Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_034529147.1 LOSG293_RS08120 amino acid ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000740055.1:WP_034529147.1 Length = 247 Score = 269 bits (688), Expect = 3e-77 Identities = 135/243 (55%), Positives = 181/243 (74%), Gaps = 3/243 (1%) Query: 9 ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68 +S L K++GA +VL G+ E++PK+V+ +IGPSG GKSTFLRCLN LE ++ G +E+ Sbjct: 7 VSVKDLHKSYGANEVLSGIDLEVFPKEVVCLIGPSGSGKSTFLRCLNGLEAVNSGVIEIN 66 Query: 69 GVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRAL 128 GV+L D +RQ +GMVFQHFNLFPHLTV++N++LAP ++ ++ A+++ + Sbjct: 67 GVNLVAKHTDINKVRQ---NIGMVFQHFNLFPHLTVIENVMLAPVQLKKMDKQTAREKGM 123 Query: 129 TYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLNV 188 L +VGL KAD P LSGGQ+QRVAIAR L M+PEI+LFDEPTSALDPE+VG+VL V Sbjct: 124 KLLAQVGLAEKADVKPASLSGGQEQRVAIARALAMEPEIMLFDEPTSALDPEMVGDVLAV 183 Query: 189 MKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLSR 248 MK LA+ GMTM VVTHEM FA+E ++RV F + G I+E G P EVF +PK++R R FLS+ Sbjct: 184 MKDLAKAGMTMVVVTHEMGFAKEAADRVAFMDSGKIQEIGTPEEVFDHPKNERTRGFLSK 243 Query: 249 IQS 251 I + Sbjct: 244 IMN 246 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: 214 Number of extensions: 11 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: 247 Length adjustment: 24 Effective length of query: 228 Effective length of database: 223 Effective search space: 50844 Effective search space used: 50844 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