Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_043744393.1 AMB_RS12355 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_000009985.1:WP_043744393.1 Length = 243 Score = 154 bits (388), Expect = 2e-42 Identities = 98/268 (36%), Positives = 141/268 (52%), Gaps = 28/268 (10%) Query: 6 MTTTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTV 65 M+ PLL VE L F GL AV+ VSFS GE+ A+IGPNGAGKTT+FN I G + P Sbjct: 1 MSAAPLLLVEGLVKNFRGLRAVDGVSFSVAAGEVVALIGPNGAGKTTVFNMIAGVFEPDE 60 Query: 66 GRLTLRHADGKEFLLERMPGYRISQ--KASVARTFQNIRLFGGMSVLENLIVAQHNKLIR 123 GR+ + A + G R Q + + RTFQ ++ FG +SV EN+ Sbjct: 61 GRIEMEGAS--------LVGLRPDQVCRTGIGRTFQLVKPFGNISVEENV---------- 102 Query: 124 ASGFSIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAM 183 L+G +T +A A+ L+ + L + A L ++ LE+ARA+ Sbjct: 103 --------LIGALRWTHDVDQARRRAREVLELLGLADKRRQMARGLTLPDRKCLEVARAL 154 Query: 184 CTEPVMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLD 243 T P +L LDE AGL P E+ + + + E + ++LIEH M VM +S VVV++ Sbjct: 155 ATGPKLLLLDEVMAGLRPAETDRMVETFRRLNRETGLTIVLIEHVMRAVMALSQRVVVIN 214 Query: 244 YGRKISDGDPAFVKNDPAVIRAYLGEEE 271 G+ + +G P V DP V+ YLG+E+ Sbjct: 215 TGKPVCEGAPEEVVRDPRVLECYLGQEK 242 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: 157 Number of extensions: 10 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: 243 Length adjustment: 25 Effective length of query: 269 Effective length of database: 218 Effective search space: 58642 Effective search space used: 58642 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