Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate AZOBR_RS18065 AZOBR_RS18065 amino acid ABC transporter permease
Query= TCDB::P48244 (228 letters) >FitnessBrowser__azobra:AZOBR_RS18065 Length = 219 Score = 92.4 bits (228), Expect = 6e-24 Identities = 73/228 (32%), Positives = 109/228 (47%), Gaps = 22/228 (9%) Query: 3 TLWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNT 62 TLW L LL A W T+ L++ S IG + G L +R+ + R Y+ + T Sbjct: 5 TLWDILRNLLLAARW-TVVLSLVSFIGGGLLGMALLYLRIGKARAGRMFVQGYVELFQGT 63 Query: 63 PLTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINT 122 PL L+ LF +F GL L G + +L A L +L+T+ F+ E R + + Sbjct: 64 PL-LMQLFLAF-----FGLGLFGIDVPAWLA------AGLALVLWTAAFLVEIWRGCVES 111 Query: 123 VHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEAS- 181 V GQ EA+ SLG+G+ R +I PQAVR A+ P + + K T + S+IG E S Sbjct: 112 VARGQWEASASLGMGYVQQMRYVILPQAVRVAVPPTVGFSVQVVKGTALTSIIGFVELSK 171 Query: 182 ---LLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAV 226 ++ AT E F V+ + A+ + L P+ L +L V Sbjct: 172 AGTVVTNATFEP-----FTVYGLVALIYFALCWPLSKSSQILERKLNV 214 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: 128 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: 219 Length adjustment: 22 Effective length of query: 206 Effective length of database: 197 Effective search space: 40582 Effective search space used: 40582 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