Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate WP_085545256.1 B9Y55_RS10130 ABC transporter ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >NCBI__GCF_900177735.1:WP_085545256.1 Length = 503 Score = 89.0 bits (219), Expect = 2e-22 Identities = 72/239 (30%), Positives = 112/239 (46%), Gaps = 29/239 (12%) Query: 17 LTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGK 76 +T F G+ A + + + GE+ A++G NGAGK+TL N ++G Y P G + + G Sbjct: 4 ITKSFQGIKANDQIDLTLKKGEVLALLGENGAGKSTLMNVLSGIYLPDGGTIDI----GG 59 Query: 77 EFLLERMPGYRISQKASVARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLP 136 L R P IS A + Q+ L +V EN+++ GL LP Sbjct: 60 TRLSFRSPNDAIS--AGIGMVHQHFMLVPSQTVWENMVL---------------GLPDLP 102 Query: 137 SYTRTER---EAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLD 193 + E ++K + V E W+ L G Q+R+EI + + +L LD Sbjct: 103 QILPKGKIISEITAISKQYGLEVDP-EAIIWQ---LSIGEQQRVEILKTLYRNAQVLILD 158 Query: 194 EPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRKISDGD 252 EP A L P+E+ L + + + +E + G++ I H + VM ISD V VL G+ I D Sbjct: 159 EPTAVLTPQEARSLFNTIKRMTEEGR-GIIFISHKLDEVMEISDRVTVLRKGKLIGTVD 216 Score = 42.0 bits (97), Expect = 3e-08 Identities = 53/225 (23%), Positives = 93/225 (41%), Gaps = 16/225 (7%) Query: 23 GLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTLRHADGKEFLLER 82 GL A++ VS G+I + G G G+T L + G T G+L L+ GKE + + Sbjct: 262 GLKALDQVSLELREGQILGLAGVAGNGQTELCQVMAGLRKMTSGKLILK---GKE-VTDS 317 Query: 83 MPGYRISQKAS-VARTFQNIRLFGGMSVLENLIVAQHNKLIRASGFSIAGLLGLPSYTRT 141 P I + + + M V EN + ++ + A G I + Sbjct: 318 SPRELIDGGIRYIPADRKGTGMVSNMDVRENSTLKRYWRRPVARGVLI-------DWKAV 370 Query: 142 EREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEPVMLCLDEPAAGLNP 201 + A+ + K + +E NL G ++L + R + P +L P GL+ Sbjct: 371 LKHALGIVKNFNVDTPSVE---TPVRNLSGGNIQKLMLGRELSDIPKVLIAMNPTWGLDV 427 Query: 202 RESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGR 246 + + + L R E + LI D+ +M++SD + V+ G+ Sbjct: 428 AATRFVREQLLEER-EKGAAIFLISEDLDELMSLSDRIAVMYRGK 471 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: 305 Number of extensions: 18 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 294 Length of database: 503 Length adjustment: 30 Effective length of query: 264 Effective length of database: 473 Effective search space: 124872 Effective search space used: 124872 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: 50 (23.9 bits)
This GapMind analysis is from Sep 24 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