Align Leucine ABC transporter subunit substrate-binding protein LivK (characterized, see rationale)
to candidate 8501892 DvMF_2607 Extracellular ligand-binding receptor (RefSeq)
Query= uniprot:A0A160A0J6 (375 letters) >FitnessBrowser__Miya:8501892 Length = 372 Score = 237 bits (605), Expect = 3e-67 Identities = 128/359 (35%), Positives = 204/359 (56%), Gaps = 2/359 (0%) Query: 11 LFAAMVLAGVASHSFAADTIKIGIAGPKTGPVAQYGDMQFSGSKMAIEQINAKGGVNGKQ 70 L A + +A +A +FAADTIK G+AG +G +A YG + +K+ + INAKGGV GKQ Sbjct: 9 LVAGLAVAVMACPAFAADTIKFGVAGAHSGDLASYGLPTVNAAKLVAKMINAKGGVLGKQ 68 Query: 71 LVAVEYDDACDPKQAVAVANKVVNDGIKFVVGHLCSSSTQPASDIYEDEGVVMITPAATS 130 + + DD C P+ A A K+V+DG V+GH+CS +T+ A IY++ +V+++P+AT+ Sbjct: 69 VEVIPQDDQCKPELATNAATKLVSDGANVVLGHICSGATKAALPIYKEANIVLMSPSATN 128 Query: 131 PDITARG-YKMIFRTIGLDSAQGPAAGNYIADHVKPKIVAVLHDKQQYGEGIASAVKKTL 189 P +T G Y FRTI D Q ++ D + K +AVLHDK YG+G A K+ + Sbjct: 129 PALTQSGDYPNFFRTIASDDQQAKLGVDFTIDKLGKKKIAVLHDKGDYGKGYAEYAKQFV 188 Query: 190 EDKGV-KVAVFEGVNAGDKDFSSMIAKLKQANVDFVYYGGYHPELGLILRQSQEKGLKAK 248 E G V +FEGV G D+S+++ K++ + + V +GGYHPE I++Q ++K + Sbjct: 189 EQSGKGTVVLFEGVTPGAVDYSAVVQKIRNSGAEAVMFGGYHPEASKIVQQLRKKRMDLP 248 Query: 249 FMGPEGVGNDSISQIAKESSEGLLVTLPKSFDQDPANIALADAFKAKKEDPSGPFVFPSY 308 F+ +GV +D+ ++A + +EG+ + K P +A + G F +Y Sbjct: 249 FVSDDGVKDDTFIKVAGKDAEGVYASSSKDVSALPLYKEAIEAHVKEFGAEPGAFYKEAY 308 Query: 309 SAVTVIADAIKAAKSEDAGKVAEAIHAGTFKTPTGDLSFDKNGDLKDFKFVVYEWHFGK 367 +A + +AI+ A S D+ K+ A+ +T G + FDK GD + F +Y+ GK Sbjct: 309 AASLALLNAIEKAGSTDSAKIMNALRTEFVETSVGKIKFDKRGDAEGVGFSMYQVKNGK 367 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: 403 Number of extensions: 23 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: 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