Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate Pf1N1B4_1079 Lipopolysaccharide ABC transporter, ATP-binding protein LptB
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1079 Length = 241 Score = 127 bits (319), Expect = 2e-34 Identities = 72/234 (30%), Positives = 127/234 (54%), Gaps = 4/234 (1%) Query: 6 LSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFD 65 L ++ Y Q + +VSL I+ G+IV L+G NGAGKTT + G +A GR++ D Sbjct: 4 LKAQHLAKSYKSRQVVRDVSLSIDSGQIVGLLGPNGAGKTTCFYMIVGLVQADQGRVLID 63 Query: 66 DKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENL-AMGGFFAERDQFQER--IKWVYE 122 D D++ + + +P+ +F +++V +N+ A+ E DQ R ++ + + Sbjct: 64 DLDVSHQPMHGRAKAGIGYLPQEASIFRKLSVADNIMAILETRKELDQAGRRQELESLLQ 123 Query: 123 LFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQ 182 F +H R ++SGGE++ + I RAL +NP+ +LLDEP G+ PI + I I Sbjct: 124 EF-HIHHIRDNLGMSLSGGERRRVEIARALATNPKFILLDEPFAGVDPISVGDIKQIIHH 182 Query: 183 LREQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 L+ +G+ + + + N + L + + Y++ +G ++ +LANE V+ YLG Sbjct: 183 LKAKGIGVLITDHNVRETLDICETAYIVNDGQLIAEGDSATILANELVKEVYLG 236 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: 106 Number of extensions: 5 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: 241 Length adjustment: 23 Effective length of query: 214 Effective length of database: 218 Effective search space: 46652 Effective search space used: 46652 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 17 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