Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate Ac3H11_3326 Amino acid ABC transporter, permease protein
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3326 Length = 260 Score = 102 bits (253), Expect = 1e-26 Identities = 69/225 (30%), Positives = 107/225 (47%), Gaps = 13/225 (5%) Query: 5 QMLGFGPEGWGG---VLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIY 61 Q+L F PE G A T+ LTL + +VG V G A A+ +R+ +R Y Sbjct: 36 QLLSFLPEPIGSNAQAFSDGARTTLWLTLISGSVGLVLGTGAALARTARWAVVRWAASFY 95 Query: 62 TTVFRGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEV 121 V RG P L+ I YF LV + +P F LA+G+ GAY AE Sbjct: 96 IWVIRGTPLLVQILFVYFALPVLVPGLN----------LPDFAAAVLALGLNVGAYNAEA 145 Query: 122 YRSAVLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVT 181 R+ +LAV RG+ EAA+++G+ + + ++ PQ + +LP + + + LKDS+L Sbjct: 146 IRAGLLAVPRGQTEAAKALGLGRMHVFFDVVFPQAFKISLPPLVSNFVALLKDSSLAYAI 205 Query: 182 GLAELLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAE 226 G+ EL +T Q YL++T++ ++ N E Sbjct: 206 GVVELTNVGNRIQSATFQPIATLSTVAITYLLLTTLVTQISNAVE 250 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: 114 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: 260 Length adjustment: 24 Effective length of query: 216 Effective length of database: 236 Effective search space: 50976 Effective search space used: 50976 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 17 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