Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Ga0059261_4235 Ga0059261_4235 ABC-type multidrug transport system, ATPase component
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__Korea:Ga0059261_4235 Length = 310 Score = 110 bits (276), Expect = 2e-29 Identities = 73/224 (32%), Positives = 119/224 (53%), Gaps = 9/224 (4%) Query: 2 SVLKVENLSVHYGMIQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSGKIE 61 + + VE L+ +G V VS EV G + +G NG+GKTT LR + GL+ P G E Sbjct: 5 AAISVEGLTKRFGNRTVVDTVSLEVGRGRICGFLGPNGSGKTTTLRMICGLLIPDGGGGE 64 Query: 62 FLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKKNREENQANLKKVFS 121 LG ++ + ++++ + + + +F LT+ ENL A E+ +K+V + Sbjct: 65 VLGMDL--LTQRELIKRRIGYMTQRFGLFEDLTIRENLAFVADAYGLDEK----MKRVDA 118 Query: 122 RFPRL--EERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEIFDII 179 RL E R Q A TLSGG +Q LA+ ++ P++LLLDEP+ G+ P+ +E +D + Sbjct: 119 ALERLGLETRAGQLAGTLSGGWKQRLALAACVLHDPEILLLDEPTAGVDPLARREFWDQV 178 Query: 180 QDIQKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKEL 223 + +GTTVL+ ++A D Y+ G ++ GT E+ Sbjct: 179 HMLSAEGTTVLVSTHYMDEAERCHDIAYI-AYGVLLARGTADEI 221 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: 154 Number of extensions: 10 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: 310 Length adjustment: 25 Effective length of query: 211 Effective length of database: 285 Effective search space: 60135 Effective search space used: 60135 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: 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