Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_067911316.1 AQZ52_RS12755 alpha-ketoacid dehydrogenase subunit beta
Query= reanno::WCS417:GFF3430 (352 letters) >NCBI__GCF_001519075.1:WP_067911316.1 Length = 352 Score = 496 bits (1276), Expect = e-145 Identities = 230/344 (66%), Positives = 286/344 (83%) Query: 8 IEVETAMTTTTMTMIQALRSAMDVMLERDDNVVVFGQDVGYFGGVFRCTEGLQTKYGSSR 67 + V + + MI+A+ A+DVM+ RDD++VV G+DVGYFGGVFR T GLQ KYG +R Sbjct: 8 LSVSDTPSMKKLNMIEAINDALDVMMARDDSIVVMGEDVGYFGGVFRATAGLQKKYGRTR 67 Query: 68 VFDAPISESGIVGVAVGMGAYGLRPVAEIQFADYVYPATDQIISEAARLRYRSAGQFTAP 127 VFD PISE GI+GVAVGMGAYGLRPV EIQFADY+YP DQ++SEAARLRYRSAG+FTAP Sbjct: 68 VFDTPISECGIIGVAVGMGAYGLRPVPEIQFADYIYPGLDQLVSEAARLRYRSAGEFTAP 127 Query: 128 LTMRMPCGGGIYGGQTHSQSIEAVFTQVCGLRTVMPSNPYDAKGLLIASIENDDPVIFLE 187 +T+R P GGGI+GGQTHSQS EA+FT V GL+TV+PS P+DAKGLLIA+IE++DPVIF E Sbjct: 128 ITVRSPFGGGIFGGQTHSQSPEALFTHVAGLKTVIPSTPHDAKGLLIAAIEDNDPVIFFE 187 Query: 188 PKRLYNGPFDGHHDRPVTPWSKHPQAQVPDGYYTVPLDVAAIVRPGSAVTVLTYGTTVYV 247 PKR+YNGPF+G++DRPV PW++H VP+GYY +PL A +VR G A+TVL YGT V+V Sbjct: 188 PKRIYNGPFNGYYDRPVEPWARHAGGAVPEGYYRIPLGKARVVRGGEAMTVLAYGTMVHV 247 Query: 248 SQVAAEETGIDAEVIDLRSLWPLDLETIVKSVKKTGRCVVVHEATRTCGFGAELVSLVQE 307 ++ E G+DAE+IDLR+L PLD+ETI SV+KTG+C++VHEATRT GFGAEL +LVQE Sbjct: 248 AEAVLAEKGVDAEIIDLRTLVPLDIETIKASVEKTGKCLIVHEATRTGGFGAELSALVQE 307 Query: 308 HCFHHLEAPIERVTGWDTPYPHAQEWAYFPGPSRVGAALKRVME 351 CF+ LEAPIERVTG+DTPYPH+ EWAYFPGP R+G A+ R+++ Sbjct: 308 RCFYSLEAPIERVTGFDTPYPHSLEWAYFPGPVRIGEAVDRLLK 351 Lambda K H 0.320 0.136 0.414 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: 467 Number of extensions: 13 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: 352 Length of database: 352 Length adjustment: 29 Effective length of query: 323 Effective length of database: 323 Effective search space: 104329 Effective search space used: 104329 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