Align Glycerol facilitator (characterized)
to candidate SMc02648 SMc02648 transport transmembrane protein
Query= TCDB::P18156 (274 letters) >FitnessBrowser__Smeli:SMc02648 Length = 233 Score = 55.8 bits (133), Expect = 8e-13 Identities = 60/202 (29%), Positives = 91/202 (45%), Gaps = 26/202 (12%) Query: 7 EVIGTMLLI--IFGAGVCA-GVNLKKSLSFQSGWIVVVFGWGLGVAMAAYAVGGISGAHL 63 E +GT LL+ + G+G+ A + +L+ + I G + + +G +SGAH Sbjct: 13 EALGTGLLVAAVVGSGIMADALTADDALALVANTIAT----GAILVVLVTILGPLSGAHF 68 Query: 64 NPALTIALAFVGDFPWKEVPVYIAAQMIGAIIGAVIIYLHYLPHWKSTDDPAAKLGV-FS 122 NPA+++ A G ++ Y+ AQ+ GAI G + +L + D P + + Sbjct: 69 NPAVSLVFALSGRLTRRDCAAYVIAQVAGAIAGTALAHLMF-------DLPPLDMSMKVR 121 Query: 123 TGPSIPHTFANVLSEVIGTFVLVLGILAIGANQFTEGLNPLIVGFLIVAIGISLGGTTGY 182 TGP A LSE + F LV ILA +F P +VG I A +T + Sbjct: 122 TGP------AQWLSEGVAAFGLVATILA--GIRFHREAVPWLVGLYITA-AYWFTASTSF 172 Query: 183 AINPARDLGPRIAHAFLPI-PG 203 A NPA L + F I PG Sbjct: 173 A-NPAVALARSFTNTFSGIRPG 193 Lambda K H 0.325 0.142 0.451 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: 188 Number of extensions: 12 Number of successful extensions: 1 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: 274 Length of database: 233 Length adjustment: 24 Effective length of query: 250 Effective length of database: 209 Effective search space: 52250 Effective search space used: 52250 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.5 bits) S2: 46 (22.3 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