Align Alr3027 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate 8501407 DvMF_2137 TRAP dicarboxylate transporter, DctM subunit (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Miya:8501407 Length = 427 Score = 192 bits (488), Expect = 2e-53 Identities = 140/442 (31%), Positives = 223/442 (50%), Gaps = 27/442 (6%) Query: 8 LGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAM--PQRIFGIMAN 65 +G ++F G ++L + PVA +LGG A +L GL + P+ L M QR++ + Sbjct: 2 VGLILFGGMVLLFALNAPVAVALGGAAFA-AVLAKGLTM--PVGLEPMLAVQRLYAGADS 58 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 + LLA+P F+ G ++ GI+ R++ L+G L GGLA V+ A +G AA Sbjct: 59 FPLLAVPLFMLAGELMSAGGISRRIVALADALVGHLPGGLAAVSVVSAMFFAGVSGSAAA 118 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIG 185 A+G I +P M+R GY LA V AA G +G IIPPS+ ++V G G S+G LF G Sbjct: 119 DTAAVGSILIPAMIRRGYPAPLAGAVQAAGGCIGVIIPPSIPMIVFGALTGASIGRLFAG 178 Query: 186 SVIPGLMMASAFALHVLIVAFIRPDV------APALPAQVREIGGKALGKRVIQVMIPPL 239 V+PGL+M ++ ++ A V A AL +R G ALG I Sbjct: 179 GVLPGLLMGASLVALCVVEARRTGRVPERRFDARALWPAIRS-GAWALGAPAI------- 230 Query: 240 ILILLVLGSIFFGFATPTEAGAVGCAGAIALAA-ANGQFTLESLRQVCDTTLRITSMVVF 298 +LG+I G AT TE+ A+ A A+ + A+ + L ++ +++V+ Sbjct: 231 -----ILGTIIGGVATATESAAMAVAYALPVGLYAHRELRWRDLPRLALCAGVTSAVVML 285 Query: 299 ILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVI 358 I+ ++ F V Q + + +L G +I L + + ++G F++ + + Sbjct: 286 IIAAASLFGWVMALERLPQAIAAWMLSLSGDRIVLLLLVNLLLLVVGAFLETTAAILLFV 345 Query: 359 PLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIP 418 P+ VP+ LGIDLV GVI+ NL LTPP G L +A + S I R ++P Sbjct: 346 PVLVPLLPALGIDLVHLGVIVVVNLAIGMLTPPLGVCLVVSCSIA--RIPLSAISRAIVP 403 Query: 419 FILLQLLVLLLIIIFPGIVSFL 440 +++ ++ LLL+ FP +V +L Sbjct: 404 MLVVLIVDLLLVTFFPPLVLWL 425 Lambda K H 0.331 0.149 0.437 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: 429 Number of extensions: 31 Number of successful extensions: 3 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