Align Transmembrane component of a broad range amino acid ABC transporter (characterized, see rationale)
to candidate WP_013403236.1 CALHY_RS06830 branched-chain amino acid ABC transporter permease
Query= uniprot:Q1MCU1 (463 letters) >NCBI__GCF_000166355.1:WP_013403236.1 Length = 312 Score = 192 bits (487), Expect = 2e-53 Identities = 115/302 (38%), Positives = 178/302 (58%), Gaps = 44/302 (14%) Query: 142 ILIYVMLAWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLSSYFG-LSFWVLLPLSGIFAA 200 I++ ++LA LN++ G+ G LG+ F A+GAY+ A+L++ + F++ + + G+FA Sbjct: 39 IMLNIILAVSLNLINGITGQFSLGHAGFMAIGAYTTAVLTTLEKPVPFYLTVLIGGLFAM 98 Query: 201 LWGVILGFPVLRLRGDYLAIVTLAFGEIIRLVLINWTDVTKGTFGISSIPKATLFGIPFD 260 + G+I+G PVLRLRGDYLAI TL FGEIIR+++ N D G GIS IP+ GI + Sbjct: 99 ICGLIIGLPVLRLRGDYLAIATLGFGEIIRVIIQN-IDYLGGASGISDIPQ----GIDW- 152 Query: 261 ATAGGFAKLFHLPISSAYYKIFLFYLILALCMLTAYVTIRLRRMPIGRAWEALREDEIAC 320 + Y+ I +L+ V + + GRA A+REDEIA Sbjct: 153 ---------------TGYFVI---------TVLSVVVILNIINSSFGRAMIAIREDEIAA 188 Query: 321 RSLGINTVTTKLTAFATGAMFAGFAGSFFAARQGFVSPESFVFLESAVILAIVVLGGMGS 380 ++GINT K+ AF GA FAG AGS ++ GF+ P+ F F +S IL IVVLGG+GS Sbjct: 189 EAMGINTTLYKVLAFMIGAFFAGVAGSIYSGSFGFIQPDMFNFFKSIDILVIVVLGGLGS 248 Query: 381 LTGIAIAAIVMVGGTELLREMSFLKLIFGPDFTPELYRMLIFGLAMVVVMLFKPRGFVGS 440 ++G I+AIV+ + LL++ + RM+++ L ++++MLF+P+G +G+ Sbjct: 249 ISGSIISAIVLTIISALLQDYPAV-------------RMVLYSLILIIIMLFRPQGLMGT 295 Query: 441 RE 442 +E Sbjct: 296 KE 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: 416 Number of extensions: 29 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: 312 Length adjustment: 30 Effective length of query: 433 Effective length of database: 282 Effective search space: 122106 Effective search space used: 122106 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