Align GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Dsui_1263 Dsui_1263 TRAP-type mannitol/chloroaromatic compound transport system, small permease component
Query= TCDB::P74225 (179 letters) >FitnessBrowser__PS:Dsui_1263 Length = 195 Score = 152 bits (383), Expect = 4e-42 Identities = 76/177 (42%), Positives = 107/177 (60%), Gaps = 5/177 (2%) Query: 1 MDKLLKIAQLIDQFTAWIGKFTAWLVLAMVLTGGWNVVGRYLGRLVGQNLASNGLLEAQW 60 M LL +++ ID +GK WLVL M + N V RY N +SNGLLE QW Sbjct: 1 MTFLLSVSRGIDALNERVGKAVIWLVLLMTILSAGNAVMRYT-----INYSSNGLLEIQW 55 Query: 61 YLFDLVFLLGAAYTLQTNDHVRVDIFYKSLGDRQRAWVNLLGTCLFLFPFCGLVIFYSWE 120 YLF ++FL A YTL N+HVR+D+ R +AW++++GT LFL P L+++ SW Sbjct: 56 YLFAVIFLFSAGYTLLRNEHVRIDVVAGKFSPRGQAWIDIIGTLLFLMPMAVLIMYLSWP 115 Query: 121 SVINSWHIWETSPDPGGLPRYPIKTMIIVGFVLLIFQGIAEVIKNLAIALGHVDTEA 177 +N+W E S +PGGL R+P + MI VGF+LL+ QG++E+IK +A G + A Sbjct: 116 IFMNAWDSGEMSSNPGGLIRWPARLMIPVGFLLLVLQGLSELIKRIAFLRGLIANPA 172 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: 132 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: 195 Length adjustment: 20 Effective length of query: 159 Effective length of database: 175 Effective search space: 27825 Effective search space used: 27825 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