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 GFF3083 HP15_3026 TRAP dicarboxylate transporter, DctM subunit
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Marino:GFF3083 Length = 499 Score = 317 bits (811), Expect = 7e-91 Identities = 170/452 (37%), Positives = 274/452 (60%), Gaps = 23/452 (5%) Query: 8 LGPV---MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMA 64 +GP+ MF V L G P+AF GG+ ++F L V D + L +P RIF +MA Sbjct: 52 IGPLTYLMFGSLAVALMMGLPLAFVTGGLGVMFIYL-----VGDAMMLNIVPGRIFPLMA 106 Query: 65 NYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVA 124 N + AIP FIFM +MLE++G+ E + + +G + GGLA A ++ +LAA GV+ Sbjct: 107 NPDIAAIPLFIFMASMLERAGLIEEMFSVVYKWMGGISGGLAAATIVASTILAAMVGVIG 166 Query: 125 ATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFI 184 A VV MG+I+LP ML+ Y+ ++A G I A GTLG +IPPS++ ++ SVG+L++ Sbjct: 167 AAVVTMGIIALPAMLKRHYDHKIAIGSIMAGGTLGILIPPSILAILYAVVAQQSVGELYL 226 Query: 185 GSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILL 244 GS++PGLM++ + +VL+ +++ P + P +P + R + L +++ +I PL L+ L Sbjct: 227 GSLLPGLMLSGLYLTYVLVRSWLNPKLGPPIPVEDRISLKEKL--KLLGNLIAPLALVGL 284 Query: 245 VLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGST 304 VLG +F G ATP EA +G GAI +A + +F++ LR+ TT + ++MV++I+ G++ Sbjct: 285 VLGLLFGGIATPVEAAGIGSFGAIIVAMMHKKFSIAGLREASVTTAKASAMVLWIMFGAS 344 Query: 305 AFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPV 364 F + G QF+ D + G LF+ M + +LG F+D+ I + +P+F+P+ Sbjct: 345 VFVGFYILQGGQQFVTDAILGTGMSAYGILFLLMVLLVVLGMFLDWVGILLLAVPIFIPI 404 Query: 365 AQKL------------GIDLV-WYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSD 411 + L G D+V W+GV+ N+Q SFL+PPFG+ALFY+RGV PPE++ Sbjct: 405 VKALEFPGLFGFPPVAGDDVVLWFGVLYLVNMQMSFLSPPFGYALFYIRGVCPPEISMGT 464 Query: 412 IYRGVIPFILLQLLVLLLIIIFPGIVSFLPSL 443 I++ + F+ +Q L + ++ PGIV++LP L Sbjct: 465 IFKSSLVFLAIQAFGLFMCVLIPGIVTWLPGL 496 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: 681 Number of extensions: 39 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: 499 Length adjustment: 33 Effective length of query: 412 Effective length of database: 466 Effective search space: 191992 Effective search space used: 191992 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