Align GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate SM_b21135 SM_b21135 amino acid ABC transporter substrate-binding protein
Query= TCDB::P74223 (296 letters) >FitnessBrowser__Smeli:SM_b21135 Length = 280 Score = 91.3 bits (225), Expect = 2e-23 Identities = 65/214 (30%), Positives = 98/214 (45%), Gaps = 7/214 (3%) Query: 37 LIPGLTVSATAQTMVLETNGIAMTSREVSLEAIRQRGKLRVGVKDNLRPLGFRDGQGELT 96 +I TV+A+ VL L+ + RG L +G P F+ + +L Sbjct: 1 MISRFTVAASFVAAVLAAMPAQAQQASSKLDEVLSRGHLILGTGSTNAPWHFKSAEDKLQ 60 Query: 97 GLEIALARRLALALLGDETAVELVPVQNQDRLPLLLNGDVDLIIAQMGQNPARDRLVDFS 156 G ++ + R +A AL GD +E V + R+P + G VD+ M R + + F+ Sbjct: 61 GFDVDMGRIIAKALFGDPEKIEFVNQSSDARIPNITTGKVDITCQFMTVTGERAQQIAFT 120 Query: 157 PPYYMDGVGLISKNSSLKNID------RNQAHTIAVLNNSGTIPVIKQAFPQATLVGVDS 210 PYY +GVGL+ K K D + TI+VL N ++ A P+AT+ +S Sbjct: 121 IPYYREGVGLMLKADG-KYADYEALKAAGSSVTISVLQNVYAEDMVHAALPEATVDQYES 179 Query: 211 YDQAYQILEQGQAMAFAGDNSVLSGWAQSQSDYY 244 D YQ LE G+A A A D S L+ + S Y Sbjct: 180 VDLIYQALESGRADAAATDQSSLAWYMTQNSGRY 213 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: 156 Number of extensions: 5 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: 280 Length adjustment: 26 Effective length of query: 270 Effective length of database: 254 Effective search space: 68580 Effective search space used: 68580 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