Align High-affinity branched-chain amino acid transport ATP-binding protein (characterized, see rationale)
to candidate 208246 DVU2740 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein
Query= uniprot:A0A159ZWL6 (233 letters) >MicrobesOnline__882:208246 Length = 241 Score = 226 bits (575), Expect = 4e-64 Identities = 115/240 (47%), Positives = 167/240 (69%), Gaps = 7/240 (2%) Query: 1 MLQFENVSTFYGKIQALHSVNVEVRQGEIVTLIGANGAGKSTLLMTLCG-----SPQAHS 55 +L +N+ YG I+ALH + V +GEIVTLIGANGAGKST L ++ +P+ + Sbjct: 2 LLSIDNLKVRYGNIEALHGLTFHVNEGEIVTLIGANGAGKSTTLKSIMRLPPPEAPRVSA 61 Query: 56 GSIRYMGEELVGQDSSHIMRK-SIAVVPEGRRVFARLTVEENLAMGGFFTDKGD-YQEQM 113 G I Y G+ L+ + ++RK IA+VPEGR +F L+V ENL + + + + Sbjct: 62 GDITYKGQSLLNVEPHDVVRKLRIALVPEGRHIFGNLSVMENLMLATYSRGSDPAIGKDL 121 Query: 114 DKVLHLFPRLKERFTQRGGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIF 173 D++ LFPRL ER QR T+SGGEQQMLA+GRALM+ +LLLLDEPS+GLAP+++ ++F Sbjct: 122 DRIFDLFPRLAERRDQRSDTLSGGEQQMLAVGRALMTNCELLLLDEPSMGLAPLLMYEMF 181 Query: 174 DIIEQLRKDGVTVFLVEQNANQALKIADRAYVLENGRVVMQGTGEALLTDPKVREAYLGG 233 ++QL ++G+T+ +VEQNA AL++ADR YVL+ G +V +G+ E L +DP+V++AYLGG Sbjct: 182 RTLKQLNREGLTIVVVEQNARLALQVADRGYVLDTGEIVAEGSSEQLASDPEVKKAYLGG 241 Lambda K H 0.320 0.137 0.381 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: 176 Number of extensions: 5 Number of successful extensions: 4 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: 233 Length of database: 241 Length adjustment: 23 Effective length of query: 210 Effective length of database: 218 Effective search space: 45780 Effective search space used: 45780 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: 46 (22.3 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