Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate AO353_16950 AO353_16950 amino acid transporter
Query= TCDB::P73721 (252 letters) >FitnessBrowser__pseudo3_N2E3:AO353_16950 Length = 254 Score = 266 bits (681), Expect = 2e-76 Identities = 139/247 (56%), Positives = 184/247 (74%), Gaps = 8/247 (3%) Query: 9 ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68 ++ + L K +G +VL+GV+ + DVIS+IG SG GKSTFLRC+N LE + G + + Sbjct: 4 LTIEGLHKCYGTHEVLKGVSLKAKTGDVISLIGASGSGKSTFLRCINFLEQPNDGAMSLD 63 Query: 69 GV------DLSGAKI-DQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPMA 121 G D G ++ D+ L+++R R+ MVFQHFNL+ H+TVL+N+ +APR+VL + Sbjct: 64 GQAIRMIKDSHGMRVADEAELQRIRTRLAMVFQHFNLWSHMTVLENITMAPRRVLGVSKK 123 Query: 122 EAKDRALTYLDKVGLGTK-ADNYPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDPE 180 +A+DRA YLDKVGL + AD YP LSGGQ+QRVAIAR L M+PE++LFDEPTSALDPE Sbjct: 124 DAEDRARRYLDKVGLAARVADQYPAFLSGGQQQRVAIARALAMEPEVMLFDEPTSALDPE 183 Query: 181 LVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKSD 240 LVGEVL V++ LAEEG TM +VTHEM FAR+VSN+V F +QG++EEEG P +V NPKS+ Sbjct: 184 LVGEVLKVIQGLAEEGRTMIMVTHEMSFARKVSNQVLFLHQGLVEEEGAPEDVLGNPKSE 243 Query: 241 RLRAFLS 247 RL+ FLS Sbjct: 244 RLKQFLS 250 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: 208 Number of extensions: 7 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: 254 Length adjustment: 24 Effective length of query: 228 Effective length of database: 230 Effective search space: 52440 Effective search space used: 52440 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 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