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 GFF3943 Psest_4013 TRAP transporter, DctM subunit
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__psRCH2:GFF3943 Length = 458 Score = 456 bits (1173), Expect = e-133 Identities = 237/453 (52%), Positives = 317/453 (69%), Gaps = 20/453 (4%) Query: 6 EWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMAN 65 E++ ++F L SGYPVAF+LGG+A+LF +G+ G FD +L A+P RIFGIM N Sbjct: 3 EFMAILLFISICFALMSGYPVAFTLGGMALLFAGVGVVTGSFDVGYLHALPNRIFGIMNN 62 Query: 66 YTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAA 125 T+LA+P F+FMG MLEKS +AE LLE+M L G +RGGLA++V +VGALLAA+TG+V A Sbjct: 63 QTMLAVPLFVFMGVMLEKSRVAEDLLESMSRLFGTMRGGLAISVCVVGALLAASTGIVGA 122 Query: 126 TVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLG--------- 176 TVV MGL++LP MLR GY+ +ATG +AA+GTLGQIIPPS++LV+LGD + Sbjct: 123 TVVTMGLLALPTMLRRGYDPAIATGTLAATGTLGQIIPPSIILVLLGDVMSSAFQQAQLK 182 Query: 177 --------ISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALG 228 +SVGDLF+G++IPGL++ + L+++ VA +P PALP + E+G G Sbjct: 183 MGIFSPKTVSVGDLFVGALIPGLLLVGMYILYLIAVAIFQPKKLPALPQE--ELGPIEWG 240 Query: 229 KRVIQVMIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDT 288 K +I ++PPL LI VLGSI G+ATPTEA A+G GA L+ A GQ L+QV Sbjct: 241 K-LIGSLLPPLALITAVLGSILAGYATPTEAAAIGALGATLLSIAKGQLNFTQLKQVAFG 299 Query: 289 TLRITSMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFI 348 T ITSMV ILIG++ FSLVFRG G+ + D L +LPGG +G V M +FLLGF + Sbjct: 300 TTEITSMVFLILIGASLFSLVFRGFGGEVLIEDALHSLPGGVLGAFLVVMLVIFLLGFIL 359 Query: 349 DFFEIAFIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVT 408 DF EI F+V+P+ P+ +G+D VW GV+ NLQTSFLTPPFGF+LFYLRGV P V Sbjct: 360 DFIEIIFVVVPIVGPILLAMGLDPVWLGVMFAINLQTSFLTPPFGFSLFYLRGVTPRSVP 419 Query: 409 TSDIYRGVIPFILLQLLVLLLIIIFPGIVSFLP 441 TS +Y+GV+PFI +Q+ +L++ ++PGIV++LP Sbjct: 420 TSVMYKGVLPFIAIQIGMLVVAYMWPGIVTWLP 452 Score = 27.3 bits (59), Expect = 0.001 Identities = 39/171 (22%), Positives = 71/171 (41%), Gaps = 20/171 (11%) Query: 53 TAMPQRIFGIMANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLV 112 T + +F I+ +L ++ + F G +L I + L G +LG L V+LV Sbjct: 301 TEITSMVFLILIGASLFSLVFRGFGGEVL----IEDALHSLPGGVLGAF-----LVVMLV 351 Query: 113 GALLAATTGVVAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLG 172 LL + V + ++ PI+L G + + A + + PP G Sbjct: 352 IFLLGFILDFIEIIFVVVPIVG-PILLAMGLDPVWLGVMFAINLQTSFLTPP------FG 404 Query: 173 DQL----GISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQV 219 L G++ + + G++ A + +L+VA++ P + LP QV Sbjct: 405 FSLFYLRGVTPRSVPTSVMYKGVLPFIAIQIGMLVVAYMWPGIVTWLPEQV 455 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: 647 Number of extensions: 31 Number of successful extensions: 4 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: 445 Length of database: 458 Length adjustment: 33 Effective length of query: 412 Effective length of database: 425 Effective search space: 175100 Effective search space used: 175100 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