Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_008497300.1 B481_RS06650 daunorubicin resistance protein DrrA family ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000342445.1:WP_008497300.1 Length = 310 Score = 117 bits (293), Expect = 3e-31 Identities = 72/238 (30%), Positives = 122/238 (51%), Gaps = 18/238 (7%) Query: 18 LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77 +L + L+K F AVD I + +G GL+GPNGAGK+T +++S I+P G+V Sbjct: 1 MLKTEKLTKKFKDTLAVDEVTIELGQGESVGLLGPNGAGKSTAISMISTLIQPTSGDVRL 60 Query: 78 NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137 NG S+ + + G V Q + L+ EN+ KF R+ + Sbjct: 61 NGKSVLKKPGEMRKVLGVVP--QKIALYEELSAYENL----------KFFGRIYGLSGKK 108 Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197 EER +LE VGL + ++ SGG ++ + +A A++ P+++++DEP G+ Sbjct: 109 LEER-----IQIVLELVGLSDRQKELVKKYSGGMQRRVNLAAAMLHEPEVLIMDEPTVGI 163 Query: 198 NPTLIGQICEHIVNWNR-QGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQ 254 +P + E I NR QG+T L H M+ + LC V+++ G+ +A GT ++++ Sbjct: 164 DPQSRNHLLETIRKLNREQGMTVLYTSHYMEEVEKLCDRVYIMDHGKVIAAGTKDELK 221 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: 179 Number of extensions: 9 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: 310 Length adjustment: 26 Effective length of query: 241 Effective length of database: 284 Effective search space: 68444 Effective search space used: 68444 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: 47 (22.7 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