Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate Ac3H11_4983 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:D8J1T6 (255 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4983 Length = 280 Score = 214 bits (544), Expect = 2e-60 Identities = 111/252 (44%), Positives = 161/252 (63%), Gaps = 2/252 (0%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL+++ V+ FGG++AL GVG + G I +IGPNGAGKT+ FN I+G Y+P G+ Sbjct: 14 LLQVQGVTLAFGGVKALTGVGFDVLPGSITAVIGPNGAGKTSLFNTISGFYRPSQGSIRF 73 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 G+ + + A+ G+ R+FQNI LF MTVL+N+ +G H K NV A+ AR Sbjct: 74 QGQDITRVPAPQRARLGLGRSFQNIALFRGMTVLDNIKLGRHAHLKTNVLDALLYFGRAR 133 Query: 125 EEEAAI-REKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183 EEA + R+ ++++DF+ I L YG Q+R+E+ARALA PQ+L LDEP AG Sbjct: 134 REEAELRRDIEERIIDFLEIDHIRHAPVSALPYGLQKRVEMARALAMQPQILMLDEPVAG 193 Query: 184 MNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 MN E + ++ ++ E G T+L++EHD+ ++M L + + VL++G+ IA+G PA VQ Sbjct: 194 MNREETEDMARFILDVREEWGVTVLMVEHDMGMVMDLSDHVVVLNFGQVIAQGTPAAVQA 253 Query: 243 NPAVIEAYLGAG 254 NP VI AYLGAG Sbjct: 254 NPEVIRAYLGAG 265 Lambda K H 0.320 0.138 0.394 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: 203 Number of extensions: 15 Number of successful extensions: 3 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: 255 Length of database: 280 Length adjustment: 25 Effective length of query: 230 Effective length of database: 255 Effective search space: 58650 Effective search space used: 58650 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: 47 (22.7 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