Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate YP_426833.1 Rru_A1746 extracellular ligand-binding receptor
Query= uniprot:A0A160A0J6 (375 letters) >NCBI__GCF_000013085.1:YP_426833.1 Length = 368 Score = 296 bits (759), Expect = 5e-85 Identities = 148/356 (41%), Positives = 222/356 (62%), Gaps = 2/356 (0%) Query: 11 LFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQ 70 L AA + S AD I +G+AGP TG A +G+ G++ A++ INAKGGV G++ Sbjct: 8 LLAATAAFAMGVGSAQAD-ITVGVAGPMTGQYASFGEQLAKGAEQAVKDINAKGGVLGEK 66 Query: 71 LVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATS 130 LV + DDACDPKQAVAVAN+ VND + FV GH CS S+ PAS +Y +EG+V I+PA+T+ Sbjct: 67 LVLKKGDDACDPKQAVAVANQFVNDKVVFVAGHFCSGSSIPASAVYNEEGIVQISPASTN 126 Query: 131 PDITARGYKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTLE 190 P +T +G++ +FRT G D QGP AG+++ H + +A++HDK YG+G+A K L Sbjct: 127 PKLTEQGFENVFRTCGRDDQQGPTAGDFLKAHFPGQKIAIIHDKTAYGKGLADETKSALN 186 Query: 191 DKGVKVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAKFM 250 GV+ A++E + AG+KD+S+++ KLK + +Y GGYH E GLI+RQ++E+GL A+ + Sbjct: 187 KAGVQEALYEAITAGEKDYSALVTKLKNEGIKIIYLGGYHTEAGLIIRQAKEQGLDARIV 246 Query: 251 GPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSYSA 310 + + + + IA + +G L T ++P A+ +F + G + +Y A Sbjct: 247 SGDALVSSEFASIAGPAGDGTLFTFSPDPRKNPEAAAVVKSFTDAGYNAEG-YTLYTYGA 305 Query: 311 VTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFG 366 V A A++ AKS D KVA+A+ +G F T G + FD GD+ +V+YEW G Sbjct: 306 VQAWAQAVEKAKSTDVDKVAKALKSGQFSTVLGPIGFDAQGDVSAPGYVMYEWKGG 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: 460 Number of extensions: 27 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: 368 Length adjustment: 30 Effective length of query: 345 Effective length of database: 338 Effective search space: 116610 Effective search space used: 116610 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: 49 (23.5 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