Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_053937456.1 WG78_RS08860 amino acid ABC transporter permease
Query= TCDB::P48244 (228 letters) >NCBI__GCF_001294205.1:WP_053937456.1 Length = 221 Score = 94.7 bits (234), Expect = 1e-24 Identities = 58/179 (32%), Positives = 93/179 (51%), Gaps = 12/179 (6%) Query: 10 PSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVL 69 P LL T+ + + +G ++ G +L +R+S +K L+ + Y++ +R TPL + + Sbjct: 12 PYLLKGTGYTLLFAVGAMVGGLLVGALLAVLRLSGIKALQWPAALYVSAMRGTPLLVQIF 71 Query: 70 FCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAE 129 +GL +G+ +L L T +V+E++R IN V GQ E Sbjct: 72 IIYYGL-PAIGIQF-----------EPITAGILALSLNTGAYVSETMRGAINGVDRGQWE 119 Query: 130 AARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLMKATI 188 AA S G+G T I++PQA+R A+ L N+LI+L K+T++ SVI V E L K I Sbjct: 120 AAFSQGMGRWQTLHYIVWPQALRLAVPSLSNSLISLIKDTSLVSVIAVTELMLATKEVI 178 Lambda K H 0.327 0.139 0.397 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: 117 Number of extensions: 6 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: 228 Length of database: 221 Length adjustment: 22 Effective length of query: 206 Effective length of database: 199 Effective search space: 40994 Effective search space used: 40994 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