Align Alr3026 protein, component of The 2-oxo monocarboxylate transporter (Pernil et al., 2010). Transports pyruvate which is inhibited by various 2-ketoacids (characterized)
to candidate 6938425 Sama_2544 TRAP-type transport system, small permease component (RefSeq)
Query= TCDB::Q8YSQ8 (184 letters) >FitnessBrowser__SB2B:6938425 Length = 168 Score = 97.8 bits (242), Expect = 9e-26 Identities = 55/168 (32%), Positives = 89/168 (52%), Gaps = 6/168 (3%) Query: 6 KISRIIDAFTERIGRYTSWLVLVMVILGVWNVVGRYLGRISGNNLTSNAYIEAQWYIFDV 65 K+ + TE +GR W L MV++ + VV RY L A Y+ Sbjct: 3 KLIGFFEGITEALGRLVGWFTLGMVLMTLAVVVLRYAFATGATALQETAL-----YLHGA 57 Query: 66 IFFLGAAYTLKHNEHVRVDIFYSNWQRRRKAIADFLGTIFFLIPFSIIVIFVSWETIVAS 125 +F L A +TLK + HVRVD+FY R + DF+GT+ FL P S+ + S++ ++ + Sbjct: 58 VFTLAAGFTLKRDAHVRVDVFYRQCSERTRHWIDFVGTLVFLFPLSLAIGLYSFDYVMNA 117 Query: 126 WQIGELSPDPGGLPRYPIKAMIIVGF-VLLIIQGISQAIKNLAIIQGR 172 W+I E S + GGLP ++ +++G V LI+QG+ + ++ + GR Sbjct: 118 WRIQESSAEAGGLPWVYLQKSLLLGLCVSLILQGLCELYRHGKALFGR 165 Lambda K H 0.328 0.144 0.448 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: 100 Number of extensions: 5 Number of successful extensions: 2 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: 184 Length of database: 168 Length adjustment: 19 Effective length of query: 165 Effective length of database: 149 Effective search space: 24585 Effective search space used: 24585 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 44 (21.6 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