Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate SMc01946 SMc01946 leucine-specific binding protein
Query= uniprot:A0A160A0J6 (375 letters) >FitnessBrowser__Smeli:SMc01946 Length = 372 Score = 305 bits (782), Expect = 1e-87 Identities = 164/359 (45%), Positives = 225/359 (62%), Gaps = 2/359 (0%) Query: 9 SKLFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNG 68 S L A + A VA A I +G+ GP TGP A +G G++ A E INA GG+NG Sbjct: 4 SLLSAVALTAMVAFSGTAWADILVGVGGPLTGPNAAFGAQLQKGAEQAAEDINAAGGING 63 Query: 69 KQLVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAA 128 +Q+ V DD DPKQ V+VA K V DG+KFVVGH S + PAS+IY + G++ +TPA+ Sbjct: 64 EQIKVVLGDDVSDPKQGVSVAQKFVADGVKFVVGHFNSGVSIPASEIYAENGILQVTPAS 123 Query: 129 TSPDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKT 188 T+P T RG FRT G D QG AG YIA + K VAV+HDK YG+G+A KK+ Sbjct: 124 TNPQFTERGLWNTFRTCGRDDQQGAVAGAYIAANFKDAKVAVIHDKTPYGQGLADETKKS 183 Query: 189 LEDKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAK 248 + + GV A++EG+N GDKDFS++IAK+KQA V VYYGG H E GLI+RQ +++GLKA Sbjct: 184 MNEAGVTEALYEGINTGDKDFSALIAKMKQAGVSIVYYGGLHTEAGLIMRQMKDQGLKAT 243 Query: 249 FMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSY 308 M +G+ ++ ++ IA ++ +G L+T + PA L + F+A +P + +Y Sbjct: 244 MMSGDGIVSNELASIAGDAVDGTLMTFAPDPRKSPAAKDLVEKFRAAGFEPEA-YTLYAY 302 Query: 309 SAVTVIADAIKAAKSEDAGKVAEAIHA-GTFKTPTGDLSFDKNGDLKDFKFVVYEWHFG 366 +A+ VIA+ KAA + D VAEAI A G FKT G+L FD+ GD+ +V+Y W G Sbjct: 303 AALQVIAEGAKAAGNTDPQAVAEAIKAKGPFKTAIGELGFDEKGDITRPDYVMYTWKKG 361 Lambda K H 0.314 0.132 0.372 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: 433 Number of extensions: 20 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: 375 Length of database: 372 Length adjustment: 30 Effective length of query: 345 Effective length of database: 342 Effective search space: 117990 Effective search space used: 117990 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 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