Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_013402767.1 CALHY_RS04220 amino acid ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_000166355.1:WP_013402767.1 Length = 220 Score = 150 bits (379), Expect = 2e-41 Identities = 76/215 (35%), Positives = 132/215 (61%), Gaps = 10/215 (4%) Query: 17 VLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYL 76 VLL A+++T+ LT A+ +G VFG + A ++S+ + L IG Y +FRG P LL I+ Sbjct: 12 VLLKASVVTIELTAIAVTIGLVFGLVAALFRISKIKVLNYIGSFYVWLFRGTPLLLQIFF 71 Query: 77 FYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEA 136 Y+G +V ++ +P F+ GA+A+ + SGAY AE+ R+A+L++ +G+ EA Sbjct: 72 IYYGLPKIVPALT----------LPAFLAGAIALIINSGAYTAEIIRAAILSIDKGQYEA 121 Query: 137 ARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVAAGS 196 A+++GM L R +++PQ + +P IGN + LKDS+L+S G+ EL+R +Q+ A + Sbjct: 122 AKALGMTYLQTMRYVIVPQTYKRLIPPIGNEFIALLKDSSLVSTIGMVELMRAAQLKASA 181 Query: 197 THQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGR 231 T + ++ +YL +T++ + +FN E +G+ Sbjct: 182 TGRDAEIYIAALVIYLALTTVFSTIFNWLEKRLGK 216 Lambda K H 0.327 0.141 0.403 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: 100 Number of extensions: 3 Number of successful extensions: 2 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: 240 Length of database: 220 Length adjustment: 23 Effective length of query: 217 Effective length of database: 197 Effective search space: 42749 Effective search space used: 42749 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 (21.7 bits) S2: 46 (22.3 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