Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >NCBI__GCF_001294205.1:WP_053937456.1 Length = 221 Score = 107 bits (268), Expect = 1e-28 Identities = 68/218 (31%), Positives = 110/218 (50%), Gaps = 12/218 (5%) Query: 18 LLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELLVIYLF 77 LL T+ + A+ G + GAL+A +LS + L+ +Y + RG P L+ I++ Sbjct: 14 LLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTPLLVQIFII 73 Query: 78 YFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRGELEAA 137 Y+G + ++G F P G LA+ + +GAY +E R A+ V RG+ EAA Sbjct: 74 YYG----LPAIGIQF--------EPITAGILALSLNTGAYVSETMRGAINGVDRGQWEAA 121 Query: 138 RSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQVAAGST 197 S GM I+ PQ LR A+P + N +KD++L+SV + EL+ ++ +T Sbjct: 122 FSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELMLATKEVISTT 181 Query: 198 HQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRSFKR 235 Q F +V A+Y ++ I +V E +GR+ R Sbjct: 182 FQPFPLYVAAAAIYWCLSLIFEQVQRLLERRLGRTLAR 219 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: 97 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: 221 Length adjustment: 23 Effective length of query: 217 Effective length of database: 198 Effective search space: 42966 Effective search space used: 42966 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