Align GluA aka CGL1950, component of Glutamate porter (characterized)
to candidate WP_004089509.1 M988_RS07270 glutamine ABC transporter ATP-binding protein GlnQ
Query= TCDB::P48243 (242 letters) >NCBI__GCF_001655005.1:WP_004089509.1 Length = 240 Score = 262 bits (670), Expect = 4e-75 Identities = 135/236 (57%), Positives = 172/236 (72%) Query: 1 MIKMTGVQKYFGDFHALTDIDLEIPRGQVVVVLGPSGSGKSTLCRTINRLETIEEGTIEI 60 MI+ V K FG L DI+L I +G+VVV++GPSGSGKSTL R IN+LE I G + + Sbjct: 1 MIEFKHVDKSFGQTAVLHDINLNINQGEVVVIIGPSGSGKSTLLRCINKLEEISAGQLLV 60 Query: 61 DGKVLPEEGKGLANLRADVGMVFQSFNLFPHLTIKDNVTLAPIKVRKMKKSEAEKLAMSL 120 DG + + +R + GMVFQ F LFPHLT +NV P +VR MKK +AEK A L Sbjct: 61 DGMDVNDPKVDERLIRQEAGMVFQQFYLFPHLTALENVMFGPTRVRHMKKEDAEKRAREL 120 Query: 121 LERVGIANQADKYPAQLSGGQQQRVAIARALAMNPKIMLFDEPTSALDPEMVNEVLDVMA 180 L +VG++ +AD YP++LSGGQQQRVAIARALA+ PK+MLFDEPTSALDPE+ +EVL VM Sbjct: 121 LAKVGLSERADHYPSELSGGQQQRVAIARALAVKPKMMLFDEPTSALDPELRHEVLTVMK 180 Query: 181 SLAKEGMTMVCVTHEMGFARKAADRVLFMADGLIVEDTEPDSFFTNPKSDRAKDFL 236 LA+EGMTMV VTHE+GFA+K A R++F+ G I ED EPD+ ++P SDR ++FL Sbjct: 181 DLAEEGMTMVIVTHEIGFAQKVASRLIFVDKGRITEDGEPDALISHPPSDRLREFL 236 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: 182 Number of extensions: 7 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: 240 Length adjustment: 23 Effective length of query: 219 Effective length of database: 217 Effective search space: 47523 Effective search space used: 47523 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