Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_043744393.1 AMB_RS12355 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000009985.1:WP_043744393.1 Length = 243 Score = 182 bits (461), Expect = 7e-51 Identities = 98/249 (39%), Positives = 154/249 (61%), Gaps = 16/249 (6%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 LL + + K F GL+A++GV ++ G++ LIGPNGAGKTT FN+I G+++PD G E+ Sbjct: 6 LLLVEGLVKNFRGLRAVDGVSFSVAAGEVVALIGPNGAGKTTVFNMIAGVFEPDEGRIEM 65 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 +G P +V + GI RTFQ ++ FG ++V ENV++G +R +V A Sbjct: 66 EGASLVGLRPDQVCRTGIGRTFQLVKPFGNISVEENVLIGA-LRWTHDVDQA-------- 116 Query: 125 EEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAGM 184 R +++++L+ +G+ ++ AR L+ D++ LE+ARALAT P+LL LDE AG+ Sbjct: 117 ------RRRAREVLELLGLADKRRQMARGLTLPDRKCLEVARALATGPKLLLLDEVMAGL 170 Query: 185 NATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQKN 243 E + E ++ E G TI+LIEH ++ +M L R+ V++ GKP+ EG P +V ++ Sbjct: 171 RPAETDRMVETFRRLNRETGLTIVLIEHVMRAVMALSQRVVVINTGKPVCEGAPEEVVRD 230 Query: 244 PAVIEAYLG 252 P V+E YLG Sbjct: 231 PRVLECYLG 239 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: 179 Number of extensions: 8 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: 255 Length of database: 243 Length adjustment: 24 Effective length of query: 231 Effective length of database: 219 Effective search space: 50589 Effective search space used: 50589 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: 46 (22.3 bits)
This GapMind analysis is from Sep 17 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