Align 2-keto-isovalerate dehydrogenase component β subunit (EC 1.2.4.4) (characterized)
to candidate YP_001326764.1 Smed_1077 pyruvate dehydrogenase subunit beta
Query= metacyc::MONOMER-11684 (327 letters) >NCBI__GCF_000017145.1:YP_001326764.1 Length = 465 Score = 267 bits (682), Expect = 4e-76 Identities = 138/322 (42%), Positives = 200/322 (62%), Gaps = 1/322 (0%) Query: 1 MSVMSYIDAINLAMKEEMERDSRVFVLGEDVGRKGGVFKATAGLYEQFGEERVMDTPLAE 60 M M+ +A+ AM EEM + VFV+GE+V G +K T GL ++FG RV+DTP+ E Sbjct: 140 MVTMTVREALRDAMAEEMRANDDVFVMGEEVAEYQGAYKITQGLLQEFGARRVVDTPITE 199 Query: 61 SAIAGVGIGAAMYGMRPIAEMQFADFIMPAVNQIISEAAKIRYRSNNDWSCPIVVRAPYG 120 AGVG+GAAM G+RPI E +F M A++QII+ AAK Y S PIV R P G Sbjct: 200 HGFAGVGVGAAMTGLRPIVEFMTFNFAMQAIDQIINSAAKTLYMSGGQMGAPIVFRGPSG 259 Query: 121 GGVHGALYHSQSVEAIFANQPGLKIVMPSTPYDAKGLLKAAVRDEDPVLFFEHKRAYRLI 180 A HSQ A +++ PGLK+VMP T DAKGLLKAA+RD +P++F E++ Y Sbjct: 260 AAARVAAQHSQCYAAWYSHIPGLKVVMPYTAADAKGLLKAAIRDPNPIIFLENEILYGQS 319 Query: 181 KGEVPADDYVLPIGKADVKREGDDITVITYGLCVHFALQAAERLEKDGISAHVVDLRTVY 240 DD+VLPIGKA + R G D T++++G+ + +A++AA LE GI ++DLRT+ Sbjct: 320 FDVPKLDDFVLPIGKARIHRAGKDATLVSFGIGMTYAIKAAAELEAQGIDVEIIDLRTIR 379 Query: 241 PLDKEAIIEAASKTGKVLLVTEDTKEGSIMSEVAAIISEHCLFDLDAPIKRLAGPDIPAM 300 P+D +IE+ KTG+++ V E + S+ +E+A + + LDAP+ +AG D+P M Sbjct: 380 PMDLPTVIESVKKTGRLVTVEEGYPQSSVGTEIATRVMQQAFDYLDAPVLTIAGKDVP-M 438 Query: 301 PYAPTMEKYFMVNPDKVEAAMR 322 PYA +EK + + +V A++ Sbjct: 439 PYAANLEKLALPSVAEVVEAVK 460 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: 420 Number of extensions: 21 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: 465 Length adjustment: 30 Effective length of query: 297 Effective length of database: 435 Effective search space: 129195 Effective search space used: 129195 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: 50 (23.9 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