Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_037568644.1 BS73_RS01520 alpha-ketoacid dehydrogenase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_000744815.1:WP_037568644.1 Length = 329 Score = 249 bits (636), Expect = 7e-71 Identities = 135/321 (42%), Positives = 202/321 (62%), Gaps = 4/321 (1%) Query: 5 SYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAESAIA 64 +Y +A+ AM+E + D RVF++GEDVGR GG F + GL E+FG ER+ DTPL+ESA Sbjct: 6 TYREAMREAMREALRADERVFLMGEDVGRYGGCFGVSLGLLEEFGPERIRDTPLSESAFV 65 Query: 65 GVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYGGGVH 124 G GIGAA+ G+RPI E+ +F + A++QI++ AA +++ S P+V+R G G Sbjct: 66 GAGIGAAINGLRPIVEIMTVNFSLLALDQILNNAATLQHMSGGQIQVPLVIRMTTGAGRQ 125 Query: 125 GALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYR---LIK 181 A HS S+E +A+ PGL+++ P+T DA+ +L AA+ D DPV+ FEH Y + Sbjct: 126 LAAQHSHSLEGWYAHIPGLRVLAPATLPDARHMLAAALADPDPVIVFEHGSLYNTAGALD 185 Query: 182 GEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVYP 241 PAD I A V+R G D++++ YG + AL+AAERL DGISA V+DLRT+ P Sbjct: 186 PGSPADSAAADITHAAVRRPGTDVSLVAYGGSLPKALEAAERLAADGISAEVLDLRTLRP 245 Query: 242 LDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAMP 301 LD+ A+ +T +V++V E + + +EVAA I+E ++LDAPI+R+ ++P +P Sbjct: 246 LDQPALTATVGRTHRVVVVDEGWRSVGLSAEVAARIAESAFYELDAPIERVCTAEVP-IP 304 Query: 302 YAPTMEKYFMVNPDKVEAAMR 322 YA +E+ + + AA R Sbjct: 305 YARGLEEAALPQAADIVAAAR 325 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: 284 Number of extensions: 17 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: 329 Length adjustment: 28 Effective length of query: 299 Effective length of database: 301 Effective search space: 89999 Effective search space used: 89999 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