Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate AZOBR_RS23525 AZOBR_RS23525 ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >FitnessBrowser__azobra:AZOBR_RS23525 Length = 269 Score = 270 bits (691), Expect = 2e-77 Identities = 143/243 (58%), Positives = 174/243 (71%), Gaps = 9/243 (3%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 +I++ V K FG L D+ L +P + VV+GPSGSGKSTL R N LET + G I I Sbjct: 1 VIEIRNVYKSFGSTEVLKDVSLTVPPSRTTVVIGPSGSGKSTLLRCCNCLETADRGEIRI 60 Query: 61 -------DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEA 113 DGK LP+ K L LRA+ GMVFQSFNLFPH+T +NV AP+ VR M K+EA Sbjct: 61 NHRTIIADGKPLPD--KELNALRAETGMVFQSFNLFPHMTTVENVMRAPVVVRGMAKAEA 118 Query: 114 EKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVN 173 +LAM LL +VG+ ++AD YP+ LSGGQ+QR AIARALAM PK+MLFDEPTSALDPE+V Sbjct: 119 RELAMELLRKVGLGDKADVYPSTLSGGQKQRAAIARALAMKPKVMLFDEPTSALDPELVG 178 Query: 174 EVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAK 233 EVL VM +LA+EGMTM+ VTHEMGFAR+ AD V+ MADG IVE P+ FTNP +R + Sbjct: 179 EVLQVMKTLAEEGMTMMVVTHEMGFAREVADTVVVMADGRIVESGSPEQIFTNPTQERTR 238 Query: 234 DFL 236 FL Sbjct: 239 GFL 241 Lambda K H 0.319 0.135 0.379 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: 192 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: 242 Length of database: 269 Length adjustment: 24 Effective length of query: 218 Effective length of database: 245 Effective search space: 53410 Effective search space used: 53410 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 (21.8 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