Align High-affinity branched-chain amino acid ABC transporter ATP-binding protein LivG (characterized, see rationale)
to candidate WP_058929663.1 AU252_RS04335 ABC transporter ATP-binding protein
Query= uniprot:A0A159ZWS6 (255 letters) >NCBI__GCF_001484605.1:WP_058929663.1 Length = 345 Score = 177 bits (450), Expect = 2e-49 Identities = 100/249 (40%), Positives = 148/249 (59%), Gaps = 2/249 (0%) Query: 5 ILKVENLSMRFGGLLAVNGVALTVKEKQVVALIGPNGAGKTTVFNCLTGFYQPTGGTILL 64 I+ EN++ FGG+ AV+ L + ++ ALIGPNGAGKTT+FN LTGF P G Sbjct: 38 IVVAENVTRSFGGINAVDVEYLEIPRHKITALIGPNGAGKTTLFNLLTGFDMPNSGKWQF 97 Query: 65 DGEPIQGLPGHHIARKGVVRTFQNVRLFKDMTAVENLLIAQHRHLNTNFFAGLFKTPAFR 124 +G + G+ + +AR G+VRTFQ ++ +T +EN+ + LFK + Sbjct: 98 EGNSLAGISPYKVARMGMVRTFQLTKVMGKLTVMENMRLGGSEQPGERLSKALFK-GLWG 156 Query: 125 KSEREAMEYAEYWLDKVNLTEFANRPAGTLAYGQQRRLEIARCMMTRPRILMLDEPAAGL 184 E+E A L+K L + A +L+ GQ++ LE+AR +M RP+++MLDEP AG+ Sbjct: 157 GREKEITAQANVLLEKFKLDAKKDDYAASLSGGQRKLLEMARSLMVRPKLVMLDEPMAGV 216 Query: 185 NPKETEDLKALIGVLREEHNVTVLLIEHDMKLVMSISDHIVVINQGTPLADGTPEQIRDN 244 NP T+ L I L+ E +TVL +EHDM +V I+D +VV+ +G +A+G P ++ N Sbjct: 217 NPALTQSLLDHIKNLKAE-GMTVLFVEHDMNMVRHIADWVVVMAEGKIVAEGPPGEVMKN 275 Query: 245 PEVIKAYLG 253 P VI AYLG Sbjct: 276 PAVIDAYLG 284 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: 248 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: 345 Length adjustment: 26 Effective length of query: 229 Effective length of database: 319 Effective search space: 73051 Effective search space used: 73051 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: 48 (23.1 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