Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate WP_013075323.1 BTUS_RS06520 alpha-ketoacid dehydrogenase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_000092905.1:WP_013075323.1 Length = 327 Score = 470 bits (1209), Expect = e-137 Identities = 225/327 (68%), Positives = 278/327 (85%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 M+V +YI+A+ A++EEMERD VFVLGEDVG +GGVF+AT GL EQFG ERV+D PLAE Sbjct: 1 MAVKTYIEAVRDALREEMERDPSVFVLGEDVGVRGGVFRATVGLIEQFGPERVLDAPLAE 60 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 SAI GV IGA++YGMRP+AE+QFADFI+PAVNQIISEAAK+RYRSNNDW CP+V+RAPYG Sbjct: 61 SAIVGVAIGASLYGMRPVAEIQFADFILPAVNQIISEAAKMRYRSNNDWYCPLVIRAPYG 120 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 GGVHGALYHSQSVEA+F + PGLK+V P+TPYD KGLLKAA+RD+DPVLFFEHK+ YR I Sbjct: 121 GGVHGALYHSQSVEALFYHVPGLKVVAPATPYDVKGLLKAAIRDDDPVLFFEHKKCYRSI 180 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240 KGEVP +DYV+PIG+A V REG DITVI+YG+ +H AL+AA +EK+GISAHV+DLRT+ Sbjct: 181 KGEVPEEDYVVPIGRARVAREGMDITVISYGMTLHTALEAAAEVEKEGISAHVLDLRTLR 240 Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300 PLD+ AI+EAA KTGKV+++ ED K G + +EV+A+I+E LF LDAP+ RLAGP+IPAM Sbjct: 241 PLDEAAILEAAEKTGKVMIIHEDNKVGGVGAEVSALIAEKALFSLDAPVMRLAGPEIPAM 300 Query: 301 PYAPTMEKYFMVNPDKVEAAMRELAEF 327 P+ +EK ++V ++ AMRELA F Sbjct: 301 PFNRELEKSYLVTAPRIAEAMRELARF 327 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: 408 Number of extensions: 14 Number of successful extensions: 1 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: 327 Length adjustment: 28 Effective length of query: 299 Effective length of database: 299 Effective search space: 89401 Effective search space used: 89401 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: 48 (23.1 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