Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_041097007.1 SUTH_RS03115 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000828635.1:WP_041097007.1 Length = 261 Score = 212 bits (540), Expect = 5e-60 Identities = 105/256 (41%), Positives = 165/256 (64%), Gaps = 1/256 (0%) Query: 1 MSQTLLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTG 60 + + +L ++++S FGG++AL + + ++ +IGPNGAGK++ NVI G+Y+P G Sbjct: 6 IGEVILDLKNISLSFGGVRALQNISFNVLEHEVRAIIGPNGAGKSSMLNVINGVYRPQEG 65 Query: 61 TFELDGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRH 120 L G+ ++ ++ AKAG+ARTFQNI LF M+VL+N+M G +++ + N+ Sbjct: 66 EIILRGEHFANMNSYKAAKAGLARTFQNIALFKGMSVLDNIMTGRNLKMQANMLQQAIWW 125 Query: 121 KAAREEEAAIREKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEP 180 A+ EE R K ++++DF+ I K L YG Q+R+++ARALA +PQ+L LDEP Sbjct: 126 GPAQREELEHRAKVEEIIDFLEIQHIRKIPVGRLPYGLQKRVDLARALAMEPQILLLDEP 185 Query: 181 AAGMNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPAD 239 AGMN EK + ++ + + G T++LIEHD+ ++M + +R+ VLDYGK I +G P + Sbjct: 186 MAGMNVEEKQDMCRFILDVNDQFGTTVVLIEHDMGVVMDISDRVVVLDYGKKIGDGTPDE 245 Query: 240 VQKNPAVIEAYLGAGH 255 V+ NP VI AYLGA H Sbjct: 246 VRANPDVISAYLGASH 261 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: 189 Number of extensions: 11 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: 261 Length adjustment: 24 Effective length of query: 231 Effective length of database: 237 Effective search space: 54747 Effective search space used: 54747 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