Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate AZOBR_RS22350 AZOBR_RS22350 ABC transporter
Query= uniprot:G8ALJ0 (294 letters) >FitnessBrowser__azobra:AZOBR_RS22350 Length = 268 Score = 193 bits (490), Expect = 4e-54 Identities = 109/269 (40%), Positives = 164/269 (60%), Gaps = 10/269 (3%) Query: 17 LTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGK 76 +++RFGG+ A+ DV FS GE+ +IIGPNGAGKT++ NCI+G Y PT G++ + D Sbjct: 7 VSLRFGGVQALTDVGFSIRKGELFSIIGPNGAGKTSMVNCISGRYRPTDGKVYFKGQD-- 64 Query: 77 EFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLP 136 + P +R S + RTFQN+ LFG M+VL+N++V +H+ L + F L L Sbjct: 65 --ITGMTPNHRAS--LGIGRTFQNLALFGHMTVLDNIMVGRHHLL--KNNFFTGSLYWLT 118 Query: 137 SYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLDEPA 196 + E + +D + + AG L YG ++R+E+ARA+ +P ++ LDEP Sbjct: 119 GARKEELAHRREVEEIIDFLEIQHVRKATAGTLSYGLRKRVELARAIALKPDLILLDEPM 178 Query: 197 AGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDGDPAFV 256 AG+N E ++A + + +E + V++IEHDM VVM IS V+VL++G+KI++G P V Sbjct: 179 AGMNLEEKEDMARYIVDLNEEFGMTVVMIEHDMGVVMDISHRVIVLEFGKKIAEGTPEEV 238 Query: 257 KNDPAVIRAYLGE--EEDEELPPEIKADL 283 DP V RAYLGE EEDE + P K ++ Sbjct: 239 LADPRVKRAYLGEDDEEDEAVAPPPKQEV 267 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: 195 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: 268 Length adjustment: 26 Effective length of query: 268 Effective length of database: 242 Effective search space: 64856 Effective search space used: 64856 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