Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate GFF2308 PS417_11770 pyruvate dehydrogenase
Query= BRENDA::Q9HIA4 (319 letters) >FitnessBrowser__WCS417:GFF2308 Length = 339 Score = 281 bits (719), Expect = 2e-80 Identities = 149/330 (45%), Positives = 210/330 (63%), Gaps = 17/330 (5%) Query: 5 QALNSAMDLKMSEDDSVIILGEDVGRD----------GGVFRVTDGLQAKYGPQRVIDTP 54 QA+N A+ +M D SV I+G+DV GGV VT GL ++ P+RV+D P Sbjct: 9 QAINEALAQEMRRDQSVFIIGQDVSGGTGSPGEQDAWGGVLGVTKGLYPEF-PERVLDAP 67 Query: 55 LSELGIVGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRT 114 LSE+G VGMA+G A G++P+ E+ F DFI +DQ++NQ AK RY GG T PLV+R Sbjct: 68 LSEVGYVGMAVGAATRGMRPVCELMFVDFIGCCLDQLLNQAAKFRYMFGGKTTTPLVIRA 127 Query: 115 PVGGGIKGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLY 174 G G++ HSQ + + H GL VV P+ PYDAKG+LI AI DPVIFLE K LY Sbjct: 128 MYGAGLRAAAQHSQMLTSMWTHIPGLKVVCPATPYDAKGMLIQAIRDNDPVIFLEHKMLY 187 Query: 175 RAQKVEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVA---SKSKYDVEVIDLR 231 Q EVP+E YT+P +AN +++G DVT+VTYG MV + A ++ D EV+DLR Sbjct: 188 SLQG-EVPEELYTVPFGEANFVREGKDVTLVTYGRMVHIALEAAAQLARQGIDCEVLDLR 246 Query: 232 TIAPMDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDT 291 T +P+D+D+I+ SV+KTGR+V++ E+ + +ISA+++++ +L API VT P T Sbjct: 247 TTSPLDQDSILESVEKTGRLVVIDESNPRCSMATDISALVAQQGFSFLRAPIQMVTAPHT 306 Query: 292 PFPY--RLEEYYLPNEGRINAALDRVMSFR 319 P P+ LE+ Y+PN +I AA+ ++ R Sbjct: 307 PVPFSDALEDLYIPNAAKIEAAVLKIADKR 336 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: 294 Number of extensions: 11 Number of successful extensions: 5 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: 339 Length adjustment: 28 Effective length of query: 291 Effective length of database: 311 Effective search space: 90501 Effective search space used: 90501 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: 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