Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate AZOBR_RS26490 AZOBR_RS26490 pyruvate dehydrogenase
Query= BRENDA::Q9HIA4 (319 letters) >FitnessBrowser__azobra:AZOBR_RS26490 Length = 324 Score = 258 bits (659), Expect = 1e-73 Identities = 145/325 (44%), Positives = 200/325 (61%), Gaps = 13/325 (4%) Query: 1 MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60 + V A+ A++ M+ D +V+++GEDV GG F+ T GL +GP+RV DTP+SE + Sbjct: 5 LRYVNAVAQALNDAMAADPAVMLMGEDVAAAGGPFKATRGLLDAHGPERVRDTPISEASL 64 Query: 61 VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120 VG A+G A+ G+KP+ EI F DF+ +MD ++NQ AK R+ GG +VP+VLRTP GGG+ Sbjct: 65 VGAAVGAALTGMKPVVEIMFMDFVTLAMDAVVNQAAKARFMFGGQCSVPMVLRTPHGGGL 124 Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQ--- 177 G HSQ EA+FAH GL VV P+ DA LL +AIE+PDPV+ +E K LY Q Sbjct: 125 NAGPQHSQCLEAWFAHIPGLRVVCPATVADAYSLLRAAIEAPDPVVVVENKALYALQGDI 184 Query: 178 KVEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASK---SKYDVEVIDLRTIA 234 V P E + KA + + G D TIVTYG+ + + A + + E++DLR I Sbjct: 185 DVNAPRE-----VGKARIDRAGRDATIVTYGATLYAARAAADRLATEGIEAEIVDLRWIQ 239 Query: 235 PMDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTP-- 292 P D + + +SV KT RVVI HEA + GVGAEI+A I+ A + L AP++RV P P Sbjct: 240 PWDEEAVFASVAKTHRVVIAHEAVQAFGVGAEIAARIAADAFDDLDAPVLRVGAPFMPIA 299 Query: 293 FPYRLEEYYLPNEGRINAALDRVMS 317 F LE YLP+ RI AA+ ++ Sbjct: 300 FAKTLEAAYLPDADRIVAAVKSTLA 324 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: 256 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: 324 Length adjustment: 28 Effective length of query: 291 Effective length of database: 296 Effective search space: 86136 Effective search space used: 86136 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 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