Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate WP_011939741.1 GURA_RS14755 alpha-ketoacid dehydrogenase subunit beta
Query= BRENDA::Q9HIA4 (319 letters) >NCBI__GCF_000016745.1:WP_011939741.1 Length = 320 Score = 348 bits (892), Expect = e-100 Identities = 175/319 (54%), Positives = 231/319 (72%), Gaps = 3/319 (0%) Query: 1 MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60 +NMVQA+N A++ +M DD V++LGEDVGRDGGVFR+T+GL ++G +R+IDTPLSE I Sbjct: 4 LNMVQAINLALNEEMERDDRVVLLGEDVGRDGGVFRITEGLLERFGSERLIDTPLSESAI 63 Query: 61 VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120 VG AIGMAV GL+PI EIQF F+Y + DQ+ A++R RS YT PLV+RTP GGGI Sbjct: 64 VGAAIGMAVYGLRPIAEIQFMGFLYAAFDQLFTHAARLRSRSRSRYTCPLVVRTPYGGGI 123 Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQKVE 180 K H +S EA+F H G+ VV PS PY AKGLL +AI PDPV+FLEP RLYR + E Sbjct: 124 KAPEMHEESTEAFFCHMPGVKVVVPSGPYTAKGLLTAAIRDPDPVLFLEPTRLYRLIREE 183 Query: 181 VPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASKSKYDVEVIDLRTIAPMDRDT 240 VP Y +PL +A V+++G+DVT++ +GSM+ V+ +Y EVIDL T+ P D +T Sbjct: 184 VPAGDYIVPLGRAQVVREGDDVTLIAWGSMLEWVLKAV--GEYSAEVIDLLTLNPFDAET 241 Query: 241 IISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTPFPY-RLEE 299 +++SV+KTGRVVIVHEA ++ G GAEI+A I+E AI +L PI+RVT PD P +L + Sbjct: 242 VLASVRKTGRVVIVHEAVKSCGFGAEIAATIAEEAILHLRGPILRVTAPDVTVPLAKLLD 301 Query: 300 YYLPNEGRINAALDRVMSF 318 +YLP+ RI AALD V+ + Sbjct: 302 HYLPSAERIRAALDEVLQY 320 Lambda K H 0.318 0.137 0.388 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: 331 Number of extensions: 13 Number of successful extensions: 3 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: 319 Length of database: 320 Length adjustment: 28 Effective length of query: 291 Effective length of database: 292 Effective search space: 84972 Effective search space used: 84972 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 48 (23.1 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