Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate AZOBR_RS15680 AZOBR_RS15680 amino acid ABC transporter permease
Query= TCDB::P48244 (228 letters) >FitnessBrowser__azobra:AZOBR_RS15680 Length = 216 Score = 100 bits (249), Expect = 2e-26 Identities = 73/216 (33%), Positives = 106/216 (49%), Gaps = 15/216 (6%) Query: 12 LLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFC 71 LL A T+ L+ + IG G ++ R S +K +R +T YI + TPL + + Sbjct: 12 LLSAVQWTLALSAIAFIGGATVGLVIALARTSDIKAVRLAATGYIQLFQGTPLLMQLFLV 71 Query: 72 SFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAEAA 131 FG +GL L N + A LG L S F+ E R I V GQ EAA Sbjct: 72 FFGATV-MGLDL-----------NPWAAAALGLTLNASAFLGEIWRGCIQAVPRGQWEAA 119 Query: 132 RSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASLLMKATIENH 191 +LGL + R +I PQAV+ A+ P L+ L K+T++A++IG E L I N+ Sbjct: 120 SALGLRYPGLMRYVILPQAVKVAVPPTVGFLVQLIKSTSLAAIIGFTE--LTRAGQIVNN 177 Query: 192 ANML-FVVFAIFAVGFMILTLPMGLGLGKLSERLAV 226 A F+VF I AV + ++ P+ L +L R A+ Sbjct: 178 ATFQPFLVFGIVAVLYFLMCWPLSLLSARLERRYAL 213 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: 144 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: 228 Length of database: 216 Length adjustment: 22 Effective length of query: 206 Effective length of database: 194 Effective search space: 39964 Effective search space used: 39964 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: 45 (21.9 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