Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_034278233.1 AMYHA_RS20915 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000504245.1:WP_034278233.1 Length = 366 Score = 139 bits (349), Expect = 2e-37 Identities = 98/306 (32%), Positives = 158/306 (51%), Gaps = 29/306 (9%) Query: 149 AWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSY-------FGLS---FWVLLPLSGIF 198 A GLNIV G AG + LG+ F A+GAY+ A LS FG++ W+L +G+ Sbjct: 59 AIGLNIVTGYAGQVSLGHAFFLAIGAYTAAALSGDPDGRTIGFGVTNVLVWLLA--AGLV 116 Query: 199 AALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIP 258 AA++GV++ RLRG YLAIVTL I V W D+T G P LFG+ Sbjct: 117 AAVFGVLVAPLATRLRGLYLAIVTLGLVFIGEHVFKEWRDLTGGAGVGRPGPVPELFGVT 176 Query: 259 FDATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIR-LRRMPIGRAWEALREDE 317 + + + ++ K+ YL++ +C++ + R L R +GRA+ A+R+ + Sbjct: 177 LNKSGD---------VLTSDQKL---YLLMLVCLVVLGILARNLARSKVGRAFAAIRDRD 224 Query: 318 IACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGG 377 IA +G+N K+ AFA + +AG AG+ GF+ P SF L S +A+V++GG Sbjct: 225 IAASVIGVNLARYKMIAFAVSSFYAGCAGALLYTITGFIEPTSFNLLLSVQYIAMVLIGG 284 Query: 378 MGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPEL----YRMLIFGLAMVVVMLFK 433 + +++G + A + L RE+ + D + L +++GL ++ ++F+ Sbjct: 285 VATISGSIMGAFFITLLPALTRELPTVAPFISSDASAPLNVFQVETVLYGLLIIGFLIFE 344 Query: 434 PRGFVG 439 PRG G Sbjct: 345 PRGLYG 350 Lambda K H 0.330 0.145 0.432 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: 472 Number of extensions: 31 Number of successful extensions: 4 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: 463 Length of database: 366 Length adjustment: 31 Effective length of query: 432 Effective length of database: 335 Effective search space: 144720 Effective search space used: 144720 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: 50 (23.9 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