Align GtrC aka GLNH aka SLL1104, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate AO353_21710 AO353_21710 ABC transporter substrate-binding protein
Query= TCDB::P74223 (296 letters) >FitnessBrowser__pseudo3_N2E3:AO353_21710 Length = 282 Score = 87.8 bits (216), Expect = 3e-22 Identities = 70/210 (33%), Positives = 101/210 (48%), Gaps = 18/210 (8%) Query: 27 SLIVASCLLFLIPGLTVSATAQTMVLETNGIAMTSREVSLEAIRQRGKLRVGVKDNLRPL 86 SL A LF +ATA + GIA + + L+ + +RG L VG P Sbjct: 6 SLFTACVFLF-------AATASAV-----GIAQAA-DSRLDNVLKRGHLIVGTGSTNAPW 52 Query: 87 GFRDGQGELTGLEIALARRLALALLGDETAVELVPVQNQDRLPLLLNGDVDLIIAQMGQN 146 F+ G+L G +I + R +A L D + VE V + R+P LL VD+ + Sbjct: 53 HFQGADGKLQGFDIDIGRMVAKGLFNDPSKVEFVVQSSDARIPNLLTDKVDMSCQFITVT 112 Query: 147 PARDRLVDFSPPYYMDGVG-LISKNSSLKNIDRNQAH----TIAVLNNSGTIPVIKQAFP 201 +R + V F+ PYY +GVG L+ NS K I+ +A T+AVL N ++ QA P Sbjct: 113 ASRAQQVAFTLPYYREGVGLLLPANSKYKEIEDLKAAGDSVTVAVLQNVYAEELVHQALP 172 Query: 202 QATLVGVDSYDQAYQILEQGQAMAFAGDNS 231 +A + DS D YQ + G+A A D S Sbjct: 173 KAKVDQYDSVDLMYQAVNSGRADTAATDQS 202 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: 168 Number of extensions: 8 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: 282 Length adjustment: 26 Effective length of query: 270 Effective length of database: 256 Effective search space: 69120 Effective search space used: 69120 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: 48 (23.1 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