Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_011938516.1 GURA_RS08195 alpha-ketoacid dehydrogenase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_000016745.1:WP_011938516.1 Length = 333 Score = 256 bits (655), Expect = 4e-73 Identities = 132/326 (40%), Positives = 208/326 (63%), Gaps = 2/326 (0%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 M ++Y +A +++ + RD RVF++GEDVG GG F + GL ++FG ER+ DTPL+E Sbjct: 7 MVKLTYREAAREGLRDALARDPRVFLMGEDVGHYGGCFAVSKGLLQEFGPERIRDTPLSE 66 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 A G+GIGAAM GMRPI E+ +F + A++QI++ AA + + S ++ P+V+R G Sbjct: 67 LAFTGMGIGAAMGGMRPIVEIMTVNFSLLALDQILNNAATLLHMSGGQFNVPLVIRMATG 126 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 G A H+ S+E +A+ PG+++V P+T D +G+L A+ D DPVL FE+ Y + Sbjct: 127 AGKQLAAQHAHSLEGWYAHIPGIRVVSPATLADVRGMLWTALEDPDPVLIFENNTLYTM- 185 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240 +GE+ D + I A V REG D+++ITY +H +L AAE L +GISA V+DLRT+ Sbjct: 186 EGELAVDAGPVDIDHARVLREGSDVSIITYSASLHKSLAAAETLAGEGISAEVIDLRTLR 245 Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300 PLD I+ + +KT + L+V E + GSI +E++A I E ++LDAP++RL ++P + Sbjct: 246 PLDDATIMGSVAKTHRALIVDEGWRSGSISAEISARIVEQAFYELDAPVERLCSAEVP-I 304 Query: 301 PYAPTMEKYFMVNPDKVEAAMRELAE 326 PYA ME+ + + + A ++ + + Sbjct: 305 PYARHMEQAAIPQAETIVATVKRMVQ 330 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: 250 Number of extensions: 14 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: 333 Length adjustment: 28 Effective length of query: 299 Effective length of database: 305 Effective search space: 91195 Effective search space used: 91195 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 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