Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate H281DRAFT_06474 H281DRAFT_06474 amino acid ABC transporter membrane protein 1, PAAT family
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__Burk376:H281DRAFT_06474 Length = 229 Score = 164 bits (416), Expect = 1e-45 Identities = 88/207 (42%), Positives = 128/207 (61%), Gaps = 1/207 (0%) Query: 13 GWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVFRGVPELL 72 G+G VLL + TV L++ +LA V G AAAKLS R LR + YTT+ R VP+L+ Sbjct: 5 GFGPVLLAGTIQTVELSVLSLAAAVVLGLAGAAAKLSFNRPLRALATGYTTLIRSVPDLV 64 Query: 73 VIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSAVLAVSRG 132 ++ L ++ V ++ F + PFV G L +G I GAY E +R A LAV RG Sbjct: 65 LMLLLFYSIQIAVNNLTDALNLPQF-DIDPFVAGVLTLGFIYGAYFTETFRGAFLAVPRG 123 Query: 133 ELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAELLRTSQV 192 +LEA + GM + + RIL PQ++RFALPGIGN WQ+ +K +AL+S+ GLA++++ +Q Sbjct: 124 QLEAGSAYGMSGVRVFARILFPQMMRFALPGIGNNWQVLVKATALVSIIGLADVVKAAQD 183 Query: 193 AAGSTHQYFTFFVVGGALYLIMTSISN 219 A ST F F ++ +YL +T++SN Sbjct: 184 AGKSTFNMFFFILIAALIYLALTTVSN 210 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: 229 Length adjustment: 23 Effective length of query: 217 Effective length of database: 206 Effective search space: 44702 Effective search space used: 44702 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