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_002720082.1 RSPH17029_RS07940 ABC transporter ATP-binding protein
Query= TCDB::P21630 (233 letters) >NCBI__GCF_000015985.1:WP_002720082.1 Length = 236 Score = 205 bits (522), Expect = 5e-58 Identities = 98/223 (43%), Positives = 154/223 (69%), Gaps = 1/223 (0%) Query: 11 YGKIQALHDVSVEVKKGEIVTLIGANGAGKSTLLMTLCGSPQAASGSIRYEGEELVGLPS 70 YG LH ++ V+KG+I ++G NGAGKST + + G + +G ++ EGE++ L Sbjct: 15 YGAADILHGCTLAVEKGQIAVIVGPNGAGKSTAMKAVFGMLRLRAGHVKLEGEDITALTP 74 Query: 71 STIMRKSIAVVPEGRRVFSRLTVEENLAMGGFFTDKDDYQVQMDKVLELFPRLKERYEQR 130 + K +A VP+ +F+ +TVEENL MG F +DD + M++V ELFP LK++ Q Sbjct: 75 QARVAKGMAFVPQTHNIFTSMTVEENLEMGAFLR-RDDIRGTMEQVYELFPILKDKRRQA 133 Query: 131 AGTMSGGEQQMLAIGRALMSKPKLLLLDEPSLGLAPIIIQQIFEIIEQLRREGVTVFLVE 190 AG +SGG++Q +A+GRALM++PK+L+LDEP+ G++PI++ ++F+ I ++ R G+++ +VE Sbjct: 134 AGELSGGQRQQVAVGRALMTQPKVLMLDEPTAGVSPIVMDELFDRIIEVARTGISILMVE 193 Query: 191 QNANQALKLADRAYVLENGRIVMHDTGAALLTNPKVRDAYLGG 233 QNA QAL +AD+ YVL G DTG AL+ +P+VR ++LGG Sbjct: 194 QNARQALMIADKGYVLVQGANRFTDTGPALMADPEVRRSFLGG 236 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: 156 Number of extensions: 6 Number of successful extensions: 2 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: 236 Length adjustment: 23 Effective length of query: 210 Effective length of database: 213 Effective search space: 44730 Effective search space used: 44730 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 10 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