Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate Ac3H11_4983 Branched-chain amino acid transport ATP-binding protein LivG (TC 3.A.1.4.1)
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4983 Length = 280 Score = 195 bits (495), Expect = 1e-54 Identities = 112/278 (40%), Positives = 173/278 (62%), Gaps = 20/278 (7%) Query: 9 TPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRL 68 TPLL V+ +T+ FGG+ A+ V F G ITA+IGPNGAGKT+LFN I+GFY P+ G + Sbjct: 12 TPLLQVQGVTLAFGGVKALTGVGFDVLPGSITAVIGPNGAGKTSLFNTISGFYRPSQGSI 71 Query: 69 TLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFS 128 + D + R+P + + + + R+FQNI LF GM+VL+N+ + +H L Sbjct: 72 RFQGQD-----ITRVPAPQRA-RLGLGRSFQNIALFRGMTVLDNIKLGRHAHL------K 119 Query: 129 IAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWE------AGNLPYGAQRRLEIARA 182 L L + R RE +L + +R+ ++F + + LPYG Q+R+E+ARA Sbjct: 120 TNVLDALLYFGRARREEAELRRDIEERI--IDFLEIDHIRHAPVSALPYGLQKRVEMARA 177 Query: 183 MCTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVL 242 + +P +L LDEP AG+N E+ ++A + +R+E + VL++EHDM +VM +SDHVVVL Sbjct: 178 LAMQPQILMLDEPVAGMNREETEDMARFILDVREEWGVTVLMVEHDMGMVMDLSDHVVVL 237 Query: 243 DYGRKISDGDPAFVKNDPAVIRAYLGEEEDEELPPEIK 280 ++G+ I+ G PA V+ +P VIRAYLG + +L +++ Sbjct: 238 NFGQVIAQGTPAAVQANPEVIRAYLGAGDVGDLRAKLQ 275 Lambda K H 0.319 0.137 0.397 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: 182 Number of extensions: 6 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: 294 Length of database: 280 Length adjustment: 26 Effective length of query: 268 Effective length of database: 254 Effective search space: 68072 Effective search space used: 68072 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