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 SM_b20297 SM_b20297 permease
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Smeli:SM_b20297 Length = 426 Score = 210 bits (534), Expect = 8e-59 Identities = 134/431 (31%), Positives = 221/431 (51%), Gaps = 17/431 (3%) Query: 12 MFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLAI 71 +F G LL +G PV F+L VA L +L G G L QR+ + ++ LLA+ Sbjct: 4 LFGGWFALLIAGMPVGFTLI-VAALAYMLWQGTG------LNFAGQRMIAGLNSFPLLAV 56 Query: 72 PYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAMG 131 P+FI ++ SG+ ER+ + L+G +RGGL ++ L + +G A +G Sbjct: 57 PFFILTAQLMNLSGVTERIFDFAKALVGHIRGGLGHVNIMASVLFSGMSGSAVADAAGLG 116 Query: 132 LISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPGL 191 + + M GY+++ + + AAS +G +IPPS+ LVV G S+G LF+G ++PGL Sbjct: 117 QLEIKAMRDAGYDEQFSGSITAASAIIGPLIPPSIPLVVYGVIANTSIGGLFLGGIVPGL 176 Query: 192 MMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIFF 251 + A++ + V ++A+ R + A A A R + + PLI +++G IF Sbjct: 177 LCAASLMIMVYVIAW-RRNYATAQRAGFRRVWS------TFWHALLPLITPFIIIGGIFA 229 Query: 252 GFATPTEAGAVGCAGAIAL-AAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFSLVF 310 G +PTEA V + A+ L + T L V T+ T+ V +++G + F V Sbjct: 230 GVFSPTEAAVVAASYALFLGVVVYREITFAKLVTVLRETVSHTAAVGLLIMGVSLFGYVI 289 Query: 311 RGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKLGI 370 Q + + FL + + LG FI+ I +++P+ VP A + G+ Sbjct: 290 AREQVPQHVATFFLTYAEDPLTFLILVNLMLLALGTFIEALAILLLIVPVLVPTALQFGV 349 Query: 371 DLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLLLI 430 D V +GV++ NL LTPP G ALF + VA ++ + RG++P ++ ++VL+LI Sbjct: 350 DPVHFGVMVVFNLMIGILTPPMGVALFVVSKVA--DIPFGVLARGILPLLIPLVVVLVLI 407 Query: 431 IIFPGIVSFLP 441 IFP +V+F+P Sbjct: 408 TIFPALVTFIP 418 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: 472 Number of extensions: 28 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: 426 Length adjustment: 32 Effective length of query: 413 Effective length of database: 394 Effective search space: 162722 Effective search space used: 162722 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