Align high-affinity branched-chain amino acid ABC transporter, ATP-binding protein LivF (characterized)
to candidate GFF3785 Psest_3854 ABC-type branched-chain amino acid transport systems, ATPase component
Query= CharProtDB::CH_003736 (237 letters) >FitnessBrowser__psRCH2:GFF3785 Length = 234 Score = 179 bits (455), Expect = 3e-50 Identities = 99/216 (45%), Positives = 137/216 (63%), Gaps = 3/216 (1%) Query: 1 MEKVMLSFDKVSAHYGKIQALHEVSLHINQGEIVTLIGANGAGKTTLLGTLCGDPRATSG 60 M + +LS ++A YG+ ALH + L ++ GE VTL+G NG GKTT L + G R SG Sbjct: 1 MTEPLLSVRDLNAWYGESHALHGIDLDVHAGETVTLLGRNGVGKTTALRAIVGIIRKRSG 60 Query: 61 RIVFDDKDITDWQTAKIMREAVAIVPEGRRVFSRMTVEENLAMGGFFAERDQFQERIKWV 120 I FD KD+ + R + VPE R +FS +TVEENL + A+ + + Sbjct: 61 SIRFDGKDMLRVPLHRTARHGIGYVPEERGIFSTLTVEENLTLPPVVAKGGM---TLAEI 117 Query: 121 YELFPRLHERRIQRAGTMSGGEQQMLAIGRALMSNPRLLLLDEPSLGLAPIIIQQIFDTI 180 Y+LFP L ERR +SGGEQQMLA+ R L + +LLLLDEP+ GLAP+IIQ+I + + Sbjct: 118 YQLFPNLEERRKSPGTKLSGGEQQMLAMARILRTGAKLLLLDEPTEGLAPVIIQRIGEVL 177 Query: 181 EQLREQGMTIFLVEQNANQALKLADRGYVLENGHVV 216 + L+++GMTI LVEQN A K+ADR YV+++G V+ Sbjct: 178 QTLKQRGMTILLVEQNFRFASKVADRFYVVDHGQVI 213 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: 142 Number of extensions: 6 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: 234 Length adjustment: 23 Effective length of query: 214 Effective length of database: 211 Effective search space: 45154 Effective search space used: 45154 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