Align Ile/Val:H+ symporter (characterized)
to candidate PP_4184 PP_4184 branched chain amino acid transporter
Query= TCDB::P25185 (437 letters) >FitnessBrowser__Putida:PP_4184 Length = 437 Score = 676 bits (1743), Expect = 0.0 Identities = 340/437 (77%), Positives = 381/437 (87%) Query: 1 MNALKGRDILALGFMTFALFVGAGNIIFPPIVGLQSGPHVWLAALGFLITAVGLPVITVI 60 M LKG+DILALGFMTFALFVGAGNIIFPPIVGLQSGPHVW+AALGFL+TAVGLPVITV+ Sbjct: 1 MKVLKGQDILALGFMTFALFVGAGNIIFPPIVGLQSGPHVWMAALGFLVTAVGLPVITVV 60 Query: 61 ALAKVGGSVDALSHPIGRYAGGLLAAVCYLAVGPLFAIPRTATVSFEVGVVPLLGESGTA 120 ALAKVGG +DALS PIG++ GGLLAAVCYL+VGPLFA PRTATVSFEVGV PL GES A Sbjct: 61 ALAKVGGGMDALSSPIGKFFGGLLAAVCYLSVGPLFATPRTATVSFEVGVAPLTGESPLA 120 Query: 121 LFVYSLAYFLLALAISLYPGRLLDTVGRFLAPLKILALAILGVAAFLWPAGPIGTAQPEY 180 LF+YSL YF++ LA+S+YPG+LLDTVGRFLAPLKI+ALA+LG+AAF PAG IG AQP Y Sbjct: 121 LFIYSLVYFIVVLAVSMYPGKLLDTVGRFLAPLKIIALAVLGIAAFALPAGSIGDAQPAY 180 Query: 181 TQAAFSQGFVNGYLTMDTLAALVFGIVIVNAIRSRGVQSPRLITRYAIVAGLIAGVGLVL 240 AAFS+GF +GYLTMDTL ALVFGIVIVNAIRSRGV+SPRLITRYAI+AGLIAGVGL L Sbjct: 181 AAAAFSKGFSDGYLTMDTLGALVFGIVIVNAIRSRGVESPRLITRYAIIAGLIAGVGLAL 240 Query: 241 VYVSLFRLGAGSHAIAADASNGAAVLHAYVQHTFGSLGSSFLAGLIALACLVTAVGLTCA 300 VY+SLFRLGA SH IAADA+NGAAVLHAYVQHTFGSLGS FLA LIALACLVTAVGLTCA Sbjct: 241 VYISLFRLGATSHDIAADATNGAAVLHAYVQHTFGSLGSGFLAVLIALACLVTAVGLTCA 300 Query: 301 CAEYFCQRLPLSYRSLVIILAGFSFIVSNLGLTKLIQVSIPVLTAIYPPCIVLVALSFCI 360 CAEYF Q LPLSYR+LV+ILAGFS ++SNLGLTKLI SIPVLTAIYPPCIV+V LSF Sbjct: 301 CAEYFSQILPLSYRALVVILAGFSLLISNLGLTKLIMFSIPVLTAIYPPCIVVVGLSFVK 360 Query: 361 GLWHSATRILAPVMLVSLAFGVLDALKAAGLGQDFPQWLLHLPLAEQGLAWLIPSVATLA 420 LW+S TRILAPVMLVSL FG++DA+K + L P ++ HLPL++ G+AWL+PSV TL Sbjct: 361 DLWNSPTRILAPVMLVSLLFGMVDAIKGSSLAHVLPDFMAHLPLSDAGMAWLVPSVVTLV 420 Query: 421 ACSLVDRLLGKPAQVAA 437 DR+LGKP + A Sbjct: 421 GAVACDRMLGKPREALA 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: 835 Number of extensions: 31 Number of successful extensions: 2 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