Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate WP_013684586.1 ARCVE_RS09645 ABC transporter ATP-binding protein
Query= CharProtDB::CH_003736 (237 letters) >NCBI__GCF_000194625.1:WP_013684586.1 Length = 223 Score = 184 bits (466), Expect = 2e-51 Identities = 100/213 (46%), Positives = 140/213 (65%), Gaps = 9/213 (4%) Query: 5 MLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSGRIVF 64 ML + A+Y + + L + L I +GE V ++G NGAGKTTL+ +CG R+ G IVF Sbjct: 1 MLKVKGLKAYYDEAEILRGIDLEIEKGEAVAVLGPNGAGKTTLIRAICGLVRS-EGEIVF 59 Query: 65 DDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWVYELF 124 D + I +T + +R +A+ PEGRR+F +TVE+NL + G E ++ VY LF Sbjct: 60 DGRKINGLKTHERIRLGMAVCPEGRRLFPNLTVEDNLLLAGDADE-------LETVYSLF 112 Query: 125 PRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTIEQLR 184 PRL ERR Q TMSGGEQQM+AIGRALM P+LL+LDEPS+GLAPI++ I + I ++R Sbjct: 113 PRLKERRKQLVKTMSGGEQQMVAIGRALMLKPKLLMLDEPSIGLAPIVVDAIGEAISKIR 172 Query: 185 -EQGMTIFLVEQNANQALKLADRGYVLENGHVV 216 E ++I +VEQN + A +++ R YVL G +V Sbjct: 173 DEMDISILIVEQNIHLAFRISQRAYVLVKGEIV 205 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: 170 Number of extensions: 8 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: 223 Length adjustment: 23 Effective length of query: 214 Effective length of database: 200 Effective search space: 42800 Effective search space used: 42800 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