Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate 17340 b3270 putative transport system permease protein (VIMSS)
Query= TCDB::P48244 (228 letters) >FitnessBrowser__Keio:17340 Length = 367 Score = 84.7 bits (208), Expect = 2e-21 Identities = 65/178 (36%), Positives = 101/178 (56%), Gaps = 14/178 (7%) Query: 17 WVTIKLTIYSA----IGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLFCS 72 W + LT+ A GA+ +G +L R S + I+R LS +I R PL + VLF S Sbjct: 156 WGGLTLTLIIASVGIAGALPWGILLALGRRSHMPIVRILSVIFIEFWRGVPL-ITVLFMS 214 Query: 73 FGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGINTVHFGQAEAAR 132 ++ L L E ++ +D R A++G IL+ S +VAE +R G+ + GQ EAA Sbjct: 215 -----SVMLPLFMAEGTS--IDKLIR-ALVGVILFQSAYVAEVVRGGLQALPKGQYEAAE 266 Query: 133 SLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEA-SLLMKATIE 189 SL LG+ T +I PQA++ I L NT+IAL K+T++ +IG+ + S + +AT++ Sbjct: 267 SLALGYWKTQGLVILPQALKLVIPGLVNTIIALFKDTSLVIIIGLFDLFSSVQQATVD 324 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: 218 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: 367 Length adjustment: 26 Effective length of query: 202 Effective length of database: 341 Effective search space: 68882 Effective search space used: 68882 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: 48 (23.1 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