Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_068463382.1 APY04_RS13115 urea ABC transporter ATP-binding subunit UrtE
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_001541235.1:WP_068463382.1 Length = 232 Score = 152 bits (384), Expect = 5e-42 Identities = 84/214 (39%), Positives = 129/214 (60%), Gaps = 2/214 (0%) Query: 4 VMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIV 63 ++LSFDKVS++YG Q L VS + QG+ + ++G NG GKTT++ T+ G T+G I Sbjct: 1 MLLSFDKVSSYYGATQILRNVSFDLEQGQCLCVLGRNGVGKTTIMRTIMGLTDRTTGSIT 60 Query: 64 FDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYEL 123 D+ I + + + VP+GR + + TV EN+ + G FA +D E + + Sbjct: 61 MGDEAIANKPPYQRAGYGIGYVPQGRGILADFTVRENILL-GTFARKDSAPEIPELCLRI 119 Query: 124 FPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQL 183 FP L E +RAG +SGG++Q LAI RAL P++LLLDEP+ G+ P I+ +I + + L Sbjct: 120 FPYLRENLDRRAGLLSGGQKQQLAIARALAVGPQVLLLDEPTEGIQPNIVHEIGEILRML 179 Query: 184 -REQGMTIFLVEQNANQALKLADRGYVLENGHVV 216 +E G+++ L EQ+ A KL D +++NG VV Sbjct: 180 NKELGISLILTEQHIKVARKLGDAFLMVDNGRVV 213 Lambda K H 0.321 0.137 0.390 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: 158 Number of extensions: 8 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: 237 Length of database: 232 Length adjustment: 23 Effective length of query: 214 Effective length of database: 209 Effective search space: 44726 Effective search space used: 44726 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