Align Polar amino acid ABC transporter, inner membrane subunit; Flags: Precursor (characterized, see rationale)
to candidate SMc00139 SMc00139 amino acid ABC transporter permease
Query= uniprot:B2TBJ7 (240 letters) >FitnessBrowser__Smeli:SMc00139 Length = 267 Score = 179 bits (453), Expect = 6e-50 Identities = 94/227 (41%), Positives = 139/227 (61%) Query: 6 MLGFGPEGWGGVLLLAALMTVALTLAALAVGAVFGALVAAAKLSRFRTLRVIGDIYTTVF 65 +L G GWG + L+T +L +A L VG V G VA AK S ++LR+ G+IYTT+F Sbjct: 37 LLACGDAGWGDEIAYGFLVTASLAVATLPVGLVIGFFVALAKQSEEKSLRLAGNIYTTIF 96 Query: 66 RGVPELLVIYLFYFGGSTLVTSVGQLFGAEGFVGVPPFVVGALAVGMISGAYQAEVYRSA 125 RG+PELL +++ Y+G LV G EG V + FV G +A+G++ AY +EV SA Sbjct: 97 RGLPELLTLFIVYYGLQILVQQFLATVGYEGAVEINAFVAGMIALGVVFSAYCSEVLLSA 156 Query: 126 VLAVSRGELEAARSIGMPTLTMARRILIPQVLRFALPGIGNVWQLSLKDSALISVTGLAE 185 A+ G+ EA ++G+ R I++PQ++R ALPG+GN+W LKD+AL+SV GL + Sbjct: 157 FKAIPHGQYEAGDALGLHRGKTMRLIILPQLIRIALPGLGNLWMALLKDTALVSVIGLPD 216 Query: 186 LLRTSQVAAGSTHQYFTFFVVGGALYLIMTSISNRVFNRAEAHVGRS 232 +LR + +AA T F FF + L+L++ IS+ VF+ E R+ Sbjct: 217 ILRQTGIAARVTKHAFEFFGIACVLFLVLAMISSVVFSALERSTKRA 263 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: 130 Number of extensions: 3 Number of successful extensions: 1 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: 267 Length adjustment: 24 Effective length of query: 216 Effective length of database: 243 Effective search space: 52488 Effective search space used: 52488 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