Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000017845.1:WP_009545830.1 Length = 238 Score = 120 bits (300), Expect = 3e-32 Identities = 77/251 (30%), Positives = 129/251 (51%), Gaps = 18/251 (7%) Query: 19 LLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFN 78 L+ + + K++G V+ ++ V G I GL+GPNGAGKTT F + + I+P++G V N Sbjct: 3 LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62 Query: 79 GDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQK 138 + +L ++ A G Q + L+V EN+ +A QT F R + K Sbjct: 63 QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVA-LEQTNVPFRQRPQRLHTLLK 121 Query: 139 EERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARAL---MSNPKLILLDEPAA 195 E R LE + A +SGG+R+ E+AR+L P +LLDEP A Sbjct: 122 EFR---------LEKI-----AHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFA 167 Query: 196 GVNPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQS 255 GV+P + +I I + + L+ +HN+ + + + +++ +G+ LA G+ E+I + Sbjct: 168 GVDPIAVSEIQTMIAQLCDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYN 227 Query: 256 DPRVLEAYLGD 266 +P V + YLG+ Sbjct: 228 NPLVRQYYLGN 238 Lambda K H 0.319 0.136 0.389 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: 130 Number of extensions: 6 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: 267 Length of database: 238 Length adjustment: 24 Effective length of query: 243 Effective length of database: 214 Effective search space: 52002 Effective search space used: 52002 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 (21.7 bits) S2: 46 (22.3 bits)
This GapMind analysis is from Apr 09 2024. 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