Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_045582841.1 AL072_RS18480 amino acid ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_001305595.1:WP_045582841.1 Length = 251 Score = 247 bits (630), Expect = 2e-70 Identities = 130/245 (53%), Positives = 170/245 (69%), Gaps = 1/245 (0%) Query: 5 TAPLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGR 64 +AP I + K+FG+ VL+GVT + V+ IIGPSG GKST LRC+N L I G Sbjct: 7 SAPFIEMRDVYKSFGSTAVLKGVTLSVRDGGVVCIIGPSGSGKSTILRCINGLMTIDRGT 66 Query: 65 LEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAK 124 + V + K D K L LR +V MVFQ +NLFPH TVLQNL +AP +VL A + Sbjct: 67 IRVGSFAVETLKSD-KQLVPLRHQVAMVFQQYNLFPHRTVLQNLTMAPVQVLGENPAAVR 125 Query: 125 DRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGE 184 +RAL L KV L K D+YP +LSGGQ+QRVAIAR L M+P+++LFDE T+ALDPE+V E Sbjct: 126 ERALALLAKVRLTGKQDSYPGELSGGQQQRVAIARALAMQPKVILFDEVTAALDPEMVSE 185 Query: 185 VLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRA 244 VLNV++ LA EGMT +VTHEM+FA+EV++ VFF ++G+I E G P +F+NP RL+A Sbjct: 186 VLNVIRDLAREGMTCVLVTHEMRFAQEVADEVFFTDRGVIVEHGPPGTIFQNPTDPRLKA 245 Query: 245 FLSRI 249 FL ++ Sbjct: 246 FLDKV 250 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: 206 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: 252 Length of database: 251 Length adjustment: 24 Effective length of query: 228 Effective length of database: 227 Effective search space: 51756 Effective search space used: 51756 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 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