Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_012568343.1 RC1_RS15325 LPS export ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000016185.1:WP_012568343.1 Length = 272 Score = 128 bits (322), Expect = 1e-34 Identities = 75/229 (32%), Positives = 120/229 (52%), Gaps = 3/229 (1%) Query: 10 KVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFDDKDI 69 K+ Y L +VSL +N+GE V L+G NGAGKTT + G G I D +I Sbjct: 40 KLGKSYKGRPVLRDVSLSVNRGEAVGLLGPNGAGKTTCFYIITGLILPDYGSITLDGTEI 99 Query: 70 TDWQTAKIMREAVAIVPEGRRVFSRMTVEENL--AMGGFFAERDQFQERIKWVYELFPRL 127 T+ + R + +P+ +F ++VE N+ + +RD + + + F Sbjct: 100 TELPMYRRARLGIGYLPQEASIFRGLSVENNIRAVLEVVEPDRDTREHMLDELLAEFSIS 159 Query: 128 HERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLREQG 187 H RR A +SGGE++ + I RAL S P +LLDEP G+ PI + I + + LRE+G Sbjct: 160 HLRRTP-ALALSGGERRRVEIARALASQPHFILLDEPFAGIDPIAVNDIRELVSHLRERG 218 Query: 188 MTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 + + + + N + L + DR Y+L +G V++ ++A++ VR YLG Sbjct: 219 IGVLITDHNVRETLDIVDRAYILHDGMVLMEGAPSEIVAHKDVRRVYLG 267 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: 136 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: 272 Length adjustment: 24 Effective length of query: 213 Effective length of database: 248 Effective search space: 52824 Effective search space used: 52824 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: 47 (22.7 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