Align GtrA aka SLL1102, component of Tripartite glutamate:Na+ symporter (characterized)
to candidate AZOBR_RS29765 AZOBR_RS29765 C4-dicarboxylate ABC transporter
Query= TCDB::P74225 (179 letters) >FitnessBrowser__azobra:AZOBR_RS29765 Length = 206 Score = 126 bits (316), Expect = 3e-34 Identities = 67/176 (38%), Positives = 104/176 (59%), Gaps = 5/176 (2%) Query: 1 MDKLLKIAQLIDQFTAWIGKFTAWLVLAMVLTGGWNVVGRYLGRLVGQNLASNGLLEAQW 60 M L+ +L+D TA +GK +WL++ +L N V R + +++SN LE QW Sbjct: 1 MTALVGACRLVDAVTARLGKAISWLIVLAILVSAVNAVVRKMF-----DISSNSWLELQW 55 Query: 61 YLFDLVFLLGAAYTLQTNDHVRVDIFYKSLGDRQRAWVNLLGTCLFLFPFCGLVIFYSWE 120 LF VFLL + +TL+ ++H+R+DI LG R R ++L G FL PF +++ SW Sbjct: 56 VLFAAVFLLCSPWTLKEDEHIRIDIVNAQLGKRARDTIDLFGHLTFLLPFSFVMLVTSWP 115 Query: 121 SVINSWHIWETSPDPGGLPRYPIKTMIIVGFVLLIFQGIAEVIKNLAIALGHVDTE 176 I S+ I E S + GGLP++P K +I +GF +L QG++E+ K AI GH++ + Sbjct: 116 FAIASYAIEEQSMNAGGLPQWPAKMLIPLGFTVLFIQGLSELAKRAAIMSGHLEDD 171 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: 133 Number of extensions: 9 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: 206 Length adjustment: 20 Effective length of query: 159 Effective length of database: 186 Effective search space: 29574 Effective search space used: 29574 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