Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate AZOBR_RS13290 AZOBR_RS13290 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__azobra:AZOBR_RS13290 Length = 259 Score = 198 bits (503), Expect = 1e-55 Identities = 115/263 (43%), Positives = 162/263 (61%), Gaps = 9/263 (3%) Query: 12 LTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLR 71 L++E L++ FGGL A++DV + GEI IIGPNGAGKTTL N ++G PT G + L Sbjct: 4 LSIERLSLSFGGLAALSDVDIAVPAGEIRGIIGPNGAGKTTLLNVVSGLVRPTGGEIRL- 62 Query: 72 HADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAG 131 DG+ L R+ ++ + V RTFQ LF GM+VLEN++ H L R S A Sbjct: 63 --DGQP--LTRLKASEVAARG-VGRTFQTSLLFKGMTVLENVMAGMHQGL-RTSVLGAA- 115 Query: 132 LLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLC 191 +GLP R ER+A + A+ L V +L FA+ + +L +G QR +EIAR++ EP +L Sbjct: 116 -IGLPGVLREERQARERAREALAFVGMLSFAERDGASLSFGQQRLVEIARSLVAEPKVLL 174 Query: 192 LDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDG 251 LDEPA GL+P EL +LL IRD+ I ++++EH + +VM + D + VL+ GRKI+DG Sbjct: 175 LDEPAVGLSPPRVAELDELLRRIRDKRGITIIMVEHVIRLVMGVCDRITVLNSGRKIADG 234 Query: 252 DPAFVKNDPAVIRAYLGEEEDEE 274 P + DP V AYLG+ D + Sbjct: 235 TPDVILADPFVKEAYLGKSPDAD 257 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: 189 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: 259 Length adjustment: 25 Effective length of query: 269 Effective length of database: 234 Effective search space: 62946 Effective search space used: 62946 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 Apr 09 2024. 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