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_197539677.1 SUTH_RS01360 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000828635.1:WP_197539677.1 Length = 233 Score = 221 bits (564), Expect = 7e-63 Identities = 119/233 (51%), Positives = 160/233 (68%), Gaps = 2/233 (0%) Query: 1 MLSFDKVSTYYGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRY 60 ML + YG I A+ +S V++ EIV LIGANGAGK++ L L + SG I Y Sbjct: 1 MLEALNLHVRYGGISAVKGISFAVEENEIVCLIGANGAGKTSTLKALARMIPS-SGEIHY 59 Query: 61 EGEELVGLPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFT-DKDDYQVQMDKVLEL 119 E + +PS ++ + +A+VPEGR +F+RLTV ENLAMG + D ++V L Sbjct: 60 RTERIEAVPSHDLIGRGLALVPEGRGIFARLTVAENLAMGAYHRRDATGIADDFERVFAL 119 Query: 120 FPRLKERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQL 179 PRLKER Q AGT+SGGEQQMLAIGRALM +PKLLLLDEPS+GLAP++++++FE+I + Sbjct: 120 LPRLKERKAQVAGTLSGGEQQMLAIGRALMGRPKLLLLDEPSMGLAPLMVEKVFEVIRAV 179 Query: 180 RREGVTVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 EG+T+ LVEQNA AL++ R YV+E+G I + D+ AALL + +VR AYLG Sbjct: 180 AAEGMTILLVEQNARLALEVCSRGYVMESGLITLADSSAALLADSRVRAAYLG 232 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: 174 Number of extensions: 5 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: 233 Length adjustment: 23 Effective length of query: 210 Effective length of database: 210 Effective search space: 44100 Effective search space used: 44100 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 Apr 09 2024. 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