Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate GFF4159 HP15_4099 branched-chain amino acid ABC transporter, ATP-binding protein
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Marino:GFF4159 Length = 269 Score = 206 bits (523), Expect = 5e-58 Identities = 107/242 (44%), Positives = 172/242 (71%), Gaps = 8/242 (3%) Query: 2 SVLKVENLSVHYGM-IQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLV-----RP 55 ++L+++N+ V Y +Q +R +S V +G +V+L+G+NGAGK+T L+++SGL+ Sbjct: 3 ALLEIDNIEVVYNKSVQVLRGLSLRVPKGAIVALLGSNGAGKSTTLKSVSGLLTLEDGEV 62 Query: 56 SSGKIEFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAF-LKKNREENQA 114 ++G++ F G++++ +P +++V GL V EGR VF LTV ENL + L ++ Sbjct: 63 TAGEVRFRGKDVKGVPPERLVRDGLFHVMEGRRVFEDLTVEENLIAATYALSGSKPSLSD 122 Query: 115 NLKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQE 174 + + V++ FPRL+ER+ Q A LSGGEQQMLA+GRAL++ P L++LDEPS+GLAP+ ++E Sbjct: 123 SYELVYNYFPRLKERRKQLAGYLSGGEQQMLALGRALIAQPDLIMLDEPSLGLAPLLVEE 182 Query: 175 IFDIIQDI-QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAY 233 IF I+ I ++QGT +LL+EQNA +LAI+ GY++E GKIV+ G +L ++E+V++ Y Sbjct: 183 IFTIVARINREQGTAILLVEQNAAVSLAIASYGYIMENGKIVIDGPADKLTANEDVQEFY 242 Query: 234 LG 235 LG Sbjct: 243 LG 244 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: 191 Number of extensions: 12 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: 236 Length of database: 269 Length adjustment: 24 Effective length of query: 212 Effective length of database: 245 Effective search space: 51940 Effective search space used: 51940 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