Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_020176258.1 A3OQ_RS0115150 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000385335.1:WP_020176258.1 Length = 247 Score = 187 bits (475), Expect = 2e-52 Identities = 97/234 (41%), Positives = 147/234 (62%), Gaps = 2/234 (0%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRY 60 +LQ +++ +YG L V+++V +GEIV L+G NGAGK+T + T+ G SG+I + Sbjct: 5 LLQVRDLNAWYGAAHVLQGVSLDVGRGEIVALVGRNGAGKTTTVRTIMGLIAKRSGTILF 64 Query: 61 MGEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKG--DYQEQMDKVLH 118 G +L+ + + + VPE RR+ LTV ENL +G +G E ++ V Sbjct: 65 DGIDLMARQTYERFGLGLGYVPEERRIVPGLTVRENLMLGLLAARRGMAGEAEAINAVAM 124 Query: 119 LFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFDIIEQ 178 FPRL ER Q TMSGGEQQMLAI RA++S+P ++LLDEPS G+ P ++ ++ ++ + Sbjct: 125 RFPRLGERLNQEAVTMSGGEQQMLAIARAMLSQPTMILLDEPSEGIMPALVDEMAELFLE 184 Query: 179 LRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 L++ G ++ L+EQN AL+I+DRAY+L+ GR+V +G LL D +RE Y G Sbjct: 185 LKRSGTSLLLIEQNVELALEISDRAYILDQGRLVHEGASAELLADADIRERYCG 238 Lambda K H 0.320 0.137 0.381 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: 170 Number of extensions: 4 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: 233 Length of database: 247 Length adjustment: 23 Effective length of query: 210 Effective length of database: 224 Effective search space: 47040 Effective search space used: 47040 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: 46 (22.3 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