Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate Ac3H11_4899 ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4899 Length = 264 Score = 234 bits (597), Expect = 1e-66 Identities = 124/243 (51%), Positives = 169/243 (69%), Gaps = 2/243 (0%) Query: 7 PLISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLE 66 P++ L+K++G+ +VL+G+ ++ +VI+IIG SG GKST LRC+N LE G L Sbjct: 22 PIVDITALRKSYGSNEVLKGIDLKVQRGEVIAIIGKSGSGKSTLLRCVNGLEEFQEGALS 81 Query: 67 VAGVDLSGAKIDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKDR 126 V G L +R+LR +VGM+FQ FNLFPHL+V +N++LAP V A+ + Sbjct: 82 VNGKKL--LHDSPTAMRELRQQVGMIFQSFNLFPHLSVGRNIMLAPTLVKARDAKTAETQ 139 Query: 127 ALTYLDKVGLGTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVL 186 A L++VGL K D PDQLSGGQ+QRVAIAR L M+P++LL DE TSALDPELVGEVL Sbjct: 140 ARKLLERVGLAEKFDAMPDQLSGGQQQRVAIARALAMEPQVLLCDEITSALDPELVGEVL 199 Query: 187 NVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFL 246 V++ LA+EGMT+ +VTHEM FAR+V +RV F +QG + E+G P +F NP++ L+ FL Sbjct: 200 RVVESLAQEGMTLMMVTHEMAFARKVGDRVIFMHQGRVHEQGTPAALFGNPQTPELQQFL 259 Query: 247 SRI 249 S + Sbjct: 260 SSL 262 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: 195 Number of extensions: 5 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: 264 Length adjustment: 24 Effective length of query: 228 Effective length of database: 240 Effective search space: 54720 Effective search space used: 54720 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: 47 (22.7 bits)
This GapMind analysis is from Sep 17 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