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 6938424 Sama_2543 C4 dicarboxylate ABC transporter permease (RefSeq)
Query= TCDB::Q8YSQ7 (445 letters) >FitnessBrowser__SB2B:6938424 Length = 453 Score = 443 bits (1140), Expect = e-129 Identities = 230/450 (51%), Positives = 310/450 (68%), Gaps = 20/450 (4%) Query: 11 VMFAGALVLLSSGYPVAFSLGGVAILFGLLGIGLGVFDPIFLTAMPQRIFGIMANYTLLA 70 ++F ++L GYPVA +LGGVA LF L G FD +P RIFGI+ N L+A Sbjct: 4 LLFLIICLVLMLGYPVALTLGGVAFLFALFASFFGAFDMGLFGLLPNRIFGILNNQILMA 63 Query: 71 IPYFIFMGAMLEKSGIAERLLETMGILLGRLRGGLALAVVLVGALLAATTGVVAATVVAM 130 +P F+FMG +LEKS IAE+LL TMG LLGR RGGL +V VG LLAA+TG+V ATVV M Sbjct: 64 VPLFVFMGVVLEKSRIAEQLLTTMGALLGRFRGGLIFSVFFVGVLLAASTGIVGATVVTM 123 Query: 131 GLISLPIMLRYGYNKELATGVIAASGTLGQIIPPSVVLVVLGDQLG-------------- 176 GL+SLP +L+ GY+ EL+ G I A+GTLGQIIPPS+ LV+LGD L Sbjct: 124 GLMSLPTLLKRGYSPELSAGAICATGTLGQIIPPSIALVLLGDVLSNAYQQAQLKMGIFN 183 Query: 177 ---ISVGDLFIGSVIPGLMMASAFALHVLIVAFIRPDVAPALPAQVREIGGKALGKRVIQ 233 +SVGDLF G++IPGLM+ S + + L + P + Q E A RVI Sbjct: 184 PKSVSVGDLFAGALIPGLMLVSLYMFYTLFRLWRSPADFGSAITQDYEPASLA---RVIS 240 Query: 234 VMIPPLILILLVLGSIFFGFATPTEAGAVGCAGAIALAAANGQFTLESLRQVCDTTLRIT 293 ++PPL+LI LVLGSI G ATPTEA +VG AGA+ +A Q ++ +L++V +T++IT Sbjct: 241 ALLPPLLLIFLVLGSILAGIATPTEAASVGAAGALLIALLKRQMSMLALKEVMQSTVKIT 300 Query: 294 SMVVFILIGSTAFSLVFRGLNGDQFMFDVLANLPGGKIGFLFVSMTTVFLLGFFIDFFEI 353 SMV ILIG++ FSLVFRGL G++ + ++ AN+PGG +G + + MT +F+LGF +DF EI Sbjct: 301 SMVFLILIGASVFSLVFRGLGGEELIHNLFANMPGGVVGAMLLVMTVIFVLGFILDFIEI 360 Query: 354 AFIVIPLFVPVAQKLGIDLVWYGVILGANLQTSFLTPPFGFALFYLRGVAPPEVTTSDIY 413 F+V+PL P+ +G+D VW G+++ NLQTSFLTPPFGFALFYLRGV+ V++ IY Sbjct: 361 TFVVVPLVAPILLAMGLDPVWLGIMIALNLQTSFLTPPFGFALFYLRGVSGDSVSSGQIY 420 Query: 414 RGVIPFILLQLLVLLLIIIFPGIVSFLPSL 443 RGVIPF++LQLL+L+L+ I+P + ++LPS+ Sbjct: 421 RGVIPFVILQLLMLILLGIWPALATWLPSV 450 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: 586 Number of extensions: 34 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: 453 Length adjustment: 33 Effective length of query: 412 Effective length of database: 420 Effective search space: 173040 Effective search space used: 173040 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