Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_011654832.1 RL_RS30155 amino acid ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000009265.1:WP_011654832.1 Length = 254 Score = 246 bits (629), Expect = 2e-70 Identities = 131/254 (51%), Positives = 171/254 (67%), Gaps = 8/254 (3%) Query: 1 MTSPTAP-----LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLN 55 MTSP+ +I+ ++++K +GA Q LR + + + I + GPSG GKST +RC+N Sbjct: 1 MTSPSPAQGAETMITMERVEKWYGAFQALRDINISVRSGERIVLCGPSGSGKSTLIRCIN 60 Query: 56 RLEPISGGRLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKV 115 LE G + V G+ L K + +R VGMVFQ FNLFPHLTVLQN +LAP K Sbjct: 61 HLETYERGEIRVGGILLGN---QAKTIDAIRREVGMVFQQFNLFPHLTVLQNCMLAPMKA 117 Query: 116 LRIPMAEAKDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTS 175 + + AEA++RA L++V + +AD YP QLSGGQ+QRVAIAR LCM+P+++LFDEPTS Sbjct: 118 VGVSRAEAEERARGLLERVKILEQADKYPVQLSGGQQQRVAIARALCMRPKVMLFDEPTS 177 Query: 176 ALDPELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFR 235 ALDPE+V EVL+ M LA+EGMTM VTHEM FAR+V++RV F G I EE P E F Sbjct: 178 ALDPEMVKEVLDTMIALADEGMTMICVTHEMGFARQVADRVIFMASGAIVEEAPPAEFFT 237 Query: 236 NPKSDRLRAFLSRI 249 NP+ +R R FL I Sbjct: 238 NPQHERTRKFLGEI 251 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: 197 Number of extensions: 6 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: 254 Length adjustment: 24 Effective length of query: 228 Effective length of database: 230 Effective search space: 52440 Effective search space used: 52440 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: 46 (22.3 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