Align 2-oxoisovalerate dehydrogenase subunit beta 2, mitochondrial; Branched-chain alpha-keto acid dehydrogenase E1 component beta chain; BCKDE1B; BCKDH E1-beta; Protein DARK INDUCIBLE 4; EC 1.2.4.4 (characterized)
to candidate WP_012277322.1 SHAL_RS11655 2-oxoisovalerate dehydrogenase subunit beta
Query= SwissProt::Q9LDY2 (358 letters) >NCBI__GCF_000019185.1:WP_012277322.1 Length = 325 Score = 431 bits (1107), Expect = e-125 Identities = 207/322 (64%), Positives = 256/322 (79%), Gaps = 1/322 (0%) Query: 38 MNLYSAINQALHIALETDPRSYVFGEDVG-FGGVFRCTTGLAERFGKSRVFNTPLCEQGI 96 MN+ AINQAL +E+D VFGEDVG FGGVFR T+GL E+FG+ R FNTPL EQGI Sbjct: 4 MNMLQAINQALSSEMESDETMTVFGEDVGHFGGVFRATSGLQEKFGRDRCFNTPLTEQGI 63 Query: 97 VGFGIGLAAMGNRVIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTIRAPYGAV 156 GF GLA+ G +AEIQFADYIFPA DQIVNE+AKFRYRSGN+F+ GGLT R PYG Sbjct: 64 AGFANGLASNGMTAVAEIQFADYIFPAIDQIVNESAKFRYRSGNEFDVGGLTFRTPYGGG 123 Query: 157 GHGGHYHSQSPEAFFCHVPGIKVVIPRSPREAKGLLLSSIRDPNPVVFFEPKWLYRQAVE 216 GGHYHSQSPEA+F PG+KVV+PR+P +AKGLL++SIRD NPV+FFEPK LYR +V Sbjct: 124 IAGGHYHSQSPEAYFTQTPGLKVVVPRNPEQAKGLLIASIRDKNPVIFFEPKRLYRASVG 183 Query: 217 DVPEDDYMIPLSEAEVMREGSDITLVGWGAQLTIMEQACLDAENEGISCELIDLKTLIPW 276 +VPE DY+I L +AEV+++GSDITL+GWGAQ+ ++E+A A +GISCE++DL+TL PW Sbjct: 184 EVPEGDYVIELGKAEVVKQGSDITLLGWGAQMEVLEKAAEMAAKKGISCEIVDLRTLSPW 243 Query: 277 DKEIVETSVRKTGRLLISHEAPVTGGFGAEIAATIVERCFLRLEAPVSRVCGLDTPFPLV 336 D + V SV+KTGRLLI+HEAP+TGGF EIAATI E CFL LE+P++RVCGLDTP+PL+ Sbjct: 244 DIDTVAASVKKTGRLLINHEAPLTGGFAGEIAATIQEECFLYLESPIARVCGLDTPYPLI 303 Query: 337 FEPFYMPTKNKILDAIRSTVNY 358 E YMP K +AI+++V + Sbjct: 304 HEKEYMPDALKTFEAIKASVKF 325 Lambda K H 0.322 0.140 0.426 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: 363 Number of extensions: 8 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: 358 Length of database: 325 Length adjustment: 29 Effective length of query: 329 Effective length of database: 296 Effective search space: 97384 Effective search space used: 97384 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 (21.9 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