Align GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate 6938425 Sama_2544 TRAP-type transport system, small permease component (RefSeq)
Query= TCDB::P74225 (179 letters) >FitnessBrowser__SB2B:6938425 Length = 168 Score = 102 bits (255), Expect = 3e-27 Identities = 57/161 (35%), Positives = 88/161 (54%), Gaps = 6/161 (3%) Query: 6 KIAQLIDQFTAWIGKFTAWLVLAMVLTGGWNVVGRYLGRLVGQNLASNGLLEAQWYLFDL 65 K+ + T +G+ W L MVL VV RY + L E YL Sbjct: 3 KLIGFFEGITEALGRLVGWFTLGMVLMTLAVVVLRYAFAT-----GATALQETALYLHGA 57 Query: 66 VFLLGAAYTLQTNDHVRVDIFYKSLGDRQRAWVNLLGTCLFLFPFCGLVIFYSWESVINS 125 VF L A +TL+ + HVRVD+FY+ +R R W++ +GT +FLFP + YS++ V+N+ Sbjct: 58 VFTLAAGFTLKRDAHVRVDVFYRQCSERTRHWIDFVGTLVFLFPLSLAIGLYSFDYVMNA 117 Query: 126 WHIWETSPDPGGLPRYPIKTMIIVGF-VLLIFQGIAEVIKN 165 W I E+S + GGLP ++ +++G V LI QG+ E+ ++ Sbjct: 118 WRIQESSAEAGGLPWVYLQKSLLLGLCVSLILQGLCELYRH 158 Lambda K H 0.328 0.145 0.476 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: 124 Number of extensions: 6 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: 179 Length of database: 168 Length adjustment: 18 Effective length of query: 161 Effective length of database: 150 Effective search space: 24150 Effective search space used: 24150 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