Align Leucine-, isoleucine-, valine-, threonine-, and alanine-binding protein; LIVAT-BP; Leu/Ile/Val/Thr/Ala-binding protein (characterized)
to candidate 8501892 DvMF_2607 Extracellular ligand-binding receptor (RefSeq)
Query= SwissProt::P21175 (373 letters) >FitnessBrowser__Miya:8501892 Length = 372 Score = 240 bits (613), Expect = 4e-68 Identities = 134/364 (36%), Positives = 203/364 (55%), Gaps = 4/364 (1%) Query: 1 MKKGTQRLSRLFAAMAIAGFASYSMAADTIKIALAGPVTGPVAQYGDMQRAGALMAIEQI 60 M+KG L A +A+A A + AADTIK +AG +G +A YG A + + I Sbjct: 1 MRKGW--FKGLVAGLAVAVMACPAFAADTIKFGVAGAHSGDLASYGLPTVNAAKLVAKMI 58 Query: 61 NKAGGVNGAQLEGVIYDDACDPKQAVAVANKVVNDGVKFVVGHVCSSSTQPATDIYEDEG 120 N GGV G Q+E + DD C P+ A A K+V+DG V+GH+CS +T+ A IY++ Sbjct: 59 NAKGGVLGKQVEVIPQDDQCKPELATNAATKLVSDGANVVLGHICSGATKAALPIYKEAN 118 Query: 121 VLMITPSATAPEITSRG-YKLIFRTIGLDNMQGPVAGKFIAERYKDKTIAVLHDKQQYGE 179 +++++PSAT P +T G Y FRTI D+ Q + F ++ K IAVLHDK YG+ Sbjct: 119 IVLMSPSATNPALTQSGDYPNFFRTIASDDQQAKLGVDFTIDKLGKKKIAVLHDKGDYGK 178 Query: 180 GIATEVKKTVEDAGI-KVAVFEGLNAGDKDFNALISKLKKAGVQFVYFGGYHPEMGLLLR 238 G A K+ VE +G V +FEG+ G D++A++ K++ +G + V FGGYHPE +++ Sbjct: 179 GYAEYAKQFVEQSGKGTVVLFEGVTPGAVDYSAVVQKIRNSGAEAVMFGGYHPEASKIVQ 238 Query: 239 QAKQAGLDARFMGPEGVGNSEITAIAGDASEGMLATLPRAFEQDPKNKALIDAFKAKNQD 298 Q ++ +D F+ +GV + +AG +EG+ A+ + P K I+A + Sbjct: 239 QLRKKRMDLPFVSDDGVKDDTFIKVAGKDAEGVYASSSKDVSALPLYKEAIEAHVKEFGA 298 Query: 299 PSGIFVLPAYSAVTVIAKGIEKAGEADPEKVAEALRANTFETPTGNLGFDEKGDLKNFDF 358 G F AY+A + IEKAG D K+ ALR ET G + FD++GD + F Sbjct: 299 EPGAFYKEAYAASLALLNAIEKAGSTDSAKIMNALRTEFVETSVGKIKFDKRGDAEGVGF 358 Query: 359 TVYE 362 ++Y+ Sbjct: 359 SMYQ 362 Lambda K H 0.316 0.133 0.377 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: 354 Number of extensions: 17 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: 373 Length of database: 372 Length adjustment: 30 Effective length of query: 343 Effective length of database: 342 Effective search space: 117306 Effective search space used: 117306 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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