Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_109969962.1 DK846_RS15735 amino acid ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_003173355.1:WP_109969962.1 Length = 225 Score = 122 bits (307), Expect = 5e-33 Identities = 66/216 (30%), Positives = 115/216 (53%), Gaps = 11/216 (5%) Query: 14 WGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLV 73 W LL +TV L AL +G + G +A ++ +R + IY FRG+P L++ Sbjct: 10 WFPYLLSGIFITVGLVAVALLIGIILGLPMALGQVYGKHLIRSVISIYVWFFRGLPVLVL 69 Query: 74 IYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGE 133 ++LFYFG +F G + +P FVVGA+ +G+ AYQ++++R A+ +++ G+ Sbjct: 70 LFLFYFG----------IFPGLG-LDLPAFVVGAVVLGLRGAAYQSQIFRGAIQSIAEGQ 118 Query: 134 LEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVA 193 + AARS+GM R I++PQ +R ALPG N + L +S++ G+AELL S Sbjct: 119 MTAARSLGMSRAQAIRSIILPQAMRIALPGWSNEYPEILTESSICYAIGVAELLTRSSQI 178 Query: 194 AGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHV 229 T+ ++ ++++++ + R E + Sbjct: 179 VSQTYVTMPIYLACAVMFILLSYAGTHLIQRLEKRI 214 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: 118 Number of extensions: 7 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: 225 Length adjustment: 23 Effective length of query: 217 Effective length of database: 202 Effective search space: 43834 Effective search space used: 43834 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