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_061534736.1 CAter10_RS19520 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_001584165.1:WP_061534736.1 Length = 252 Score = 221 bits (563), Expect = 1e-62 Identities = 117/228 (51%), Positives = 164/228 (71%), Gaps = 6/228 (2%) Query: 11 YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGS-PQAAS--GSIRYEGEELVG 67 YGK++ALH S++V G+IVT+IG NGAGKST+L + G+ P S G++R G++ G Sbjct: 19 YGKVEALHGASLQVGAGQIVTVIGPNGAGKSTMLNAIAGAMPNNGSMRGTVRLLGQDTAG 78 Query: 68 LPSSTIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDD---YQVQMDKVLELFPRLK 124 + T + + + +VPE R +F+ +TVE+NL +G + K Y QM V +LFPRL+ Sbjct: 79 VAIETRVARGMCLVPEKRELFASMTVEDNLLLGSYRRYKAGERAYADQMAVVYDLFPRLQ 138 Query: 125 ERYEQRAGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGV 184 ER +Q+AG++SGGE+QMLA+GRALM+KP+LL+LDEPSLGLAP+I+++IF II +L++ GV Sbjct: 139 ERRKQQAGSLSGGERQMLAVGRALMAKPQLLMLDEPSLGLAPLIVKEIFHIIVRLKQTGV 198 Query: 185 TVFLVEQNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLG 232 + LVEQNA AL+ AD AYVLE G +V+ A L +PKV D YLG Sbjct: 199 AILLVEQNARAALQAADYAYVLETGDMVLQGPAAELANDPKVIDTYLG 246 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: 176 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: 252 Length adjustment: 23 Effective length of query: 210 Effective length of database: 229 Effective search space: 48090 Effective search space used: 48090 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 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