Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate WP_009545830.1 CCE_RS09615 LPS export ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >NCBI__GCF_000017845.1:WP_009545830.1 Length = 238 Score = 113 bits (283), Expect = 3e-30 Identities = 73/236 (30%), Positives = 124/236 (52%), Gaps = 6/236 (2%) Query: 2 LQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCGSPQAHSGSIRYM 61 L EN+ YGK ++ VN++V GEIV L+G NGAGK+T G + + G + Sbjct: 3 LILENIHKTYGKRDIVNRVNLKVAPGEIVGLLGPNGAGKTTTFYIATGLIKPNKGRVWLN 62 Query: 62 GEELVGQDSSHIMRKSIAVVPEGRRVFARLTVEENLAMGGFFTDKGDYQ--EQMDKVLHL 119 +E+ + R I + + +F L+V EN+ + T+ Q +++ +L Sbjct: 63 QQEVTRLPLNKRARLGIGYMTQQPSIFRHLSVAENIQVALEQTNVPFRQRPQRLHTLLKE 122 Query: 120 FPRLKERFTQRGGTMSGGEQQMLAIGRAL---MSKPKLLLLDEPSLGLAPIIIQQIFDII 176 F RL++ +G +SGGE++ + R+L P LLLDEP G+ PI + +I +I Sbjct: 123 F-RLEKIAHTKGSQVSGGERRRTELARSLAVGQQGPDFLLLDEPFAGVDPIAVSEIQTMI 181 Query: 177 EQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLG 232 QL + + + + N L I +RAY++ +G+++ G+ E + +P VR+ YLG Sbjct: 182 AQLCDRQMGILITDHNVQATLAITNRAYIMRDGQILAAGSAEEIYNNPLVRQYYLG 237 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: 132 Number of extensions: 7 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: 233 Length of database: 238 Length adjustment: 23 Effective length of query: 210 Effective length of database: 215 Effective search space: 45150 Effective search space used: 45150 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 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