Align GluC aka CGL1952, component of Glutamate porter (characterized)
to candidate WP_012048835.1 SWIT_RS13330 ABC transporter permease subunit
Query= TCDB::P48244 (228 letters) >NCBI__GCF_000016765.1:WP_012048835.1 Length = 374 Score = 76.3 bits (186), Expect = 8e-19 Identities = 64/222 (28%), Positives = 104/222 (46%), Gaps = 14/222 (6%) Query: 13 LPAFWVTIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPL-TLVVLFC 71 LP ++T + + +G I GT L + + TL TA+ + L TL + Sbjct: 152 LPGLFLTNRGITVTTVG--ITGTALPMIVTVLGGLTLTLITAWRGHLHKASLCTLGTIVA 209 Query: 72 SFGLYQNLGLTLAGRESSTF---------LVDNNFRLAVLGFILYTSTFVAESLRSGINT 122 L+ L L LA R+ F + F + G ++Y S F AE +R G++ Sbjct: 210 GSALWIVLDLGLA-RDVPHFDRFNFTGGLTLTPEFVAVLWGSVIYASAFAAEIVRGGLDG 268 Query: 123 VHFGQAEAARSLGLGFGATFRSIIFPQAVRAAIVPLGNTLIALTKNTTIASVIGVGEASL 182 V GQ EA+R+LGL + R +I PQA+R + P+ + I + KN+T+A V+G + + Sbjct: 269 VPRGQWEASRALGLSKRQSLRLVIVPQALRMIVPPMNSQFITILKNSTLALVVGYPDLNF 328 Query: 183 LMKATIENHANMLFVVFAIFAVGFMILTLPMGLGLGKLSERL 224 + I NH AI + F L + L + +L+ R+ Sbjct: 329 VANTAI-NHTGQGLEGVAILMLVFFTLASAISLAMNRLNARV 369 Score = 30.8 bits (68), Expect = 4e-05 Identities = 16/52 (30%), Positives = 29/52 (55%) Query: 19 TIKLTIYSAIGAMIFGTILTTMRVSPVKILRTLSTAYINTVRNTPLTLVVLF 70 +I LT+ + + + G + R S + RTL+ +++ VRN PL + +LF Sbjct: 82 SIALTLLIIVLSTMAGVPIALARHSGHMLARTLAGGFVDLVRNVPLVVQLLF 133 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: 210 Number of extensions: 7 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 228 Length of database: 374 Length adjustment: 26 Effective length of query: 202 Effective length of database: 348 Effective search space: 70296 Effective search space used: 70296 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 Apr 09 2024. 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