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 WP_011602030.1 FRAAL_RS03430 ABC transporter
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000058485.1:WP_011602030.1 Length = 548 Score = 165 bits (418), Expect = 1e-45 Identities = 98/234 (41%), Positives = 146/234 (62%), Gaps = 6/234 (2%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 +L F++VS+ Y + L +VS+ V+ GEIV L+GANGAGK+TL+ T G A++G + Sbjct: 308 LLVFERVSSGYNEGPVLREVSLVVRAGEIVALLGANGAGKTTLIRTAAGLVPASAGRVGM 367 Query: 61 EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELF 120 GE ST+ R+ +AVVP+GR RLTV ENL + ++ ++++VL F Sbjct: 368 FGEWFRRPAPSTLARRGLAVVPQGRGALGRLTVRENLRLAA----GRSHRGEIERVLGWF 423 Query: 121 PRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLR 180 P L ++ AG +SGGE+Q LA+ AL+ +P+LLL+DE S GLAP + ++ E++ ++ Sbjct: 424 PALGGLLDRPAGELSGGERQRLALAVALVRRPRLLLVDELSFGLAPGVAPRLLELLREIA 483 Query: 181 REGVT-VFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDA-YLG 232 E T V LVEQ A AL++ADR YVL+ GR+ + A L P + +A YLG Sbjct: 484 AETSTGVLLVEQFAALALRVADRGYVLDRGRVALAAPAAQLAARPDLIEASYLG 537 Score = 117 bits (292), Expect = 6e-31 Identities = 75/224 (33%), Positives = 115/224 (51%), Gaps = 12/224 (5%) Query: 12 GKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPSS 71 G + + DVS + G + LIG NGAGK+TL+ L G +GS+ +G L GLP+ Sbjct: 7 GGTRIVEDVSFGLAAGSVTGLIGPNGAGKTTLIDALTGFATIFAGSVNLDGTALTGLPAH 66 Query: 72 TIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTD--KDDYQVQMDKVLELFPRLKERYEQ 129 R +A + +F L V EN+A+ T D ++ + + + P Sbjct: 67 ERQRLGLARTFQALELFDSLAVAENIAVVARPTSGSMDADRLGLAAIADRLP-------- 118 Query: 130 RAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTVFLV 189 T+S E+ +A+GRA+ + PK+LLLDEP+ GL P +++ I ++ GV V LV Sbjct: 119 --ATLSHDERAAVALGRAMAATPKVLLLDEPAAGLDPGDRRELAARIRRIAGHGVAVLLV 176 Query: 190 EQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233 + + + D+ VL+ GRIV A + +P VR AYLGG Sbjct: 177 DHDVQLVFDVCDQVLVLDGGRIVARGLPAQVRADPAVRAAYLGG 220 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: 307 Number of extensions: 13 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 233 Length of database: 548 Length adjustment: 29 Effective length of query: 204 Effective length of database: 519 Effective search space: 105876 Effective search space used: 105876 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: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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