Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_084545052.1 H566_RS24850 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000482785.1:WP_084545052.1 Length = 344 Score = 129 bits (323), Expect = 2e-34 Identities = 107/329 (32%), Positives = 162/329 (49%), Gaps = 26/329 (7%) Query: 111 ALIALLLYPMVVVAIKGPQGSLTYVDNFGIQILIYVMLAWGLNIVVGLAGLLDLGYVAFY 170 A A LL +V + + P + V +++L+ + A L ++VG GL+ LG+ AF+ Sbjct: 22 AFDAGLLLALVALPLLAPGWQVDLV----LKVLVLALFAVSLELLVGHTGLVSLGHAAFF 77 Query: 171 AVGAYSYALLSSYFGLSFWVLLPLSGIFAAL-WGVILGFPVLRLRGDYLAIVTLAFGEII 229 +GAY ALL+S +LL + + AA + + +G LR +G Y +VTLAFG++ Sbjct: 78 GIGAYVPALLASDSEPGSLLLLGGAAMLAAAGYALAVGLLTLRSQGIYFIMVTLAFGQMA 137 Query: 230 RLVLINWTDVTKGTFGISSIPKATLFGIPFDATAGGFAKLFHLPISSAYYKIFLFYLILA 289 V + T + GT GI + L A G A L Y + L L+ A Sbjct: 138 YHVAHD-TKLAGGTDGIYLYLRPLL--------AVGSATLVDTEDRVQLYWLVLGTLVAA 188 Query: 290 LCMLTAYVTIRLRRMPIGRAWEALREDEIACRSLGINTVTTKLTAFATGAMFAGFAGSFF 349 + L + R GRA +R +E R+ G T K+ F A+ A AG F Sbjct: 189 IGCLNLVLHSRF-----GRALAGVRVNETRMRATGYATYPYKVAIFVLAAVLAALAGFFQ 243 Query: 350 AARQGFVSPESFVFLESAVILAIVVLGGMGSLTGIAIAAIVMVGGTELLREMSFLKLIFG 409 + GFVSPES + +S +L + +LGG+GSL G + A+ VG L+E+ + +FG Sbjct: 244 TVKDGFVSPESLSWHQSGAVLVMCILGGLGSLRGAVLGAVAFVG----LQELFQSEALFG 299 Query: 410 PDFTPELYRMLIFGLAMVVVMLFKPRGFV 438 DF + L FGLA++V + PRG V Sbjct: 300 -DFA--RHWQLGFGLAIIVCVALMPRGLV 325 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: 424 Number of extensions: 32 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: 344 Length adjustment: 31 Effective length of query: 432 Effective length of database: 313 Effective search space: 135216 Effective search space used: 135216 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