Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate CCNA_03714 CCNA_03714 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >FitnessBrowser__Caulo:CCNA_03714 Length = 252 Score = 145 bits (367), Expect = 6e-40 Identities = 84/250 (33%), Positives = 133/250 (53%), Gaps = 16/250 (6%) Query: 6 LKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILLD 65 L V+++ FG V V+L +K +V L+GPNGAGKTT F +TG G I LD Sbjct: 11 LFVDSVGKSFGDRPVVKNVSLRLKRGEVAGLLGPNGAGKTTCFYMVTGLIAADYGAIYLD 70 Query: 66 GEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFRK 125 GE I P AR GV Q +F+ MT +N++ + Sbjct: 71 GENITAQPMFQRARLGVGYLPQEASIFRGMTVEQNVMAVVEMR---------------ER 115 Query: 126 SEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGLN 185 R+A E L+++ +T PA L+ G++RR+EIAR + + P ++LDEP AG++ Sbjct: 116 DPRKAREQVTSILEELRITHIRKSPAVALSGGERRRVEIARALASEPSFMLLDEPFAGID 175 Query: 186 PKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDNP 245 P D++ +IG L+ + +L+ +H+++ + I D +I+ G L +G+P +I +NP Sbjct: 176 PLAIADIREVIGYLK-GRGIGILITDHNVRETLDIIDRASIIHAGEVLFEGSPREIVENP 234 Query: 246 EVIKAYLGEA 255 EV + YLGE+ Sbjct: 235 EVKRVYLGES 244 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: 184 Number of extensions: 15 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: 252 Length adjustment: 24 Effective length of query: 231 Effective length of database: 228 Effective search space: 52668 Effective search space used: 52668 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 Apr 09 2024. 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