Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_052592082.1 VV02_RS13170 amino acid ABC transporter permease
Query= TCDB::P48244 (228 letters) >NCBI__GCF_001190945.1:WP_052592082.1 Length = 226 Score = 225 bits (573), Expect = 6e-64 Identities = 112/228 (49%), Positives = 163/228 (71%), Gaps = 2/228 (0%) Query: 1 MSTLWADLGPSLLPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVR 60 MS L+++ + AFW+TIKLT+ +AIG+++ GT++ +R+SPV +LR L T+Y+N R Sbjct: 1 MSQLFSEF--EVWSAFWMTIKLTVLAAIGSLVIGTLVAVLRLSPVPMLRFLGTSYVNVFR 58 Query: 61 NTPLTLVVLFCSFGLYQNLGLTLAGRESSTFLVDNNFRLAVLGFILYTSTFVAESLRSGI 120 NTPLTL++L C+ L+ LG+TLA + F NNFRLA++G +Y +++V E+LRSG+ Sbjct: 59 NTPLTLIILSCNLVLWAKLGVTLADDKDPKFFDINNFRLALVGLTIYHASYVCEALRSGV 118 Query: 121 NTVHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEA 180 NT+ GQAEAARS+GL F + R ++ PQA R ++VPLGNTLIALTKNTT+A IGV E Sbjct: 119 NTIPLGQAEAARSIGLTFRQSLREVVLPQAFRGSVVPLGNTLIALTKNTTVAVTIGVAEM 178 Query: 181 SLLMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERLAVKK 228 + ++ E+ L F + A F++LTLP+GL +G+L +RLAVK+ Sbjct: 179 AAVLAKVTEDDPGKLNQAFFVSAALFVLLTLPVGLLIGRLGKRLAVKR 226 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: 196 Number of extensions: 2 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: 228 Length of database: 226 Length adjustment: 22 Effective length of query: 206 Effective length of database: 204 Effective search space: 42024 Effective search space used: 42024 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