Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_011317351.1 AVA_RS02375 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000204075.1:WP_011317351.1 Length = 259 Score = 262 bits (669), Expect = 6e-75 Identities = 136/252 (53%), Positives = 179/252 (71%), Gaps = 1/252 (0%) Query: 2 SQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGT 61 S+ +L+ + +++RFGGL A+N V T+ +I+GLIGPNGAGKTT FN+IT L P +G Sbjct: 6 SRVILEAKSLTRRFGGLIAVNNVSFTVNHYEIFGLIGPNGAGKTTLFNLITALIPPSSGE 65 Query: 62 FELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHK 121 K + PHE+A GIARTFQNIRLFGE++ LENV++ H+ TK +F V Sbjct: 66 LIYQNKAIAQLGPHEIASLGIARTFQNIRLFGELSALENVIIARHLHTKSTIFTGVLGLP 125 Query: 122 AAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPA 181 A +EEA REK+ +LL+ VG+ A+ AR+ +YGDQRRLEIARALA +PQ+L LDEPA Sbjct: 126 PAPKEEARSREKALELLEMVGLSDRAQEKARNFAYGDQRRLEIARALALEPQILLLDEPA 185 Query: 182 AGMNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADV 240 AGMN +EK L E + +I+ TI+LIEH V L+MGLC+RI VLD+G+ IA G P+ V Sbjct: 186 AGMNPSEKQQLSEFIREIRDRFNLTIILIEHHVPLVMGLCDRIAVLDFGQLIALGEPSVV 245 Query: 241 QKNPAVIEAYLG 252 + +PAVIEAYLG Sbjct: 246 RNDPAVIEAYLG 257 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: 209 Number of extensions: 12 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: 259 Length adjustment: 24 Effective length of query: 231 Effective length of database: 235 Effective search space: 54285 Effective search space used: 54285 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 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