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 3607284 Dshi_0699 TRAP C4-dicarboxylate transport system permease DctM subunit (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__Dino:3607284 Length = 437 Score = 239 bits (611), Expect = 1e-67 Identities = 149/436 (34%), Positives = 230/436 (52%), Gaps = 11/436 (2%) Query: 12 MFAGALV-LLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70 + GA+V L++ G PVA + + +LG + + + + G + Y L+ Sbjct: 9 LLLGAIVALMALGMPVALAF----LAANILGAWVFMGGERGIVQLLNNGLGALTTYALVP 64 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 IP F+ MG + +G+ R+ + LLGRL G L+ VL G + +G + + Sbjct: 65 IPLFLLMGEIFFHTGLGGRMFTAIDRLLGRLPGRLSYVTVLGGTGFSTLSGSSMGSTALL 124 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLGISVGDLFIGSVIPG 190 G + +P M GY ++ G I +G L IIPPS + V+L I VG L I VIPG Sbjct: 125 GSLMVPEMNARGYKSHMSIGPILGTGGLAIIIPPSALAVLLATLAQIDVGALLIAGVIPG 184 Query: 191 LMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQVMIPPLILILLVLGSIF 250 LM+A + + I P APA +G K LG +++ ++P + ++++++ + Sbjct: 185 LMLAGFYIATIWIQTRRDPSAAPAYEVAEVSLGAK-LGL-LLRDVVPMVGVMVVIVSLMI 242 Query: 251 FGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRITSMVVFILIGSTAFS--L 308 FG TP+EA A G G I LAAA T+E+LR+ L++T M I+ GS FS L Sbjct: 243 FGIVTPSEAAAFGALGVIILAAAFRCLTVEALRRSVVGALKVTLMAYMIVFGSATFSQLL 302 Query: 309 VFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEIAFIVIPLFVPVAQKL 368 F G +G + +L I L + +LG F++ I + +P+F P+AQ L Sbjct: 303 AFSGASGGLIGWATGFDLD--PIWMLLAMFGVLLVLGMFMEQISIMLLTVPIFFPLAQSL 360 Query: 369 GIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIYRGVIPFILLQLLVLL 428 G DL+W+ +I+ L+ SF TPPFG LF ++GVAPP T +IY IPFI LL++ Sbjct: 361 GFDLIWFALIMLLALEISFTTPPFGLLLFVMKGVAPPSTTMREIYLAAIPFIACSLLLVA 420 Query: 429 LIIIFPGIVSFLPSLG 444 L+I+FP + ++LP LG Sbjct: 421 LLILFPPLATWLPGLG 436 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: 536 Number of extensions: 32 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: 437 Length adjustment: 32 Effective length of query: 413 Effective length of database: 405 Effective search space: 167265 Effective search space used: 167265 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