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 GFF3942 Psest_4012 TRAP-type mannitol/chloroaromatic compound transport system, small permease component
Query= TCDB::Q8YSQ8 (184 letters) >FitnessBrowser__psRCH2:GFF3942 Length = 181 Score = 99.0 bits (245), Expect = 4e-26 Identities = 66/178 (37%), Positives = 97/178 (54%), Gaps = 6/178 (3%) Query: 4 LLKISRIIDAFTERIGRYTSWLVLVMVILGVWNVVGRYLGRISGNNLTSNAYIEAQWYIF 63 LL+++ +IDA R+G+ +W+ L +VI VV RY G + + A EA Y Sbjct: 8 LLRVAGLIDACNMRLGQLCAWITLFLVIGTTIVVVLRY-----GFGIGAIALQEAVMYGH 62 Query: 64 DVIFFLGAAYTLKHNEHVRVDIFYSNWQRRRKAIADFLGTIFFLIPFSIIVIFVSWETIV 123 ++F AA+TL+ N HVRVDIFY + RR+A D LG + FL+P + + + SW+ + Sbjct: 63 ALVFMGAAAWTLQRNGHVRVDIFYQKFSGRRQATVDGLGHLLFLLPVCLFLGWNSWDYVS 122 Query: 124 ASWQIGELSPDPGGLP-RYPIKAMIIVGFVLLIIQGISQAIKNLAIIQGRLEPQEENH 180 SW E S + GGL Y K++I++ L +Q +S IK I GRL E H Sbjct: 123 NSWSTLEGSNESGGLKFVYLQKSIILLLVGSLALQAVSDLIKAGYRIAGRLPEAEVKH 180 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: 123 Number of extensions: 10 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: 181 Length adjustment: 19 Effective length of query: 165 Effective length of database: 162 Effective search space: 26730 Effective search space used: 26730 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