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 AZOBR_RS14700 AZOBR_RS14700 C4-dicarboxylate ABC transporter permease
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__azobra:AZOBR_RS14700 Length = 433 Score = 220 bits (560), Expect = 8e-62 Identities = 138/440 (31%), Positives = 236/440 (53%), Gaps = 25/440 (5%) Query: 11 VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70 V+ L++L +G VA +L GV G + + L P+ + M I+G ++TL A Sbjct: 9 VVVVTMLLMLGTGIWVALALAGV----GFVAMALFTTRPVGMV-MATNIWGASTSWTLTA 63 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 +P FI+MG +L ++ I+ + + + G L G L ++ + AA +G AAT + Sbjct: 64 LPLFIWMGEILFRTRISSDMFKGLAPWTGWLPGRLMHVNIVGCTIFAAVSGSSAATAATI 123 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190 G +++P + R GY+ + G +A +GTLG +IPPS++++V G +S+ LFI VIPG Sbjct: 124 GRMTIPELTRRGYDPMMIVGSLAGAGTLGLLIPPSIIMIVYGVAADVSIARLFIAGVIPG 183 Query: 191 LMMASAFALHVLIVAFIRPDVAP------ALPAQVREIGGKALGKRVIQVMIPPLILILL 244 +++ F L+V + + PD P +L ++R+ G +IP ++LI Sbjct: 184 IVLTGLFMLYVGGWSLLNPDRVPPREARQSLMEKIRDTGS----------LIPVMLLIAG 233 Query: 245 VLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGST 304 VLGSI+ G ATPTEA +G G++ LA G + + R + M+ FIL G+ Sbjct: 234 VLGSIYAGIATPTEAAGIGVLGSLLLALVTGTMSWATFRDSVMGAAHTSCMIGFILAGA- 292 Query: 305 AFSLVFRGLNG-DQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVP 363 AF V G G + + + + ++ L V ++G F+D + + + +P Sbjct: 293 AFLTVAMGYTGIPRLLAEWITSMQLTTASLLVVLTLFFIVMGCFLDGISMVVLTTSVILP 352 Query: 364 VAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQ 423 + Q GIDL+W+G+ + ++ + +TPP GF LF L+ + + T I + +PF L+ Sbjct: 353 MVQNAGIDLLWFGIYIIIVVEMAQITPPVGFNLFVLQSMTGKNIFT--IAKASLPFFLMM 410 Query: 424 LLVLLLIIIFPGIVSFLPSL 443 ++++ L+ IFPG+VS+LPSL Sbjct: 411 IVMVALLWIFPGMVSWLPSL 430 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: 463 Number of extensions: 28 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: 433 Length adjustment: 32 Effective length of query: 413 Effective length of database: 401 Effective search space: 165613 Effective search space used: 165613 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