Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate 17272 b3201 predicted transporter subunit: ATP-binding component of ABC superfamily (NCBI)
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__Keio:17272 Length = 241 Score = 131 bits (330), Expect = 1e-35 Identities = 74/233 (31%), Positives = 124/233 (53%), Gaps = 2/233 (0%) Query: 6 LSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVFD 65 L+ ++ Y + + +VSL +N GEIV L+G NGAGKTT + G +G I+ D Sbjct: 4 LTAKNLAKAYKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNIIID 63 Query: 66 DKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYELFP 125 D DI+ R + +P+ +F R++V +NL + ++R EL Sbjct: 64 DDDISLLPLHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLSAEQREDRANELME 123 Query: 126 RLHERRIQRA--GTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQL 183 H ++ + ++SGGE++ + I RAL +NP+ +LLDEP G+ PI + I IE L Sbjct: 124 EFHIEHLRDSMGQSLSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKRIIEHL 183 Query: 184 REQGMTIFLVEQNANQALKLADRGYVLENGHVVLSDTGDALLANEAVRSAYLG 236 R+ G+ + + + N + L + +R Y++ GH++ T +L +E V+ YLG Sbjct: 184 RDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPTEILQDEHVKRVYLG 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: 128 Number of extensions: 3 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