Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate Ac3H11_1694 Branched-chain amino acid transport system permease protein LivM (TC 3.A.1.4.1)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1694 Length = 358 Score = 246 bits (629), Expect = 7e-70 Identities = 148/353 (41%), Positives = 213/353 (60%), Gaps = 33/353 (9%) Query: 110 IALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAF 169 I +ALL+ P+++ + + + L+YV+LA GLNIVVG AGLLDLGYVAF Sbjct: 10 IGAVALLVLPLILQSFGNAWVRIADL------ALLYVLLALGLNIVVGYAGLLDLGYVAF 63 Query: 170 YAVGAYSYALLSSYF--------------GL--SFWVLLPLSGIFAALWGVILGFPVLRL 213 YAVGAY +AL++S GL S W+++P++ + AA +G +LG P L+L Sbjct: 64 YAVGAYLFALMASPHLADNFAAFAAMFPNGLHTSLWIVIPVAALLAAFFGAMLGAPTLKL 123 Query: 214 RGDYLAIVTLAFGEIIRLVLINW---TDVTKGTFGISSIPKATLFGIPFDATAGGFAKLF 270 RGDYLAIVTL FGEIIR+ L N ++T G G+ I +FG+ G ++F Sbjct: 124 RGDYLAIVTLGFGEIIRIFLNNLDHPVNLTNGPKGLGQIDSVKVFGLDL----GKRLEVF 179 Query: 271 HLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTT 330 I+S +YL L L +++ + RL+ IGRAW A+REDEIA +++GINT Sbjct: 180 GFDINSV---TLYYYLFLVLVVVSVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNM 236 Query: 331 KLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIV 390 KL AF GA F G +G+ F A QGFVSPESF +ES +I+A+VVLGG+G + G+ + A++ Sbjct: 237 KLLAFGMGASFGGVSGAMFGAFQGFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVL 296 Query: 391 MVGGTELLREMSF-LKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGSRE 442 + E+LR ++ L+ + + R L+ LAM+++ML +PRG S E Sbjct: 297 LSALPEVLRYVAGPLQAMTDGRLDSAILRQLLIALAMIIIMLLRPRGLWPSPE 349 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: 510 Number of extensions: 27 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: 358 Length adjustment: 31 Effective length of query: 432 Effective length of database: 327 Effective search space: 141264 Effective search space used: 141264 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 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