Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_110208105.1 DNK54_RS16590 ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_003194585.1:WP_110208105.1 Length = 263 Score = 159 bits (403), Expect = 4e-44 Identities = 91/240 (37%), Positives = 138/240 (57%), Gaps = 12/240 (5%) Query: 28 FGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSIGQLAP 87 FGG+ AV+ A E ITGLIGPNGAGKTT FN+++ RP G V F G + + A Sbjct: 13 FGGVTAVNQARFTADERRITGLIGPNGAGKTTCFNVITGLQRPTSGSVRFGGRDVTRTAV 72 Query: 88 HQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEERANREKA 147 H+ A RG RTFQ + LTV +N+ +A G F + + A ++A Sbjct: 73 HRRARRGMARTFQRLEAFGSLTVRDNVRVALDIAGG---------FGGLMRSSSARVDEA 123 Query: 148 MAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPTLIGQICE 207 L+ VG+ A + A ++ G +LLE+AR L+ +PKL+LLDEP++G++ + E Sbjct: 124 ---LDRVGISEYAAERADSIPTGTARLLELARCLVGDPKLLLLDEPSSGLDESETDAFGE 180 Query: 208 HIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPRVLEAYLGDS 267 ++ +G L++EH+MD++MT+C + VL G + G+P ++++D RV AYLG S Sbjct: 181 LLIALASEGKAILMVEHDMDLVMTVCDDIHVLDFGEIICSGSPAEVRADARVQAAYLGAS 240 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: 162 Number of extensions: 3 Number of successful extensions: 2 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: 263 Length adjustment: 25 Effective length of query: 242 Effective length of database: 238 Effective search space: 57596 Effective search space used: 57596 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