Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_089136028.1 CES79_RS00805 amino acid ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >NCBI__GCF_002217945.1:WP_089136028.1 Length = 246 Score = 275 bits (704), Expect = 5e-79 Identities = 140/244 (57%), Positives = 186/244 (76%), Gaps = 2/244 (0%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 MI+ VQKY+GDFHAL DI+L I G+ VV++GPSGSGKSTL RT+N LE I+EG + + Sbjct: 3 MIEFHNVQKYYGDFHALHDINLTIDAGETVVLIGPSGSGKSTLIRTVNGLERIQEGQLIV 62 Query: 61 DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120 +G+ L + +R +VGMVFQ FNL+ + TI +N+ LAP V K + E +K+AM + Sbjct: 63 NGQDLANRKTDMNRIRKNVGMVFQHFNLYANKTILENIMLAPRLVLKRPEEENKKIAMDM 122 Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMA 180 L+RVG+A+QA K PAQLSGGQQQR+AIAR+LAM PK +LFDEPTSALDPEM+++VL+VM Sbjct: 123 LDRVGLADQAPKMPAQLSGGQQQRIAIARSLAMRPKALLFDEPTSALDPEMIDDVLNVMK 182 Query: 181 SLAKE-GMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFT-NPKSDRAKDFLGK 238 +A++ MTM+ VTHEMGFAR+ A+RV+FMADG I+ED + FF P ++RA+ FL K Sbjct: 183 DIARDSSMTMLVVTHEMGFAREVANRVVFMADGHILEDDSKEKFFDGQPSNERARQFLSK 242 Query: 239 ILAH 242 I+ H Sbjct: 243 IITH 246 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: 190 Number of extensions: 6 Number of successful extensions: 3 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: 246 Length adjustment: 24 Effective length of query: 218 Effective length of database: 222 Effective search space: 48396 Effective search space used: 48396 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: 46 (22.3 bits)
This GapMind analysis is from Sep 24 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