Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_085544746.1 B9Y55_RS07490 amino acid ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_900177735.1:WP_085544746.1 Length = 253 Score = 122 bits (305), Expect = 1e-32 Identities = 81/238 (34%), Positives = 126/238 (52%), Gaps = 19/238 (7%) Query: 24 LSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLFNGDSI- 82 L KSFG L + + V EG + +IGP+G+GK+TL + + DQGE+ G I Sbjct: 10 LHKSFGKLNVLKGVSLDVAEGEVVSVIGPSGSGKSTLARCICHLEDIDQGEIYLYGKRID 69 Query: 83 -GQLA-PHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQKEE 140 G L+ Q L G + FQ + L+VLEN+ L+ I R + E Sbjct: 70 KGNLSWKEQSQLVGMI--FQQFNLFPHLSVLENITLSP------------IKVRGISGE- 114 Query: 141 RANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGVNPT 200 +AN E+A+ +L VGL K LSGGQ++ + +ARAL P++++ DEP + ++P Sbjct: 115 KAN-EEALELLSKVGLVDKKDSRPSELSGGQQQRVAIARALAMEPRIMVFDEPTSALDPE 173 Query: 201 LIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDPR 258 L+G++ E I + + G+T ++I H M + V +A+G + GTPE+I PR Sbjct: 174 LVGEVLEVIADLAKSGMTMVIITHEMSFAKDVSDRVIFMADGVIVEQGTPEEILGKPR 231 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: 171 Number of extensions: 6 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: 253 Length adjustment: 24 Effective length of query: 243 Effective length of database: 229 Effective search space: 55647 Effective search space used: 55647 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