Align ABC-type branched-chain amino acid transport system, ATPase component protein (characterized, see rationale)
to candidate WP_041099057.1 SUTH_RS10320 ABC transporter ATP-binding protein
Query= uniprot:D8J1T6 (255 letters) >NCBI__GCF_000828635.1:WP_041099057.1 Length = 274 Score = 209 bits (533), Expect = 4e-59 Identities = 110/252 (43%), Positives = 160/252 (63%), Gaps = 2/252 (0%) Query: 5 LLKIRDVSKRFGGLQALNGVGITIERGQIYGLIGPNGAGKTTFFNVITGLYQPDTGTFEL 64 +L+I V+ FGG++ALNGV + G I +IGPNGAGKT+ FN I+G Y+P G Sbjct: 8 ILEIDQVTLAFGGVKALNGVSFEVAPGSITSVIGPNGAGKTSLFNTISGFYRPTAGHIRF 67 Query: 65 DGKPYSPSAPHEVAKAGIARTFQNIRLFGEMTVLENVMVGCHVRTKQNVFGAVFRHKAAR 124 G+ + + AK G+AR+FQNI LF MTVL+N+ +G H V A+F + AR Sbjct: 68 LGEDITQRPAPQRAKLGLARSFQNIALFRGMTVLDNIKLGRHCHLHTGVLDALFYYGKAR 127 Query: 125 EEEAAIR-EKSQKLLDFVGIGQFAKRTARHLSYGDQRRLEIARALATDPQLLALDEPAAG 183 EE +R + ++++DF+ I LSYG Q+R+E+ARALA P++L LDEP AG Sbjct: 128 REEVRLRADIEERIIDFLEIDHIRNAPVAALSYGLQKRVEMARALAMQPKVLMLDEPVAG 187 Query: 184 MNATEKLGLRELLVKIQAE-GKTILLIEHDVKLMMGLCNRITVLDYGKPIAEGVPADVQK 242 MN E + ++ ++ E G TIL++EHD+ ++M + + + VL++G+ IA+G PA VQ Sbjct: 188 MNREETEDMARFILDVREEWGVTILMVEHDMGMVMDISDHVVVLNFGEVIADGTPAAVQG 247 Query: 243 NPAVIEAYLGAG 254 NP VI AYLG+G Sbjct: 248 NPEVIRAYLGSG 259 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: 200 Number of extensions: 12 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: 274 Length adjustment: 25 Effective length of query: 230 Effective length of database: 249 Effective search space: 57270 Effective search space used: 57270 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