Align BztD, component of Glutamate/glutamine/aspartate/asparagine porter (characterized)
to candidate WP_037453109.1 N825_RS14315 ATP-binding cassette domain-containing protein
Query= TCDB::Q52666 (263 letters) >NCBI__GCF_000576635.1:WP_037453109.1 Length = 250 Score = 231 bits (590), Expect = 9e-66 Identities = 126/245 (51%), Positives = 165/245 (67%), Gaps = 12/245 (4%) Query: 28 MNKWYGQFHVLRDINLTVHRGERIVIAGPSGSGKSTMIRCINRLEEHQSGKIIVDGIELT 87 + K +G VL I++T+ E + + GPSGSGKST++RCIN LE+ G+I+VDG EL Sbjct: 7 VRKSFGAVEVLSGIDMTILPREVVCLLGPSGSGKSTLLRCINHLEKLSGGRILVDG-ELI 65 Query: 88 SDLKNIDKV-----------RSEVGMVFQHFNLFPHLTILENLTLAPIWVRKVPKREAEE 136 + D++ R ++GMVFQ FNLFPHL ++ N+T AP+ ++ + EA Sbjct: 66 GYRERGDRLHELGSAELARQRRDIGMVFQRFNLFPHLDVVGNITQAPMLIKGESRAEATR 125 Query: 137 TAMYYLEKVKIPEQAQKYPGQLSGGQQQRVAIARSLCMKPKIMLFDEPTSALDPEMIKEV 196 A LE V + +A YP QLSGGQQQRVAIAR+L M+PK+MLFDEPTSALDPE++ EV Sbjct: 126 RAHELLEIVDLAGKANAYPHQLSGGQQQRVAIARALAMRPKLMLFDEPTSALDPELVGEV 185 Query: 197 LDTMIQLAEEGMTMLCVTHEMGFAQAVANRVIFMADGQIVEQNNPHDFFHNPQSERTKQF 256 L M +LA EGMTML VTHEMGFA+ VA+RVIFM G +VEQ D P+ +RTK F Sbjct: 186 LAVMKRLALEGMTMLVVTHEMGFAREVADRVIFMDRGVVVEQGTAADVIARPRHDRTKAF 245 Query: 257 LSQIL 261 L ++L Sbjct: 246 LKRVL 250 Lambda K H 0.320 0.134 0.391 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: 195 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: 263 Length of database: 250 Length adjustment: 24 Effective length of query: 239 Effective length of database: 226 Effective search space: 54014 Effective search space used: 54014 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: 47 (22.7 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