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 201484 SO2340 alpha keto acid dehydrogenase complex, E1 component, beta subunit (NCBI ptt file)
Query= SwissProt::Q9LDY2 (358 letters) >FitnessBrowser__MR1:201484 Length = 325 Score = 437 bits (1124), Expect = e-127 Identities = 214/322 (66%), Positives = 254/322 (78%), Gaps = 1/322 (0%) Query: 38 MNLYSAINQALHIALETDPRSYVFGEDVG-FGGVFRCTTGLAERFGKSRVFNTPLCEQGI 96 MN+ A+N+AL IA++ D R VFGEDVG FGGVFR T+GL E+FG++R FNTPL EQGI Sbjct: 4 MNMLQAVNEALSIAMQADERMVVFGEDVGHFGGVFRATSGLQEKFGRARCFNTPLTEQGI 63 Query: 97 VGFGIGLAAMGNRVIAEIQFADYIFPAFDQIVNEAAKFRYRSGNQFNCGGLTIRAPYGAV 156 GF GLA+ G +AEIQFADYIFPAFDQIVNE+AKFRYRSGN+FN G L R PYG Sbjct: 64 AGFANGLASNGMTAVAEIQFADYIFPAFDQIVNESAKFRYRSGNEFNVGSLVFRTPYGGG 123 Query: 157 GHGGHYHSQSPEAFFCHVPGIKVVIPRSPREAKGLLLSSIRDPNPVVFFEPKWLYRQAVE 216 GGHYHSQSPEA+F PG+KVV+PR+P +AKGLLL+SIRD NPVVFFEPK LYR +V Sbjct: 124 IAGGHYHSQSPEAYFTQTPGLKVVVPRNPAQAKGLLLASIRDKNPVVFFEPKRLYRASVG 183 Query: 217 DVPEDDYMIPLSEAEVMREGSDITLVGWGAQLTIMEQACLDAENEGISCELIDLKTLIPW 276 DVP DY I L +AEV+REG DITLV WGAQ+ I+E+A A EGISCE+IDL+TL PW Sbjct: 184 DVPAGDYEIELGKAEVLREGKDITLVAWGAQMEIIEKAADMAAKEGISCEIIDLRTLAPW 243 Query: 277 DKEIVETSVRKTGRLLISHEAPVTGGFGAEIAATIVERCFLRLEAPVSRVCGLDTPFPLV 336 D V SV+KTGRLL++HEAP+TGGF EIAATI + CFL LE+P+SRVCGLDTP+PLV Sbjct: 244 DVNTVADSVKKTGRLLVNHEAPLTGGFAGEIAATIQQECFLYLESPISRVCGLDTPYPLV 303 Query: 337 FEPFYMPTKNKILDAIRSTVNY 358 E YMP K +AI+++VN+ Sbjct: 304 HEKEYMPDALKTFEAIKASVNF 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: 367 Number of extensions: 6 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 17 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