Align Branched chain amino acid (Leucine/isoleucine/valine) uptake transporter of 469 aas and 12 TMSs, BcaP or CitA (characterized)
to candidate WP_025765060.1 X939_RS0120010 amino acid permease
Query= TCDB::S6EX81 (469 letters) >NCBI__GCF_000566685.1:WP_025765060.1 Length = 484 Score = 298 bits (763), Expect = 3e-85 Identities = 164/482 (34%), Positives = 282/482 (58%), Gaps = 18/482 (3%) Query: 3 FMRKADFELYRDADKHYNQV---LTTRDFLALGVGTIISTSIFTLPGQVAAQFAGPGVVF 59 + +K +L +++ NQ+ L++ +ALG+G II +F+L G AA+ +GP V Sbjct: 6 WFKKPIEKLLQESTGEENQLKRSLSSLSLVALGIGAIIGAGLFSLTGIAAAEHSGPAVTI 65 Query: 60 SYLLAALVAGFVALAYAEMSTVMPFAGSAYSWISVLFGEGFGWIAGWALLAEYFIAVAFV 119 S+++AA+ GF L YAE ++++P AGSAY++ GE WI GW L+ EY + A V Sbjct: 66 SFIVAAVGCGFAGLCYAEFASMIPIAGSAYTYSYATMGEFVAWIIGWDLVLEYALGAATV 125 Query: 120 GSGFSANLQQLLAPLGFHLP-KVLANPF-------GT--DGGVVDIISLLVILLSAIIVF 169 +S L + L+ HLP +++++PF GT D G++++ ++L++ + ++++ Sbjct: 126 SVSWSRYLLEFLSKFDIHLPTQLVSSPFEVLTLSDGTIIDNGIINLPAILIVWMLSLLLI 185 Query: 170 RGASDAGRISQILVVLKVAAVIAFIIVGITVIKPANYHPFIPPHNPKTGFGGFSGIWSGV 229 RG + ++ LV+LKVA V+ FI +G + I P NY P+IP + G+SGI +G Sbjct: 186 RGTEGSAYLNNFLVILKVAVVLIFIGLGWSHINPENYVPYIPENTGNYENFGWSGIATGA 245 Query: 230 SMIFLAYIGFDSIAANSAEAKNPQKTMPRGIIGSLLIAVVLFAAVTLVLVGMHPYSAYAG 289 +++F A+IGFD+++ + EAKNPQK MP GI+GSL++ +L+ V+ G+ Y +A Sbjct: 246 AVVFFAFIGFDAVSTAAQEAKNPQKGMPIGILGSLIVCTILYVLFAHVMTGLVNYKEFAN 305 Query: 290 NAAPVGWALQQSGYSVLSEVVTAIALAGMFIALLGMVLAGSRLLYAFGRDGLLPKGLGKM 349 +A P A +GY L + LAG +L M+L SR+ Y+ +DGLLPK ++ Sbjct: 306 DAKPAATAFAATGYDSLQTGLIVAILAGYTSVMLVMLLGQSRVFYSMSKDGLLPKFFSEI 365 Query: 350 NAR-NLP-ANGVWTLAIVAIVIGAFFPFAFLAQLISAGTLIAFMFVTLGIYSLRRRQGKD 407 + + + P ++ + V+I G F P + L ++S GTL AF V +G++ LR ++ D Sbjct: 366 HPKFSTPWKTNIFFMLFVSIFAG-FVPVSDLGHMVSIGTLFAFSLVCVGVWMLRVKR-PD 423 Query: 408 LPEATYKMPFYPVLPALGFIGSLFVFWGLDVQAKLYSGIWFLIGILIYFAYGNRRSRKSE 467 LP +++ P P +P +G I +++ + L +++ IW +G+ IYF YG + S+ + Sbjct: 424 LPR-SFRTPLVPFVPLMGIIVCVYLMYSLPIESWYRLAIWLALGLAIYFFYGKKNSKLGK 482 Query: 468 EK 469 E+ Sbjct: 483 EQ 484 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: 650 Number of extensions: 36 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: 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 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