Align Leucine/isoleucine/valine ABC transporter,ATPase component; EC 3.6.3.- (characterized, see rationale)
to candidate 207079 DVU1627 ABC transporter, ATP-binding protein
Query= uniprot:G8ALJ0 (294 letters) >MicrobesOnline__882:207079 Length = 241 Score = 125 bits (314), Expect = 9e-34 Identities = 89/263 (33%), Positives = 132/263 (50%), Gaps = 31/263 (11%) Query: 11 LLTVEHLTMRFGGLVAVNDVSFSANNGEITAIIGPNGAGKTTLFNCITGFYTPTVGRLTL 70 +L E L RFG V VS S GEI ++GPNGAGKTT F +TG PT G + L Sbjct: 4 VLQGEDLRKRFGQREVVRGVSVSVQQGEIVGLLGPNGAGKTTTFYMLTGIIKPTAGIVRL 63 Query: 71 RHADGKEFLLERMPGYRISQKASVARTF--QNIRLFGGMSVLENL-IVAQHNKLIRASGF 127 DG++ + + + ++A V ++ Q +F ++V ENL I+ +H Sbjct: 64 ---DGQD-----IADWPLHERARVGLSYLPQESSVFKRLTVRENLEIILEHT-------- 107 Query: 128 SIAGLLGLPSYTRTEREAVDLAKYWLDRVRLLEFADWEAGNLPYGAQRRLEIARAMCTEP 187 GLP+ + ER +A + + A A +L G +RRLEIAR M EP Sbjct: 108 ------GLPAARQKERAEALMADF-----GIAHLASSRAMHLSGGERRRLEIARCMIREP 156 Query: 188 VMLCLDEPAAGLNPRESGELADLLTYIRDEHKIGVLLIEHDMSVVMTISDHVVVLDYGRK 247 + LDEP AG++P G++ L+ +RD IGVL+ +H++ +TI D ++ G+ Sbjct: 157 KFVLLDEPFAGIDPLAVGDIQGLIRKLRD-RGIGVLISDHNVRETLTICDRAYLVHQGQV 215 Query: 248 ISDGDPAFVKNDPAVIRAYLGEE 270 I DG P + D YLG + Sbjct: 216 ILDGTPEHIVGDEQARLVYLGAD 238 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: 180 Number of extensions: 12 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: 241 Length adjustment: 25 Effective length of query: 269 Effective length of database: 216 Effective search space: 58104 Effective search space used: 58104 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