Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_057508907.1 ABB28_RS12160 methionine ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_001431535.1:WP_057508907.1 Length = 335 Score = 178 bits (451), Expect = 1e-49 Identities = 106/245 (43%), Positives = 144/245 (58%), Gaps = 8/245 (3%) Query: 8 LISFDQLQKNFG----ALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGG 63 +I F +L K++ A+ L+ + I +V IIG SG GKST +R +NRLE SGG Sbjct: 1 MIEFQRLHKSYAVAGRAISALQPLDLTIQEGEVFGIIGHSGAGKSTLIRMINRLEDPSGG 60 Query: 64 RLEVAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEA 123 RL +AG D++ ++ LR LR R+GM+FQHFNL TV N+ P ++ P A+ Sbjct: 61 RLLIAGEDVTA--LETAGLRTLRRRIGMIFQHFNLLSSRTVASNVAF-PLELAGTPRAQI 117 Query: 124 KDRALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVG 183 R L VGL AD YP QLSGGQKQRV IAR L P+ILL DE TSALDP+ Sbjct: 118 DARVAELLQTVGLQAHADKYPAQLSGGQKQRVGIARALATGPQILLCDEATSALDPQTTA 177 Query: 184 EVLNVMKQLAEE-GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRL 242 VL ++ ++ E G+T+ ++THEM R V +RV + G + E G +VF +P+ Sbjct: 178 SVLALLSKINRELGLTIVLITHEMDVIRRVCDRVAVLDAGEMVEMGPVTDVFLHPQHPTT 237 Query: 243 RAFLS 247 R F+S Sbjct: 238 RRFVS 242 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: 209 Number of extensions: 12 Number of successful extensions: 4 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: 335 Length adjustment: 26 Effective length of query: 226 Effective length of database: 309 Effective search space: 69834 Effective search space used: 69834 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: 48 (23.1 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