Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate RR42_RS29450 RR42_RS29450 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__Cup4G11:RR42_RS29450 Length = 265 Score = 196 bits (499), Expect = 4e-55 Identities = 112/265 (42%), Positives = 166/265 (62%), Gaps = 9/265 (3%) Query: 8 TTPLLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGR 67 T LL+V L++RFGG++A+ VSF GE+ +IGPNGAGKTT+FN I+ Y PT G Sbjct: 2 TDTLLSVRDLSVRFGGVLALGGVSFDVRRGEVFTLIGPNGAGKTTVFNLISRIYPPTSGE 61 Query: 68 LTLRHADGKEFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGF 127 + + + L R+P + I+ + +ARTFQNI LF +VL+NL++ H RASGF Sbjct: 62 ILWQGSS-----LTRLPPHAIAAQG-IARTFQNIELFEHATVLQNLLIGHHTH--RASGF 113 Query: 128 SIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187 A LL P+ R+E A A+ ++ + L D LPYG ++ +E+ARA+C+ P Sbjct: 114 W-ADLLFTPAARRSELAARHKAEEMIELLDLQAHRDALVAGLPYGVRKVVELARALCSSP 172 Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247 +L LDEP++GLN E+ ++A + I+ E I VL++EHDMS+V +SD V+ ++ G+ Sbjct: 173 RLLLLDEPSSGLNVEETEDMAWWIRDIQSELGITVLMVEHDMSLVSRVSDRVLAMNQGQV 232 Query: 248 ISDGDPAFVKNDPAVIRAYLGEEED 272 ++ G PA V+ P VI AYLG +D Sbjct: 233 LAQGTPAEVQEHPGVIEAYLGTVDD 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: 188 Number of extensions: 9 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