Align Ile/Val:H+ symporter (characterized)
to candidate GFF1754 PS417_08920 branched-chain amino acid ABC transporter substrate-binding protein
Query= TCDB::P25185 (437 letters) >FitnessBrowser__WCS417:GFF1754 Length = 437 Score = 654 bits (1688), Expect = 0.0 Identities = 335/437 (76%), Positives = 370/437 (84%) Query: 1 MNALKGRDILALGFMTFALFVGAGNIIFPPIVGLQSGPHVWLAALGFLITAVGLPVITVI 60 M LK +D+LALGFMTFALFVGAGNIIFPPIVGLQSGPHVW+AALGFL+TAVGLPV+TVI Sbjct: 1 MKVLKSQDVLALGFMTFALFVGAGNIIFPPIVGLQSGPHVWMAALGFLVTAVGLPVVTVI 60 Query: 61 ALAKVGGSVDALSHPIGRYAGGLLAAVCYLAVGPLFAIPRTATVSFEVGVVPLLGESGTA 120 ALAKVGG +DALS PIG+ AGGLLAA YLAVGPLFA PRTATVSFEVG+ PL GES A Sbjct: 61 ALAKVGGGMDALSSPIGKIAGGLLAAAAYLAVGPLFATPRTATVSFEVGLAPLTGESPLA 120 Query: 121 LFVYSLAYFLLALAISLYPGRLLDTVGRFLAPLKILALAILGVAAFLWPAGPIGTAQPEY 180 LF+YS YFL+ +SLYPGRLLDTVGRFLAPLKI+ALAILG+AAF PAG +G A EY Sbjct: 121 LFLYSSVYFLVVFFVSLYPGRLLDTVGRFLAPLKIIALAILGIAAFALPAGDVGVATQEY 180 Query: 181 TQAAFSQGFVNGYLTMDTLAALVFGIVIVNAIRSRGVQSPRLITRYAIVAGLIAGVGLVL 240 A FSQGF+NGYLTMDTL ALVFGIVIVNAIRSRGV+SP+LITRYAI+AGLIAGVGL L Sbjct: 181 VAAPFSQGFINGYLTMDTLGALVFGIVIVNAIRSRGVESPKLITRYAIIAGLIAGVGLAL 240 Query: 241 VYVSLFRLGAGSHAIAADASNGAAVLHAYVQHTFGSLGSSFLAGLIALACLVTAVGLTCA 300 VY+SLFRLG+GSH +AA A+NGAAVLHAYVQHTFGSLGS FLA LI+LACLVTAVGLTCA Sbjct: 241 VYISLFRLGSGSHEVAAGAANGAAVLHAYVQHTFGSLGSGFLAVLISLACLVTAVGLTCA 300 Query: 301 CAEYFCQRLPLSYRSLVIILAGFSFIVSNLGLTKLIQVSIPVLTAIYPPCIVLVALSFCI 360 CAEYF + LPLSY++LV+ILA FS VSNLGLTKLI SIPVLTAIYPPCIVLVALSFC Sbjct: 301 CAEYFSRILPLSYKTLVVILALFSLFVSNLGLTKLIAFSIPVLTAIYPPCIVLVALSFCK 360 Query: 361 GLWHSATRILAPVMLVSLAFGVLDALKAAGLGQDFPQWLLHLPLAEQGLAWLIPSVATLA 420 W RI+ PVMLVS FG +DALK AGL P L +LPL+EQGLAWL+PSV TLA Sbjct: 361 DFWLEQGRIVGPVMLVSFIFGCIDALKGAGLADWMPAQLANLPLSEQGLAWLVPSVMTLA 420 Query: 421 ACSLVDRLLGKPAQVAA 437 VDR+LGK ++ A Sbjct: 421 VAFAVDRMLGKRSEAIA 437 Lambda K H 0.328 0.143 0.431 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: 849 Number of extensions: 33 Number of successful extensions: 1 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: 437 Length of database: 437 Length adjustment: 32 Effective length of query: 405 Effective length of database: 405 Effective search space: 164025 Effective search space used: 164025 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 (21.8 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