Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_086510700.1 BZY95_RS14915 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_002151265.1:WP_086510700.1 Length = 256 Score = 184 bits (466), Expect = 2e-51 Identities = 97/251 (38%), Positives = 153/251 (60%), Gaps = 1/251 (0%) Query: 4 TLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFE 63 +++ +R V K FGGL+ +N I +E+G I GLIGPNGAGK+T FN+I G D+G Sbjct: 3 SIIDVRHVYKAFGGLKVINDCSIQVEKGSITGLIGPNGAGKSTLFNIIAGALPLDSGQVL 62 Query: 64 LDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAA 123 LDG+ + +E+ G+ RTFQ F +MT LEN+M+ + +++F A + Sbjct: 63 LDGEDITNRPANELFHKGLLRTFQIAHEFSQMTALENLMMVPPKQAGESLFSAWLKPGLV 122 Query: 124 REEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183 ++E A+R+K+ +++DF+G+ A +LS G ++ LE+ R + TD +++ LDE AAG Sbjct: 123 NQQETAVRQKALEVIDFIGLHHVRNELAGNLSGGQKKLLELGRTMMTDARVVLLDEIAAG 182 Query: 184 MNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 +N T L E + ++ E G T L+IEHD+ ++ LC+ + VL G + EG ++Q Sbjct: 183 VNRTLLGDLVENIERLNREMGYTFLVIEHDMDMIARLCDPVIVLAQGSVMVEGTIEEIQN 242 Query: 243 NPAVIEAYLGA 253 NP VIEAY G+ Sbjct: 243 NPQVIEAYFGS 253 Lambda K H 0.320 0.138 0.394 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: 161 Number of extensions: 5 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: 255 Length of database: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 47 (22.7 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