Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_076948807.1 C1M55_RS07375 amino acid ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >NCBI__GCF_002893965.1:WP_076948807.1 Length = 261 Score = 258 bits (660), Expect = 6e-74 Identities = 128/249 (51%), Positives = 172/249 (69%), Gaps = 10/249 (4%) Query: 2 IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEID 61 ++ G+ K FG L +DL + +G+V V+LGPSGSGKSTL RT+N LE ++ GT+ ID Sbjct: 13 VEARGIHKSFGTLEVLAGVDLLVRKGEVTVILGPSGSGKSTLLRTLNHLEKVDRGTVRID 72 Query: 62 GKVLPEEGKG----------LANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKS 111 G+++ KG + R+ +G VFQ+FNLFPHLT +NV AP+ +K + Sbjct: 73 GELIGYRRKGNRLHELRDREILKQRSHIGFVFQNFNLFPHLTALENVVEAPLSAQKRDRD 132 Query: 112 EAEKLAMSLLERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEM 171 E + A +LLERVG+ +AD+YP QLSGGQQQRVAIARALA+ P ++LFDEPTSALDPE+ Sbjct: 133 EVYREARALLERVGVGEKADEYPRQLSGGQQQRVAIARALALRPAVILFDEPTSALDPEL 192 Query: 172 VNEVLDVMASLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDR 231 V EVL+V+A LA++G T+V VTHE+GFAR+ AD +FM G+IVE P NP +R Sbjct: 193 VGEVLEVLAQLARDGATLVIVTHEVGFAREVADTAVFMDGGVIVEQGPPSQVIDNPVHER 252 Query: 232 AKDFLGKIL 240 K FL ++L Sbjct: 253 TKAFLSRVL 261 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: 167 Number of extensions: 5 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: 261 Length adjustment: 24 Effective length of query: 218 Effective length of database: 237 Effective search space: 51666 Effective search space used: 51666 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