Align 2-oxoisovalerate dehydrogenase subunit beta; EC 1.2.4.4 (characterized)
to candidate WP_011445624.1 SARO_RS09920 alpha-ketoacid dehydrogenase subunit beta
Query= CharProtDB::CH_121283 (339 letters) >NCBI__GCF_000013325.1:WP_011445624.1 Length = 351 Score = 509 bits (1310), Expect = e-149 Identities = 236/336 (70%), Positives = 285/336 (84%) Query: 3 TTTMTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPISE 62 T + MI+A+ A+D+M+ERD NVVV G+DVGYFGGVFR T GLQ KYGK+RVFD PISE Sbjct: 15 TRRLNMIEAINDALDIMMERDPNVVVMGEDVGYFGGVFRATAGLQKKYGKTRVFDTPISE 74 Query: 63 SGIVGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSEMARLRYRSAGEFIAPLTLRMPCG 122 GI+G AVGMGAYGLRPV EIQFADY YP DQ+VSE ARLRYRSAGEFIAP+T+R P G Sbjct: 75 CGIIGVAVGMGAYGLRPVPEIQFADYIYPGLDQLVSEAARLRYRSAGEFIAPMTVRSPFG 134 Query: 123 GGIYGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGP 182 GGI+GGQTHSQSPEA+FT V GL+TV+PS P+DAKGLLIA+IE +DPVIF EPKR+YNGP Sbjct: 135 GGIFGGQTHSQSPEALFTHVAGLKTVVPSTPHDAKGLLIAAIEDNDPVIFFEPKRIYNGP 194 Query: 183 FDGHHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAEES 242 F+G++D+PV PWSKH SAVP+GYY++PL KA + RPG +VL YGT V+VA E Sbjct: 195 FNGYYDKPVEPWSKHADSAVPEGYYSIPLGKARVVRPGQAFTVLAYGTMVHVAAAVCAEK 254 Query: 243 GVDAEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEA 302 GVDAE+IDLR+L PLD++T+ +SV+KTG+C++VHEATRT GFGAEL +LVQE CF+HLEA Sbjct: 255 GVDAEIIDLRTLVPLDIETVEKSVEKTGKCLIVHEATRTSGFGAELSALVQERCFYHLEA 314 Query: 303 PIERVTGWDTPYPHAQEWAYFPGPSRVGAALKKVME 338 PIERVTG+DTPYPH+ EWAYFPGP R+G A+ ++M+ Sbjct: 315 PIERVTGFDTPYPHSLEWAYFPGPVRIGEAVDRLMK 350 Lambda K H 0.320 0.137 0.424 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: 487 Number of extensions: 8 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: 339 Length of database: 351 Length adjustment: 29 Effective length of query: 310 Effective length of database: 322 Effective search space: 99820 Effective search space used: 99820 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