Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate RR42_RS14410 RR42_RS14410 leucine/isoleucine/valine transporter ATP-binding subunit
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Cup4G11:RR42_RS14410 Length = 259 Score = 266 bits (679), Expect = 5e-76 Identities = 143/260 (55%), Positives = 186/260 (71%), Gaps = 9/260 (3%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 LL V L MRFGGL+AV+ + F E+ AIIGPNGAGKTT+FNC+ GFY PT G + L Sbjct: 9 LLKVSGLQMRFGGLLAVDGIDFDVRRDEVFAIIGPNGAGKTTVFNCVGGFYKPTAGEVML 68 Query: 71 RHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIA 130 DG + R+P ++++++ V RTFQNIRLF ++V+ENL+VAQH ++ SG + Sbjct: 69 ---DGHS--IARLPSHQVARRGLV-RTFQNIRLFKQLTVVENLLVAQHLQV--RSGL-LR 119 Query: 131 GLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVML 190 GL P+Y R EREA++ A WL+R+ L A+ EAG L YG QRRLEIAR M T P +L Sbjct: 120 GLFATPAYRRAEREALERAALWLERMGLRGVANREAGTLSYGHQRRLEIARCMITNPRLL 179 Query: 191 CLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISD 250 LDEPAAGLNP+E EL+ L+ +R EHKI VLLIEHDMS+VM +SD ++V+++GR I Sbjct: 180 MLDEPAAGLNPQEKVELSQLIDQLRREHKISVLLIEHDMSLVMGVSDRILVMEHGRPILV 239 Query: 251 GDPAFVKNDPAVIRAYLGEE 270 G PA V+NDP VI+AYLGE+ Sbjct: 240 GKPAEVRNDPRVIKAYLGED 259 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: 221 Number of extensions: 7 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 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