Align Branched chain amino acid transporter 2 of 439 aas and 12 TMSs, BrnQ (characterized)
to candidate BWI76_RS06240 BWI76_RS06240 branched-chain amino acid transport system 2 carrier protein BrnQ
Query= TCDB::P0AD99 (439 letters) >FitnessBrowser__Koxy:BWI76_RS06240 Length = 439 Score = 791 bits (2044), Expect = 0.0 Identities = 398/439 (90%), Positives = 419/439 (95%) Query: 1 MTHQLRSRDIIALGFMTFALFVGAGNIIFPPMVGLQAGEHVWTAAFGFLITAVGLPVLTV 60 MTHQL+SRDIIALGFMTFALFVGAGNIIFPPMVGLQAGEHVWTAA GFLITAVGLPVLTV Sbjct: 1 MTHQLKSRDIIALGFMTFALFVGAGNIIFPPMVGLQAGEHVWTAAIGFLITAVGLPVLTV 60 Query: 61 VALAKVGGGVDSLSTPIGKVAGVLLATVCYLAVGPLFATPRTATVSFEVGIAPLTGDSAL 120 VALAKVGGGV+SLSTPIGKVAG+LLA VCYLAVGPLFATPRTATVSFEVGIAPLTGD AL Sbjct: 61 VALAKVGGGVESLSTPIGKVAGILLAVVCYLAVGPLFATPRTATVSFEVGIAPLTGDGAL 120 Query: 121 PLFIYSLVYFAIVILVSLYPGKLLDTVGNFLAPLKIIALVILSVAAIVWPAGSISTATEA 180 PL IYS++YFA+VILVSLYPGKLLDTVGNFLAPLKIIAL+ILSVAAIVWPAG +S A EA Sbjct: 121 PLLIYSVIYFALVILVSLYPGKLLDTVGNFLAPLKIIALIILSVAAIVWPAGPLSHAMEA 180 Query: 181 YQNAAFSNGFVNGYLTMDTLGAMVFGIVIVNAARSRGVTEARLLTRYTVWAGLMAGVGLT 240 Y+ A FSNGFVNGYLTMDTLGAMVFGIVIVNAARSRGVTEARLLTRYTVWAGLMAGVGLT Sbjct: 181 YRTAPFSNGFVNGYLTMDTLGAMVFGIVIVNAARSRGVTEARLLTRYTVWAGLMAGVGLT 240 Query: 241 LLYLALFRLGSDSASLVDQSANGAAILHAYVQHTFGGGGSFLLAALIFIACLVTAVGLTC 300 LLYLALFRLGSDS +LV+QSANGAAILHAYVQHTFGG GSF+LAALIFIACLVTAVGLTC Sbjct: 241 LLYLALFRLGSDSGTLVEQSANGAAILHAYVQHTFGGAGSFMLAALIFIACLVTAVGLTC 300 Query: 301 ACAEFFAQYVPLSYRTLVFILGGFSMVVSNLGLSQLIQISVPVLTAIYPPCIALVVLSFT 360 ACAEFFAQY+P SYRTLVFILG FSM VSNLGLS LIQIS+PVLTAIYPPCIALVVLSFT Sbjct: 301 ACAEFFAQYLPFSYRTLVFILGLFSMAVSNLGLSHLIQISIPVLTAIYPPCIALVVLSFT 360 Query: 361 RSWWHNSSRVIAPPMFISLLFGILDGIKASAFSDILPSWAQRLPLAEQGLAWLMPTVVMV 420 R WWHNSSRVIAP MFISL+FGI+DGIKASAF+DI+PSW RLPLAEQGLAWLMPT VMV Sbjct: 361 RGWWHNSSRVIAPAMFISLMFGIIDGIKASAFADIMPSWTARLPLAEQGLAWLMPTAVMV 420 Query: 421 VLAIIWDRAAGRQVTSSAH 439 +LA+IWDRAAGRQ+TSSAH Sbjct: 421 ILAVIWDRAAGRQMTSSAH 439 Lambda K H 0.327 0.140 0.424 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: 781 Number of extensions: 13 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: 439 Length of database: 439 Length adjustment: 32 Effective length of query: 407 Effective length of database: 407 Effective search space: 165649 Effective search space used: 165649 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 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