Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_011842446.1 RSPH17029_RS17985 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000015985.1:WP_011842446.1 Length = 232 Score = 181 bits (458), Expect = 1e-50 Identities = 102/232 (43%), Positives = 141/232 (60%), Gaps = 1/232 (0%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64 ML + A YG+++ LH VS+ G ++GANG GKTTL + G SG I+ Sbjct: 1 MLEVRDLRAGYGRMEVLHGVSVSAVSGRPTVVMGANGVGKTTLCRAITGLIPLRSGAILL 60 Query: 65 DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYELF 124 D +D++ A+ +R VA+VPEGR+VF MTV ENL +G + + + V ELF Sbjct: 61 DGEDLSRCDPAERVRRGVALVPEGRQVFPEMTVRENLRLGAY-VHGEPTAAQFDDVTELF 119 Query: 125 PRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLR 184 P L ER+ Q AG +SGGEQQMLA+ RALM+ PR+LLLDEPS GLAP + Q+ + ++ Sbjct: 120 PILAERQGQMAGLLSGGEQQMLALARALMARPRVLLLDEPSQGLAPKAVAQVGQAVTRIA 179 Query: 185 EQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 +G+ + LVEQN A +A VLE+G V D LL++ AV ++YLG Sbjct: 180 SRGVAVLLVEQNLTLAEMIARHAVVLESGAVAAEGPADELLSSGAVEASYLG 231 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: 141 Number of extensions: 10 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: 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 10 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