Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_054557498.1 I595_RS00860 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_001306415.1:WP_054557498.1 Length = 219 Score = 102 bits (254), Expect = 6e-27 Identities = 63/218 (28%), Positives = 113/218 (51%), Gaps = 7/218 (3%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLL---GTLCGDPRATSGR 61 M++ + +YG ++ L VS+ I +GE+++++G +GAGKTTLL GTL Sbjct: 1 MITATNIKKNYGDLKVLKGVSISIKKGEVISIVGPSGAGKTTLLQLVGTLDTPSNPKDSS 60 Query: 62 IVFDDKDITDW---QTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIK 118 I+ + D+TD Q AK E + + + ++ T EN+ + F + + + ++ Sbjct: 61 IMINGVDVTDLRDKQLAKFRNENIGFIFQFHQLLPEFTALENVCIPAFIKKTPKAKAEVR 120 Query: 119 WVYEL-FPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIF 177 L F L +R R +SGGEQQ +A+ RAL++NP ++ DEPS L + + Sbjct: 121 GRELLDFLGLSQRYDHRPRELSGGEQQRVAVARALINNPSVIFADEPSGNLDSESAENLH 180 Query: 178 DTIEQLREQGMTIFLVEQNANQALKLADRGYVLENGHV 215 +LRE+ F++ + + +ADR ++ +G + Sbjct: 181 QLFFKLREEFGQTFVIVTHNKELANMADRKLIMVDGQI 218 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: 98 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: 219 Length adjustment: 23 Effective length of query: 214 Effective length of database: 196 Effective search space: 41944 Effective search space used: 41944 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