Align ABC transporter ATP-binding protein-branched chain amino acid transport, component of The branched chain hydrophobic amino acid transporter, LivJFGHM (characterized)
to candidate Pf6N2E2_1429 Branched-chain amino acid transport ATP-binding protein LivF (TC 3.A.1.4.1)
Query= TCDB::Q8DQH7 (236 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1429 Length = 253 Score = 199 bits (507), Expect = 3e-56 Identities = 111/241 (46%), Positives = 162/241 (67%), Gaps = 8/241 (3%) Query: 3 VLKVENLSVHYGM-IQAVRDVSFEVNEGEVVSLIGANGAGKTTILRTLSGLVRPSSG--- 58 +L+++++ V Y I AVR VS EV +G+VV L+GANGAGK+T L+ S LVR G Sbjct: 7 ILQIDDIEVLYEQTILAVRSVSLEVGKGQVVVLLGANGAGKSTTLKAASNLVRAERGEVV 66 Query: 59 --KIEFLGQEIQKMPAQKIVAGGLSQVPEGRHVFPGLTVMENLEMGAFLKK-NREENQAN 115 +I + G+++ + + A GL QV EGRH F LTV ENL GA ++ R + A+ Sbjct: 67 RGRIVYQGRDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLAD 126 Query: 116 LKKVFSRFPRLEERKNQDAATLSGGEQQMLAMGRALMSTPKLLLLDEPSMGLAPIFIQEI 175 L+ V+ FPRL+ R+ A SGGEQQM+A+GRALM+ P+L+LLDEPSMGLAP ++EI Sbjct: 127 LESVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMAKPQLVLLDEPSMGLAPQIVEEI 186 Query: 176 FDIIQDI-QKQGTTVLLIEQNANKALAISDRGYVLETGKIVLSGTGKELASSEEVRKAYL 234 F+I++ + Q+ G + L+ EQN N AL + GYVLE+G++V G+ ++LA+ +++ YL Sbjct: 187 FEIVRQLNQRDGVSFLIAEQNINIALRYAHHGYVLESGRVVSEGSAEQLAARGDLQDFYL 246 Query: 235 G 235 G Sbjct: 247 G 247 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: 153 Number of extensions: 9 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: 253 Length adjustment: 24 Effective length of query: 212 Effective length of database: 229 Effective search space: 48548 Effective search space used: 48548 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