Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_013011147.1 DACET_RS09425 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_000025725.1:WP_013011147.1 Length = 250 Score = 185 bits (469), Expect = 9e-52 Identities = 93/252 (36%), Positives = 158/252 (62%), Gaps = 7/252 (2%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +LK+ N+ + FGG+ A+N V+ E V ALIGPNGAGKTT+FN +TGF PT G + Sbjct: 1 MLKINNIGVSFGGVRALNEVSFQTPEIGVTALIGPNGAGKTTLFNVITGFVPPTDGQVSF 60 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGL--FKTPA 122 DG+ I G + G+ RTFQN+ + ++T +N+ + N + + Sbjct: 61 DGKDITGCEPECVFPLGISRTFQNLNIIPELTLRQNMYLGFIGKENPSALKSMLGINRGY 120 Query: 123 FRKSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAA 182 ++K+ER EY E+ VN+TE+A+ ++ YG + E+ R +++RP++L+LDEPAA Sbjct: 121 WKKAERLIDEYMEF----VNVTEYASMTPDSIPYGVLKNFELGRALLSRPKMLLLDEPAA 176 Query: 183 GLNPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIR 242 GLN E ++L ++ + E +++L++EHDM+ + S+++++V +N G + GT +++R Sbjct: 177 GLNLNEKDNLAGMVQKIAGE-GISILMVEHDMQFISSLAEYVVCLNFGEVIGKGTYKEVR 235 Query: 243 DNPEVIKAYLGE 254 +N EV++AYLG+ Sbjct: 236 ENKEVLRAYLGD 247 Lambda K H 0.321 0.138 0.398 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: 203 Number of extensions: 10 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: 250 Length adjustment: 24 Effective length of query: 231 Effective length of database: 226 Effective search space: 52206 Effective search space used: 52206 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 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