVLSEVVTAI---ALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKMNAR-NLPANGV 359 L+ + TA+ A+AG+ +L M++ +R+ Y RDGLLP+ LGK++AR P Sbjct: 324 PQLAWLKTAVEIGAIAGLSSVVLVMMMGQTRIAYTISRDGLLPRFLGKVHARFKTPYVAT 383 Query: 360 WTLAIVAIVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKDLPEAT--YKMPF 417 + ++A + P L +L+S GTL+AF V +G+ LR + PE +++P Sbjct: 384 IIVGVIAAALAGMMPLNVLGELVSMGTLLAFATVCIGVLVLRYTR----PELVRPFRVPM 439 Query: 418 YPVLPALGFIGSLFVF-WGLDVQAKLYSGIWFLIGILIYFAYGNRRSR 464 ++ LG + L +F L+ G W ++G+LIYF YG R S+ Sbjct: 440 AWLICPLGALACLTLFAMAFREHWHLFVG-WTVLGLLIYFGYGMRNSK 486 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: 641 Number of extensions: 39 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: 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 24 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