Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate GFF2283 PGA1_c23150 acetoin:2,6-dichlorophenolindophenol oxidoreductase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >FitnessBrowser__Phaeo:GFF2283 Length = 331 Score = 275 bits (704), Expect = 9e-79 Identities = 140/324 (43%), Positives = 205/324 (63%), Gaps = 2/324 (0%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 M ++ A+N A+ EEM RD VF++GEDV G FK +GL E+FG ERV+DTP+AE Sbjct: 1 MREITLSQAVNEALAEEMRRDETVFIIGEDVAEAGTPFKVLSGLVEEFGTERVVDTPIAE 60 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 G+ +GAAM G RP+ ++ F DFI ++Q+ ++AAK Y S S P+V+R G Sbjct: 61 PGFMGLAVGAAMTGTRPVVDLMFGDFIYLIMDQLCNQAAKTHYMSGGKMSAPLVLRTNMG 120 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 A HSQS+ A+ A+ PGLK+ MPS+ Y+AKGL+K A+RD +PV+ FE K Y Sbjct: 121 ATRRSAAQHSQSLHALVAHIPGLKVAMPSSAYEAKGLMKTAIRDNNPVVIFEDKLMYN-D 179 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240 K VP +++++P G+A++KR G+DIT+I V AAE L K+GI A V+D RT+ Sbjct: 180 KAPVPEEEFLIPFGEANIKRAGNDITLIATSSMVQVCEAAAEILAKEGIDAEVIDPRTIV 239 Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300 PLD+E +I +A KT +V++V E + I E+A I+E + LDAP+ R+ D+P + Sbjct: 240 PLDEETLIASAKKTSRVIVVDEGHQSYGITGEIAGRINEKAFYHLDAPVLRMGAMDVP-V 298 Query: 301 PYAPTMEKYFMVNPDKVEAAMREL 324 P++P +E + P+ V A R+L Sbjct: 299 PFSPALEDITVPTPEAVAANARKL 322 Lambda K H 0.319 0.136 0.392 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: 270 Number of extensions: 12 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: 327 Length of database: 331 Length adjustment: 28 Effective length of query: 299 Effective length of database: 303 Effective search space: 90597 Effective search space used: 90597 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: 49 (23.5 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