Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein
Query= TCDB::P48243 (242 letters) >NCBI__GCF_000621325.1:WP_028489030.1 Length = 348 Score = 154 bits (389), Expect = 2e-42 Identities = 86/237 (36%), Positives = 138/237 (58%), Gaps = 6/237 (2%) Query: 2 IKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEID 61 +++ V KY+G HA+ + LEI G+ +V +GPSG GKSTL R I LE I G + +D Sbjct: 4 LELKNVDKYYGKLHAIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILD 63 Query: 62 GKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSLL 121 G+ + E + + D+ MVFQS+ L+PH+T+++N++ A +++ K+ + ++ Sbjct: 64 GRDITE----VPPSQRDLAMVFQSYALYPHMTVEENMSFA-LRLAKVDPAIIQEKVKMAA 118 Query: 122 ERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMAS 181 +++ + + P LSGGQ+QRVAI R++ +PK+ LFDEP S LD + +AS Sbjct: 119 DKLNLTAYLQRTPKALSGGQRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIAS 178 Query: 182 LAKE-GMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFLG 237 L +E G T V VTH+ A ADRV+ + DG+I + P + P + F+G Sbjct: 179 LHRELGATTVYVTHDQVEAMTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIG 235 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: 197 Number of extensions: 8 Number of successful extensions: 4 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: 348 Length adjustment: 26 Effective length of query: 216 Effective length of database: 322 Effective search space: 69552 Effective search space used: 69552 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 Apr 09 2024. 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