Align GtrB aka SLL1103, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::P74224 (445 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 193 bits (490), Expect = 1e-53 Identities = 135/443 (30%), Positives = 216/443 (48%), Gaps = 29/443 (6%) Query: 7 LGPMMFVGALVFLGCGYPVAFSLGGVAILFAIIGAALGSFDPIFLSAM--PQRIFGIMAN 64 +G ++F G ++ PVA +LGG A FA + A G P+ L M QR++ + Sbjct: 2 VGLILFGGMVLLFALNAPVAVALGGAA--FAAV-LAKGLTMPVGLEPMLAVQRLYAGADS 58 Query: 65 GTLLAIPFFIFLGSMLERSGIAEQLLETMGIILGHLRGGLALAVILVGTMLAATTGVVAA 124 LLA+P F+ G ++ GI+ +++ ++GHL GGLA ++ A +G AA Sbjct: 59 FPLLAVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAA 118 Query: 125 TVVAMGLISLPIMLRYGYSKELASGVIVASGTLGQIIPPSVVLIVLADQLGVSVGDLFIG 184 A+G I +P M+R GY LA V A G +G IIPPS+ +IV G S+G LF G Sbjct: 119 DTAAVGSILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAG 178 Query: 185 SLLPGLMMAGSFALYVLIIAWLKPDLAPALPAEVRNIGGQELRRRIVQVMLP-------P 237 +LPGL+M S ++ E R G RR + + P Sbjct: 179 GVLPGLLMGASLVALCVV--------------EARRTGRVPERRFDARALWPAIRSGAWA 224 Query: 238 LVLILLVLGSIFFGIASPTEAGAVGSIGAIALAHFNQR-LNWKALWEVCDATLRITSMVM 296 L ++LG+I G+A+ TE+ A+ A+ + + R L W+ L + +++VM Sbjct: 225 LGAPAIILGTIIGGVATATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVM 284 Query: 297 LILLGSTAFSLVFRGLEGDRFMFDLLANLPGGQIGFLAISMITIFILGFFIDFFEIAFIV 356 LI+ ++ F V + + + +L G +I L + + + ++G F++ + Sbjct: 285 LIIAAASLFGWVMALERLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLF 344 Query: 357 LPLFKPVAEALNLDLIWYGVIVGANLQTSFLTPPFGFALFYLRGVAPASLTTGQIYRGAV 416 +P+ P+ AL +DL+ GVIV NL LTPP G L +A L+ I R V Sbjct: 345 VPVLVPLLPALGIDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCSIARIPLSA--ISRAIV 402 Query: 417 PFIGLQVLVLLLIIIFPALINWL 439 P + + ++ LLL+ FP L+ WL Sbjct: 403 PMLVVLIVDLLLVTFFPPLVLWL 425 Lambda K H 0.331 0.148 0.443 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: 510 Number of extensions: 36 Number of successful extensions: 4 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: 445 Length of database: 427 Length adjustment: 32 Effective length of query: 413 Effective length of database: 395 Effective search space: 163135 Effective search space used: 163135 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 51 (24.3 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