Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_012965554.1 FERP_RS05240 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000025505.1:WP_012965554.1 Length = 227 Score = 192 bits (488), Expect = 5e-54 Identities = 99/214 (46%), Positives = 151/214 (70%), Gaps = 6/214 (2%) Query: 4 VMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIV 63 ++L + A+YGK Q LH ++L I +GE L+G NGAGKTTL+ ++CG + T G+I+ Sbjct: 1 MLLEVKDLKAYYGKAQILHGINLGIEEGEFFALLGPNGAGKTTLINSICGLVK-TEGKII 59 Query: 64 FDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYEL 123 F+ KDI+ + + ++ + + PEGR++F M+VE+NL + A D ++R+++VY L Sbjct: 60 FNGKDISKLKPYERVKLGIGVCPEGRKLFPEMSVEDNLLL----ACEDGCEDRLEFVYSL 115 Query: 124 FPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQL 183 FPR+ E R + MSGGEQQM+AIGRALM+NP+LLLLDEPS+GLAPI++ I D + ++ Sbjct: 116 FPRIKELRKNKVKNMSGGEQQMVAIGRALMTNPKLLLLDEPSMGLAPIVLLNIRDALMRI 175 Query: 184 REQ-GMTIFLVEQNANQALKLADRGYVLENGHVV 216 +E+ ++I +VEQN + AL+LADR +L G +V Sbjct: 176 KEETNISILIVEQNVHLALELADRVALLIKGEIV 209 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: 158 Number of extensions: 9 Number of successful extensions: 4 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: 227 Length adjustment: 23 Effective length of query: 214 Effective length of database: 204 Effective search space: 43656 Effective search space used: 43656 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