Align 2-oxoisovalerate dehydrogenase subunit beta; EC 1.2.4.4 (characterized)
to candidate WP_041379667.1 SWIT_RS10825 alpha-ketoacid dehydrogenase subunit beta
Query= CharProtDB::CH_121283 (339 letters) >NCBI__GCF_000016765.1:WP_041379667.1 Length = 334 Score = 518 bits (1333), Expect = e-151 Identities = 242/333 (72%), Positives = 284/333 (85%) Query: 6 MTMIQALRSAMDVMLERDDNVVVYGQDVGYFGGVFRCTEGLQTKYGKSRVFDAPISESGI 65 M MIQA+ SA+DV + RDD +VV G+DVGYFGGVF+ TEGLQ +YGK+RVFD PISE GI Sbjct: 1 MNMIQAINSAIDVAMGRDDRIVVLGEDVGYFGGVFKATEGLQKRYGKTRVFDTPISECGI 60 Query: 66 VGTAVGMGAYGLRPVVEIQFADYFYPASDQIVSEMARLRYRSAGEFIAPLTLRMPCGGGI 125 +G AVGM YGLRPV EIQFADY YPA DQ+VSE ARLRYRSAGE+ AP+T+R P GGGI Sbjct: 61 IGVAVGMATYGLRPVPEIQFADYIYPALDQLVSEAARLRYRSAGEYTAPITVRTPFGGGI 120 Query: 126 YGGQTHSQSPEAMFTQVCGLRTVMPSNPYDAKGLLIASIECDDPVIFLEPKRLYNGPFDG 185 +GGQTHSQSPE +FT V GL+TV+PSNPYDAKGLLIA+IE +DPVIF EPKR+YNGPFDG Sbjct: 121 FGGQTHSQSPEGIFTHVAGLKTVIPSNPYDAKGLLIAAIEDNDPVIFFEPKRIYNGPFDG 180 Query: 186 HHDRPVTPWSKHPHSAVPDGYYTVPLDKAAITRPGNDVSVLTYGTTVYVAQVAAEESGVD 245 H+DRPV PWSK SAVP+GYYTV L KA + R GNDV+VL YGT V+VA EE+G+D Sbjct: 181 HYDRPVQPWSKFAESAVPEGYYTVQLGKARVVREGNDVTVLAYGTMVHVAHSVIEETGID 240 Query: 246 AEVIDLRSLWPLDLDTIVESVKKTGRCVVVHEATRTCGFGAELVSLVQEHCFHHLEAPIE 305 AE+IDLR+L PLD++T+VESV+KTGRC+VVHEAT+T GFGAEL +LVQEHCFH LEAP++ Sbjct: 241 AELIDLRTLVPLDIETVVESVRKTGRCMVVHEATKTSGFGAELSALVQEHCFHWLEAPVQ 300 Query: 306 RVTGWDTPYPHAQEWAYFPGPSRVGAALKKVME 338 RVTGWDTPYPH+ EWAYFPGP R+ A K+VM+ Sbjct: 301 RVTGWDTPYPHSLEWAYFPGPVRLTEAFKRVMQ 333 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: 450 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: 339 Length of database: 334 Length adjustment: 28 Effective length of query: 311 Effective length of database: 306 Effective search space: 95166 Effective search space used: 95166 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