Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_089136612.1 CES79_RS05995 amino acid ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_002217945.1:WP_089136612.1 Length = 246 Score = 202 bits (515), Expect = 4e-57 Identities = 107/240 (44%), Positives = 158/240 (65%), Gaps = 4/240 (1%) Query: 8 LISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEV 67 +I + L+K + +L + I +V++++GPSG GKST +RCLN LEP G + Sbjct: 5 VIKVEHLEKYYQKDHILHDINFSIDQGEVVALLGPSGSGKSTLIRCLNGLEPYQNGTVSF 64 Query: 68 AGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDRA 127 G + +K+ ++LR ++GMVFQ ++LFP+LTVL N+LL P KV + AK A Sbjct: 65 NGDQVVPT---EKNWQKLRQKIGMVFQSYDLFPNLTVLDNILLGPVKVQKQSRETAKAAA 121 Query: 128 LTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLN 187 LD+VGL + YP QLSGGQKQR+AI R L + PE++LFDE T++LDPE+V VLN Sbjct: 122 EKLLDQVGLREYENVYPRQLSGGQKQRIAIVRALALNPELMLFDEVTASLDPEMVRGVLN 181 Query: 188 VMKQLAEEG-MTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246 ++ +LA++ MTM VVTHEM FA+++++RV F G I E+ ++ F+ P++DR + FL Sbjct: 182 IISKLAQDSDMTMIVVTHEMNFAQQIADRVLFLEDGKILEQTKGDQFFKQPQTDRAKEFL 241 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: 186 Number of extensions: 8 Number of successful extensions: 3 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: 246 Length adjustment: 24 Effective length of query: 228 Effective length of database: 222 Effective search space: 50616 Effective search space used: 50616 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