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 3607992 Dshi_1400 ABC transporter related (RefSeq)
Query= TCDB::P21630 (233 letters) >FitnessBrowser__Dino:3607992 Length = 251 Score = 170 bits (431), Expect = 2e-47 Identities = 98/232 (42%), Positives = 138/232 (59%), Gaps = 5/232 (2%) Query: 2 LSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLC--GSPQAASGSIR 59 LS + YYG+ + +S V +GEI+ L+G NGAGK+T L + G PQ G I Sbjct: 21 LSVWDLHAYYGESYIVQGISFNVHEGEILALLGRNGAGKTTTLRAIARLGDPQVRHGEIW 80 Query: 60 YEGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLEL 119 + L + S + +VPE RR+ LTVEENL + K +D++ +L Sbjct: 81 LDHARLHEMESHEAAVAGLGLVPEDRRIIPGLTVEENLQLAQIVEPKG---WSLDRLYDL 137 Query: 120 FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179 FPRL ER +Q T+SGGEQQML+I RAL K+LLLDEP GLAP+I+ +I + + + Sbjct: 138 FPRLGERRKQEGVTLSGGEQQMLSIARALARDLKVLLLDEPYEGLAPVIVDEIEKTLRVI 197 Query: 180 RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYL 231 + +G+T +VEQNA +AL+LADRA +L+ G IV A +L N ++R YL Sbjct: 198 KEQGMTTVIVEQNAVRALELADRAVILDTGSIVFDGAAAEVLENAELRAEYL 249 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: 158 Number of extensions: 9 Number of successful extensions: 3 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: 251 Length adjustment: 23 Effective length of query: 210 Effective length of database: 228 Effective search space: 47880 Effective search space used: 47880 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