Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_083492030.1 ABB28_RS12765 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_001431535.1:WP_083492030.1 Length = 261 Score = 93.2 bits (230), Expect = 4e-24 Identities = 76/252 (30%), Positives = 120/252 (47%), Gaps = 26/252 (10%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGD--PRA-TSGR 61 M+ D+ S G+++ LH +SL I QG+ L+G NG GK+T + + + P A G Sbjct: 1 MIELDRASVMRGQVKVLHGLSLRIAQGQHTALLGPNGCGKSTFIKLITRELYPLAHADGH 60 Query: 62 IVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRM---TVEENLAMGGFFAE--------- 109 + WQ ++ + + + + M TVE+ + + GFFA Sbjct: 61 VPVKVLGQNRWQVDRLRSQLGIVTGDLSNNLADMPGLTVEQAV-LTGFFASYVLPAFREI 119 Query: 110 ----RDQFQERIKWVYELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPS 165 RD+ + + L LH R +S GE + + I RAL++ P LLLDEPS Sbjct: 120 SQDMRDRARATLAMSGAL--ALHGRTYAE---LSAGETRRVLIARALVNRPHALLLDEPS 174 Query: 166 LGLAPIIIQQIFDTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALL 225 GL + QQ+ DT++ L QG+T+ LV + + + +R +L +G V+ T LL Sbjct: 175 TGLDLVARQQLVDTMQSLARQGITLVLVTHHVEEIIPEIERVVLLRDGRVLADGTRAELL 234 Query: 226 ANEAVRSAYLGG 237 +A SA GG Sbjct: 235 C-DAPLSALFGG 245 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: 147 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: 237 Length of database: 261 Length adjustment: 24 Effective length of query: 213 Effective length of database: 237 Effective search space: 50481 Effective search space used: 50481 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