Align BgtA aka SLR1735, component of Arginine/lysine/histidine/glutamine porter (characterized)
to candidate RR42_RS29660 RR42_RS29660 amino acid transporter
Query= TCDB::P73721 (252 letters) >FitnessBrowser__Cup4G11:RR42_RS29660 Length = 264 Score = 253 bits (646), Expect = 3e-72 Identities = 133/248 (53%), Positives = 175/248 (70%), Gaps = 9/248 (3%) Query: 9 ISFDQLQKNFGALQVLRGVTGEIYPKDVISIIGPSGCGKSTFLRCLNRLEPISGGRLEVA 68 ++ + K+FG +VL+GV+ DVISIIG SG GKSTFLRC+N LE G++ + Sbjct: 13 LAVQDIHKSFGDNEVLKGVSLTAKKGDVISIIGASGSGKSTFLRCINYLERPKSGQIFLD 72 Query: 69 GVDLSGAK--------IDQKHLRQLRVRVGMVFQHFNLFPHLTVLQNLLLAPRKVLRIPM 120 G ++ K ++ K L+++R ++ MVFQHFNL+ H+ VL+N++ AP VL + Sbjct: 73 GEEIRTKKDKTGDLVVVEPKQLQRMRTKLSMVFQHFNLWAHMNVLENIIEAPTHVLGLSR 132 Query: 121 AEAKDRALTYLDKVGLGTKADN-YPDQLSGGQKQRVAIARGLCMKPEILLFDEPTSALDP 179 EA++RA YL+KVGL + + YP LSGGQ+QRVAIAR L M P+++LFDEPTSALDP Sbjct: 133 KEAEERAREYLEKVGLPPRVEKQYPSHLSGGQQQRVAIARALAMNPDVMLFDEPTSALDP 192 Query: 180 ELVGEVLNVMKQLAEEGMTMAVVTHEMQFAREVSNRVFFFNQGIIEEEGDPNEVFRNPKS 239 ELVGEVL VM++LAEEG TM VVTHEM FAR VSN V F +QG EE+G P EV +P+S Sbjct: 193 ELVGEVLKVMQKLAEEGRTMIVVTHEMGFARNVSNHVMFLHQGRTEEQGPPEEVLNSPRS 252 Query: 240 DRLRAFLS 247 +RLR FLS Sbjct: 253 ERLRQFLS 260 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: 213 Number of extensions: 5 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: 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