Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate 7026373 Shewana3_3515 ABC transporter related (RefSeq)
Query= TCDB::P48243 (242 letters) >FitnessBrowser__ANA3:7026373 Length = 349 Score = 149 bits (377), Expect = 6e-41 Identities = 80/222 (36%), Positives = 133/222 (59%), Gaps = 4/222 (1%) Query: 17 LTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEIDGKVLPEEGKGLANLR 76 L +DL + +G+++ +LGPSG GK+TL R + L+ I +G I+I+GK + G+ + + + Sbjct: 20 LKGLDLTLAQGEILALLGPSGCGKTTLLRAVAGLQAISQGEIQINGKTVSGAGQFVPSEQ 79 Query: 77 ADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSLLERVGIANQADKYPAQ 136 +GM+FQ + LFPHLT+ +N+ V K+ ++ + +L V + A +YP + Sbjct: 80 RGIGMIFQDYALFPHLTVAENILFG---VAKLTPAQRKARLDDMLALVKLEGLAKRYPHE 136 Query: 137 LSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMASLAKE-GMTMVCVTHE 195 LSGGQQQRV+IARALA P+++L DEP S +D ++ + ++ + S+ K+ ++ V VTH Sbjct: 137 LSGGQQQRVSIARALAYEPQLLLLDEPFSNIDAQVRHSMMAEIRSILKQRNVSAVFVTHS 196 Query: 196 MGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLG 237 A AD + G+IV+ ++ + P S DFLG Sbjct: 197 KDEAFVFADTLAIFNQGVIVQHGRAENLYAAPNSRYVADFLG 238 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: 173 Number of extensions: 5 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: 349 Length adjustment: 26 Effective length of query: 216 Effective length of database: 323 Effective search space: 69768 Effective search space used: 69768 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: 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