Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_043744393.1 AMB_RS12355 ABC transporter ATP-binding protein
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000009985.1:WP_043744393.1 Length = 243 Score = 173 bits (438), Expect = 4e-48 Identities = 102/249 (40%), Positives = 141/249 (56%), Gaps = 16/249 (6%) Query: 18 LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77 LLL +GL K+F GLRAVD V G + LIGPNGAGKTT+FN+++ PD+G + Sbjct: 6 LLLVEGLVKNFRGLRAVDGVSFSVAAGEVVALIGPNGAGKTTVFNMIAGVFEPDEGRIEM 65 Query: 78 NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137 G S+ L P Q+ G RTFQ+ K ++V EN+L+ T + V Sbjct: 66 EGASLVGLRPDQVCRTGIGRTFQLVKPFGNISVEENVLIGALRWTHD-----------VD 114 Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197 + R RE +LE +GL K + A L+ RK LE+ARAL + PKL+LLDE AG+ Sbjct: 115 QARRRARE----VLELLGLADKRRQMARGLTLPDRKCLEVARALATGPKLLLLDEVMAGL 170 Query: 198 NPTLIGQICEHIVNWNRQ-GITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSD 256 P ++ E NR+ G+T ++IEH M +M L V V+ G+ + +G PE++ D Sbjct: 171 RPAETDRMVETFRRLNRETGLTIVLIEHVMRAVMALSQRVVVINTGKPVCEGAPEEVVRD 230 Query: 257 PRVLEAYLG 265 PRVLE YLG Sbjct: 231 PRVLECYLG 239 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: 202 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: 243 Length adjustment: 24 Effective length of query: 243 Effective length of database: 219 Effective search space: 53217 Effective search space used: 53217 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 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