Align NatA aka BRAF aka SLR0467, component of Leucine/proline/alanine/serine/glycine (and possibly histidine) porter, NatABCDE (characterized)
to candidate WP_012402388.1 BPHY_RS15490 branched-chain amino acid ABC transporter ATP-binding protein/permease
Query= TCDB::Q55164 (267 letters) >NCBI__GCF_000020045.1:WP_012402388.1 Length = 594 Score = 173 bits (439), Expect = 7e-48 Identities = 101/248 (40%), Positives = 145/248 (58%), Gaps = 2/248 (0%) Query: 18 LLLAQGLSKSFGGLRAVDHADIVVKEGSITGLIGPNGAGKTTLFNLLSNFIRPDQGEVLF 77 LL+ K FGGL AV+ VK G I GLIGPNGAGK+T FNL++ ++ G + F Sbjct: 346 LLVVDKARKQFGGLVAVNDVSFEVKAGQIIGLIGPNGAGKSTTFNLVTGVLQATSGAITF 405 Query: 78 NGDSIGQLAPHQIALRGSVRTFQVAKVLSRLTVLENMLLADQHQTGEKFLPRLINFRRVQ 137 G+ I L +I RG RTFQ K+L +TVLEN+ + H G + R + Sbjct: 406 RGERIDALNSREIVKRGIGRTFQHVKLLPGMTVLENVAIGG-HLRGRAGVWRSVARLNGA 464 Query: 138 KEERANREKAMAMLESVGLGAKAQDYAGALSGGQRKLLEMARALMSNPKLILLDEPAAGV 197 +E R E A + VGL D AG+L+ G++++LE+ARAL +P L+LLDEPAAG+ Sbjct: 465 EEGRLMAEAAR-QIRRVGLEEHMYDEAGSLALGKQRILEIARALCCDPTLLLLDEPAAGL 523 Query: 198 NPTLIGQICEHIVNWNRQGITFLVIEHNMDVIMTLCHHVWVLAEGRNLADGTPEQIQSDP 257 Q+ + +G++ L++EH+MD +M L + V+ G +A+G P+ +Q+DP Sbjct: 524 RYQEKQQLATLLRKLREEGMSLLLVEHDMDFVMNLTDRLVVMEFGTRIAEGLPQDVQNDP 583 Query: 258 RVLEAYLG 265 VLEAYLG Sbjct: 584 AVLEAYLG 591 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: 371 Number of extensions: 20 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: 594 Length adjustment: 31 Effective length of query: 236 Effective length of database: 563 Effective search space: 132868 Effective search space used: 132868 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: 50 (23.9 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