Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_069958141.1 BEN30_RS09700 ABC transporter permease subunit
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_001746755.1:WP_069958141.1 Length = 232 Score = 182 bits (461), Expect = 7e-51 Identities = 90/209 (43%), Positives = 139/209 (66%), Gaps = 1/209 (0%) Query: 12 EGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPEL 71 +G+G +L +T+ L LAAL VG + G L A AKLS +R++G+ Y+T+ RG+PE Sbjct: 5 QGFGALLFAGTQVTLQLALAALVVGLILGLLGATAKLSEHAPVRLLGNGYSTLVRGLPEF 64 Query: 72 LVIYLFYFGGSTLVTSVGQ-LFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVS 130 LV+ FYFG + ++ +V LFG +G++ V F G A+G I GAY +E++R A++++ Sbjct: 65 LVVLTFYFGATDILMAVASTLFGYDGYIEVSAFAAGTTALGFIFGAYASELFRGAIISIP 124 Query: 131 RGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTS 190 G+ EAAR++GM RI +PQV R ALPG+GN++ + +KD+ALISV GL EL+R + Sbjct: 125 GGQAEAARALGMTKRQTFFRITLPQVWRIALPGLGNLFMILMKDTALISVVGLEELMRVT 184 Query: 191 QVAAGSTHQYFTFFVVGGALYLIMTSISN 219 A G T + FT ++ +YL++TSI++ Sbjct: 185 AFAVGRTKEPFTLYLTAAVIYLLLTSIAS 213 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: 128 Number of extensions: 4 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: 232 Length adjustment: 23 Effective length of query: 217 Effective length of database: 209 Effective search space: 45353 Effective search space used: 45353 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