Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_011428131.1 RHE_RS25475 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000092045.1:WP_011428131.1 Length = 233 Score = 173 bits (438), Expect = 3e-48 Identities = 93/212 (43%), Positives = 131/212 (61%), Gaps = 3/212 (1%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64 +L ++A YG+ LH V + + +GE +T++G NG GKTT L T+ G RA GRI F Sbjct: 4 LLEVQGLNAWYGESHVLHGVDMRVAEGETITILGRNGVGKTTTLRTITGIVRARKGRISF 63 Query: 65 DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYELF 124 D+ K + VPE R +FS +TV ENL + A+ + I YELF Sbjct: 64 AGSDMMQVPLHKTAHRGIGFVPEERGIFSTLTVSENLLLPPVVAKGGMTLDEI---YELF 120 Query: 125 PRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLR 184 P L+ERR +SGGEQQMLAI R L + RLL+LDEP+ GLAP+I+Q+I + ++ L+ Sbjct: 121 PNLYERRSSPGTKLSGGEQQMLAIARILRTGVRLLILDEPTEGLAPVIVQRIGEVLQALK 180 Query: 185 EQGMTIFLVEQNANQALKLADRGYVLENGHVV 216 +GMTI LVEQN A ++ADR Y++++G +V Sbjct: 181 GRGMTILLVEQNFRFASRIADRFYLMDHGQMV 212 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: 148 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: 233 Length adjustment: 23 Effective length of query: 214 Effective length of database: 210 Effective search space: 44940 Effective search space used: 44940 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