Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_043532174.1 JH15_RS16045 ATP-binding cassette domain-containing protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000759345.1:WP_043532174.1 Length = 262 Score = 233 bits (595), Expect = 2e-66 Identities = 127/244 (52%), Positives = 162/244 (66%), Gaps = 8/244 (3%) Query: 14 LQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDL- 72 LQK++G + VL V+ + + V+SIIG SG GKST LRC+N LE G L +A + Sbjct: 18 LQKHYGEVPVLHDVSLSVTDRHVVSIIGSSGSGKSTLLRCMNLLEIPDRGELTIANEAIR 77 Query: 73 -------SGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKD 125 ID++ + +LR +V MVFQ FNL+PHL+VL N++ AP +V + EA + Sbjct: 78 FQRNAQGDNVGIDRRQVHKLRSQVSMVFQQFNLWPHLSVLGNVIEAPLRVHGLSRREAIE 137 Query: 126 RALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEV 185 R YL KVGL K + +P LSGGQ+QRVAIAR L M+P +LLFDEPTSALDPELV EV Sbjct: 138 RGEHYLAKVGLADKRNAFPSFLSGGQQQRVAIARALAMEPRVLLFDEPTSALDPELVNEV 197 Query: 186 LNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAF 245 L V+ LA EG TM +VTHEM FAREVSN + F +QG +EE G P +VF +SDR R F Sbjct: 198 LGVIGGLAGEGRTMLLVTHEMSFAREVSNEIVFLHQGHVEEAGSPQQVFEQARSDRCRQF 257 Query: 246 LSRI 249 LS + Sbjct: 258 LSSV 261 Lambda K H 0.321 0.139 0.397 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: 185 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: 252 Length of database: 262 Length adjustment: 24 Effective length of query: 228 Effective length of database: 238 Effective search space: 54264 Effective search space used: 54264 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 (21.9 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