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 GFF2674 PGA1_c27160 TRAP transporter, subunit DctM
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Phaeo:GFF2674 Length = 500 Score = 230 bits (587), Expect = 7e-65 Identities = 153/499 (30%), Positives = 243/499 (48%), Gaps = 65/499 (13%) Query: 3 LAYEWLGPVMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGI 62 ++YE + +MFAG +++L +G V ++G V L G+L G G + F AM + Sbjct: 1 MSYELIAIMMFAGMMLMLMTGQRVFGAIGFVGALAGMLLWGTGGSEIPFSAAMK-----L 55 Query: 63 MANYTLLAIPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGV 122 M Y LL +P FIFMG +L +S IA+ L + +G ++GGLA+ + + L++A G+ Sbjct: 56 MKWYPLLTLPMFIFMGYVLSESKIADDLYRMFHVWMGPVKGGLAIGTIGLMVLISAMNGL 115 Query: 123 VAATVVAMGLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDL 182 A + I+LP +LR GY+K L TG I A +LG ++PPSVVLV+ VG L Sbjct: 116 SVAGMAIGATIALPELLRRGYDKTLVTGTIQAGSSLGILVPPSVVLVLYAMIARQPVGQL 175 Query: 183 FIGSVIPGLMMASAF-----------------------------------------ALHV 201 ++ V+PGL+MA+ F AL V Sbjct: 176 WLAGVVPGLLMATMFIIYIYLRARMQPELGPAMSPEDLAEYERISDHPLRLNYVALALLV 235 Query: 202 LIVAFIRPDVAPALPAQVREIGGKALG------------------KRVIQVMIPPLILIL 243 L+ ++ V A PA + G L R++ + PL + Sbjct: 236 LVPLVVKLGVIEAKPAIGVALAGSVLAFVTRGIPAFYHDVFMREKYRLLFSGVLPLAIFA 295 Query: 244 LVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGS 303 ++ G+ + E+ A+G A A G+ E +TL I+ M ++I++ + Sbjct: 296 AMMVPFVNGWTSLVESSAIGAMTAFIAAILKGRMNKEVFETSVRSTLGISCMFMWIILAA 355 Query: 304 TAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFL-LGFFIDFFEIAFIVIPLFV 362 F +F GL + + D+ G + + M F+ +G F+D + IV PL+V Sbjct: 356 LGFGAIFDGLGAVKAIEDLFTTQLGLSPWMILILMQLSFIVMGTFLDDTAMLVIVAPLYV 415 Query: 363 PVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILL 422 P+ LG DL+WYGV+ Q +++TPPFG+ LF +R +APPE+ DIY +IPF + Sbjct: 416 PLVGALGFDLIWYGVLYTITTQIAYMTPPFGYNLFLMRAMAPPEIGLKDIYVSIIPFAAV 475 Query: 423 QLLVLLLIIIFPGIVSFLP 441 ++ L L++IFP I +LP Sbjct: 476 MVVALALVMIFPQIALWLP 494 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: 561 Number of extensions: 30 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 445 Length of database: 500 Length adjustment: 33 Effective length of query: 412 Effective length of database: 467 Effective search space: 192404 Effective search space used: 192404 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