Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_085770502.1 B1812_RS04380 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_002117405.1:WP_085770502.1 Length = 293 Score = 211 bits (538), Expect = 1e-59 Identities = 112/251 (44%), Positives = 161/251 (64%), Gaps = 1/251 (0%) Query: 6 LKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFELD 65 L + ++S FGG+QAL+ + ++ G+I +IGPNGAGK++ NVITGLY+PD G +LD Sbjct: 35 LALTNISLSFGGIQALSEIDFSVAAGEICSIIGPNGAGKSSLINVITGLYRPDWGRIQLD 94 Query: 66 GKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAARE 125 +S +A G+ARTFQN+ LF ++V +N+ VG T+ + VF AR Sbjct: 95 KNSFSRMPTERLASLGVARTFQNLALFRGLSVFDNIAVGRVSATRSHWLEQVFGLPRARA 154 Query: 126 EEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGMN 185 + A +++L F+G+GQ R A L YG Q+R+E+ARALA P+LL LDEP AGM Sbjct: 155 DRLATEIIVEEMLVFLGLGQVRNRIAGTLPYGMQKRVELARALAIRPRLLLLDEPMAGMT 214 Query: 186 ATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKNP 244 A EK + E + + G +I+LIEHD+ ++M L +R+ VLDYG+ IA+G P+DV + Sbjct: 215 AGEKAEMGEFIQLTRDRFGASIVLIEHDIGVVMELSDRVAVLDYGRKIADGPPSDVMNDE 274 Query: 245 AVIEAYLGAGH 255 AVI+AYLG H Sbjct: 275 AVIDAYLGVAH 285 Lambda K H 0.320 0.138 0.394 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: 191 Number of extensions: 8 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: 255 Length of database: 293 Length adjustment: 25 Effective length of query: 230 Effective length of database: 268 Effective search space: 61640 Effective search space used: 61640 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 (21.8 bits) S2: 47 (22.7 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