Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_011385946.1 AMB_RS18160 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000009985.1:WP_011385946.1 Length = 265 Score = 198 bits (503), Expect = 1e-55 Identities = 111/271 (40%), Positives = 169/271 (62%), Gaps = 8/271 (2%) Query: 5 SMTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPT 64 S+T P+L V +++ FGG+ A+ +VSF N GE+ +IIGPNGAGKT++ NC++G Y PT Sbjct: 2 SVTDNPVLEVRDVSLAFGGVRALTEVSFQVNKGELFSIIGPNGAGKTSMLNCVSGRYKPT 61 Query: 65 VGRLTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRA 124 GR+ + DG++ + P R + + RTFQN+ LFG MSVL+N++V +H+ L Sbjct: 62 SGRVFM---DGRD-VTGLSPNVRAT--LGLGRTFQNLALFGHMSVLDNIMVGRHHLL--G 113 Query: 125 SGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMC 184 + + L L + E + +D + + AG LPYG ++R+E+ARAM Sbjct: 114 NNAATGALYWLSGARKEELAHRRKVEDIIDFLEIAHIRKAVAGTLPYGLRKRVELARAMA 173 Query: 185 TEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDY 244 EP ++ LDEP AG+N E ++A + + +E + V++IEHDM VVM IS V+VL++ Sbjct: 174 VEPKVILLDEPMAGMNLEEKEDMARYIVDLNEEWGMTVIMIEHDMGVVMDISHRVMVLEF 233 Query: 245 GRKISDGDPAFVKNDPAVIRAYLGEEEDEEL 275 GRKI++G P V N+ V AYLG +EDE++ Sbjct: 234 GRKIAEGLPDEVMNNERVKVAYLGIDEDEDV 264 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: 196 Number of extensions: 13 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: 265 Length adjustment: 26 Effective length of query: 268 Effective length of database: 239 Effective search space: 64052 Effective search space used: 64052 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