Align High-affinity branched-chain amino acid transport ATP-binding protein BraG, component of Branched chain amino acid uptake transporter. Transports alanine (characterized)
to candidate AO356_28370 AO356_28370 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_28370 Length = 265 Score = 184 bits (466), Expect = 2e-51 Identities = 110/243 (45%), Positives = 150/243 (61%), Gaps = 13/243 (5%) Query: 1 MLSFDKVSTYYGK-IQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGS-- 57 +L D + Y + I A+ VS+EV+KG++V L+GANGAGKST L +A G Sbjct: 7 ILQIDDIEVLYEQTILAVRSVSLEVEKGQVVVLLGANGAGKSTTLKAASNLVRAERGEVV 66 Query: 58 ---IRYEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMD 114 I Y+G+++ T+ + V EGR F++LTVEENL G Q+ D Sbjct: 67 RGRIVYQGKDVTRSAPHTLAASGLVQVLEGRHCFAQLTVEENLLAGALARQVPRRQLLAD 126 Query: 115 KVLEL----FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQ 170 LEL FPRLK R + AG SGGEQQM+AIGRALM++P+L+LLDEPS+GLAP I++ Sbjct: 127 --LELVYGHFPRLKLRRKSLAGYTSGGEQQMIAIGRALMARPQLVLLDEPSMGLAPQIVE 184 Query: 171 QIFEIIEQL-RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDA 229 +IFEI+ QL +R+GV+ + EQN N AL+ A YVLE+GR+V + L ++D Sbjct: 185 EIFEIVRQLNQRDGVSFLIAEQNINVALRYAHHGYVLESGRVVSEGSAEQLAARSDLQDF 244 Query: 230 YLG 232 YLG Sbjct: 245 YLG 247 Lambda K H 0.318 0.136 0.374 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: 159 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: 265 Length adjustment: 24 Effective length of query: 209 Effective length of database: 241 Effective search space: 50369 Effective search space used: 50369 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: 41 (21.7 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