Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate WP_029134705.1 A3GO_RS0118750 ABC transporter ATP-binding protein
Query= TCDB::P73721 (252 letters) >NCBI__GCF_000428045.1:WP_029134705.1 Length = 353 Score = 144 bits (364), Expect = 2e-39 Identities = 88/233 (37%), Positives = 136/233 (58%), Gaps = 9/233 (3%) Query: 18 FGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVAGVDLSGAKI 77 FG +V++ V+ ++ D+ ++GPSGCGK+T LR + EP+ G + + G + Sbjct: 14 FGTTEVVKRVSLKLREGDIGCLLGPSGCGKTTLLRAIAGFEPLRQGSIALHGKVVCDT-- 71 Query: 78 DQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMAEAKD-RALTYLDKVGL 136 Q + + RVGMVFQ F LFPHL+V +N+ LR A+AK R L VGL Sbjct: 72 -QHMIAPEQRRVGMVFQDFALFPHLSVAENIGFG----LRGRTAQAKQARIAELLTLVGL 126 Query: 137 GTKADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPELVGEVLN-VMKQLAEE 195 A +P QLSGGQ+QR+A+AR + +PEILL DEP SALDPEL G++ + V L ++ Sbjct: 127 TDAAQQHPHQLSGGQQQRIALARAMAPRPEILLLDEPFSALDPELRGQLASEVRTLLKQD 186 Query: 196 GMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSDRLRAFLSR 248 G+T +VTH+ A +++++ NQG + + ++ +P + + F+ R Sbjct: 187 GITAILVTHDQTEAFTMADQIGVMNQGELHQWDSGYNLYHHPATTFVADFVGR 239 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: 11 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: 353 Length adjustment: 26 Effective length of query: 226 Effective length of database: 327 Effective search space: 73902 Effective search space used: 73902 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