Align GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate GFF3942 Psest_4012 TRAP-type mannitol/chloroaromatic compound transport system, small permease component
Query= TCDB::P74225 (179 letters) >FitnessBrowser__psRCH2:GFF3942 Length = 181 Score = 99.8 bits (247), Expect = 2e-26 Identities = 65/162 (40%), Positives = 92/162 (56%), Gaps = 6/162 (3%) Query: 4 LLKIAQLIDQFTAWIGKFTAWLVLAMVLTGGWNVVGRYLGRLVGQNLASNGLLEAQWYLF 63 LL++A LID +G+ AW+ L +V+ VV RY G + + L EA Y Sbjct: 8 LLRVAGLIDACNMRLGQLCAWITLFLVIGTTIVVVLRY-----GFGIGAIALQEAVMYGH 62 Query: 64 DLVFLLGAAYTLQTNDHVRVDIFYKSLGDRQRAWVNLLGTCLFLFPFCGLVIFYSWESVI 123 LVF+ AA+TLQ N HVRVDIFY+ R++A V+ LG LFL P C + + SW+ V Sbjct: 63 ALVFMGAAAWTLQRNGHVRVDIFYQKFSGRRQATVDGLGHLLFLLPVCLFLGWNSWDYVS 122 Query: 124 NSWHIWETSPDPGGLP-RYPIKTMIIVGFVLLIFQGIAEVIK 164 NSW E S + GGL Y K++I++ L Q ++++IK Sbjct: 123 NSWSTLEGSNESGGLKFVYLQKSIILLLVGSLALQAVSDLIK 164 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: 150 Number of extensions: 11 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: 181 Length adjustment: 19 Effective length of query: 160 Effective length of database: 162 Effective search space: 25920 Effective search space used: 25920 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