Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_092347340.1 BLU87_RS09485 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_900107645.1:WP_092347340.1 Length = 254 Score = 211 bits (538), Expect = 9e-60 Identities = 107/249 (42%), Positives = 162/249 (65%), Gaps = 1/249 (0%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 +L++EN+S FGGL A++ V TV + Q+ ALIGPNGAGK+T+ NC+TG +P+ G I Sbjct: 1 MLRLENVSKNFGGLPALSEVTFTVPKGQLTALIGPNGAGKSTLINCMTGVIEPSSGQIFF 60 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 + I LP + I+R G+ RTFQN+++F +T +EN+L + + + P R Sbjct: 61 QQQQIASLPAYKISRLGISRTFQNLKIFPRLTVLENILTGLTSEGGDSMLMAMLRLPYLR 120 Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 ER A LD+ L + AN PA LAYG ++R+E+AR + +P++++LDEP AGL Sbjct: 121 HRERSLKLRALEALDRFGLADKANWPAEVLAYGDKKRVELARATVGKPQLILLDEPVAGL 180 Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244 N +ET + + +LR + T+LL+EHDM LVM I+D +VV++ G +A GTP+++R N Sbjct: 181 NAEETATVAEQLRLLRSAGH-TMLLVEHDMDLVMEIADQVVVLDSGKCIATGTPDEVRCN 239 Query: 245 PEVIKAYLG 253 P V++AYLG Sbjct: 240 PLVLEAYLG 248 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: 177 Number of extensions: 3 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: 254 Length adjustment: 24 Effective length of query: 231 Effective length of database: 230 Effective search space: 53130 Effective search space used: 53130 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