Align GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate Synpcc7942_1276 Synpcc7942_1276 extracellular solute-binding protein, family 3
Query= TCDB::P74223 (296 letters) >FitnessBrowser__SynE:Synpcc7942_1276 Length = 260 Score = 164 bits (415), Expect = 2e-45 Identities = 95/229 (41%), Positives = 131/229 (57%), Gaps = 6/229 (2%) Query: 66 LEAIRQRGKLRVGVKDNLRPLGFRDGQGELTGLEIALARRLALALLGDETAVELVPVQNQ 125 LE I++RG L VGV+ N+ PL ++D QG+ G E+ LAR LA LLG+ AV +Q++ Sbjct: 38 LETIKRRGYLIVGVQANVAPLSWQDAQGQWQGFEVDLARSLAAELLGNSAAVRFEGLQSR 97 Query: 126 DRLPLLLNGDVDLIIAQMGQNPARDRLVDFSPPYYMDGVGLISKNSSLKNIDRNQAHTIA 185 DRLP LL VDL+IAQM AR R+ FS PYY D +GL+++ Q +A Sbjct: 98 DRLPALLADRVDLLIAQMTVTDARQRVAQFSRPYYRDRIGLLTRRGI------TQPQRVA 151 Query: 186 VLNNSGTIPVIKQAFPQATLVGVDSYDQAYQILEQGQAMAFAGDNSVLSGWAQSQSDYYH 245 VL S IP+++ P+ LVGV SY A L++GQ A D VL W + Y Sbjct: 152 VLQGSSAIPLLRWQAPELALVGVKSYAAAQTALDRGQVDGIAADRLVLQQWQRQSDRYQL 211 Query: 246 LPLQLTVNPLAIAMAKGLQHQALQREVNQTLLQLRASGWLRQQWQAWGL 294 LP Q PLAIA+ +GLQ+++LQ +++ + A LR + WGL Sbjct: 212 LPQQWGDFPLAIALPQGLQYRSLQIAIDRLIQNWDADDKLRDIRKRWGL 260 Lambda K H 0.322 0.136 0.397 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: 213 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: 296 Length of database: 260 Length adjustment: 25 Effective length of query: 271 Effective length of database: 235 Effective search space: 63685 Effective search space used: 63685 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 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