Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate 208246 DVU2740 high-affinity branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >MicrobesOnline__882:208246 Length = 241 Score = 229 bits (585), Expect = 3e-65 Identities = 117/240 (48%), Positives = 172/240 (71%), Gaps = 6/240 (2%) Query: 3 VLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRP-----SS 57 +L ++NL V YG I+A+ ++F VNEGE+V+LIGANGAGK+T L+++ L P S+ Sbjct: 2 LLSIDNLKVRYGNIEALHGLTFHVNEGEIVTLIGANGAGKSTTLKSIMRLPPPEAPRVSA 61 Query: 58 GKIEFLGQEIQKMPAQKIVAG-GLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANL 116 G I + GQ + + +V ++ VPEGRH+F L+VMENL + + + + +L Sbjct: 62 GDITYKGQSLLNVEPHDVVRKLRIALVPEGRHIFGNLSVMENLMLATYSRGSDPAIGKDL 121 Query: 117 KKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIF 176 ++F FPRL ER++Q + TLSGGEQQMLA+GRALM+ +LLLLDEPSMGLAP+ + E+F Sbjct: 122 DRIFDLFPRLAERRDQRSDTLSGGEQQMLAVGRALMTNCELLLLDEPSMGLAPLLMYEMF 181 Query: 177 DIIQDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYLGG 236 ++ + ++G T++++EQNA AL ++DRGYVL+TG+IV G+ ++LAS EV+KAYLGG Sbjct: 182 RTLKQLNREGLTIVVVEQNARLALQVADRGYVLDTGEIVAEGSSEQLASDPEVKKAYLGG 241 Lambda K H 0.315 0.134 0.358 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: 162 Number of extensions: 6 Number of successful extensions: 2 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: 236 Length of database: 241 Length adjustment: 23 Effective length of query: 213 Effective length of database: 218 Effective search space: 46434 Effective search space used: 46434 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 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