Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate 8500844 DvMF_1582 inner-membrane translocator (RefSeq)
Query= uniprot:Q1MCU1 (463 letters) >FitnessBrowser__Miya:8500844 Length = 313 Score = 139 bits (350), Expect = 1e-37 Identities = 97/328 (29%), Positives = 158/328 (48%), Gaps = 40/328 (12%) Query: 117 LYPMVVVAIKGPQ---GSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVG 173 L P+VV+A+ G +YV + I +++ + N++ G G + G+ AF+ +G Sbjct: 5 LVPLVVLAMLAGLPLLGLNSYVMHILILSIMWTLAGMAWNLLGGYCGQVSFGHAAFFGMG 64 Query: 174 AYSYALLSSYFGLSFWVLLPLSGIFAALWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVL 233 AYS L+ + GLS W +S AL + +G VLRLRG Y + TLA GE++R+ Sbjct: 65 AYSAGLIHLHLGLSPWWGFLVSLPLVALVALAMGSVVLRLRGPYFVLATLAIGEVLRITC 124 Query: 234 INWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILALCML 293 N TD TKGT GI + + Y +Y+IL L +L Sbjct: 125 ENLTDFTKGTLGIM---------------------ITRTWVEKTQY----YYIILGLALL 159 Query: 294 TAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFFAARQ 353 V + G + A+RED+ A S+GI+T K A AM G AG+F+ Sbjct: 160 GFVVCRAIVHSRWGYYFVAIREDQDAAESMGIDTTRYKTIALTVSAMLTGLAGAFYTNYM 219 Query: 354 GFVSPESFVFLE--SAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFGPD 411 G++ P L S +I+ +V++GG+ + G A+ A +MV E +R + + + + Sbjct: 220 GYIDPGVVFSLGEISILIIMVVMVGGVATEWGPALGAGIMVILAEYIRSLPLIGVAY--- 276 Query: 412 FTPELYRMLIFGLAMVVVMLFKPRGFVG 439 +FG+ ++V++++ P G VG Sbjct: 277 -------QTMFGVLLIVIIIYLPNGLVG 297 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: 456 Number of extensions: 32 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 463 Length of database: 313 Length adjustment: 30 Effective length of query: 433 Effective length of database: 283 Effective search space: 122539 Effective search space used: 122539 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