Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate YP_004139480.1 Mesci_0257 pyruvate dehydrogenase (acetyl-transferring)
Query= BRENDA::Q9HIA4 (319 letters) >NCBI__GCF_000185905.1:YP_004139480.1 Length = 724 Score = 182 bits (463), Expect = 2e-50 Identities = 103/278 (37%), Positives = 161/278 (57%), Gaps = 5/278 (1%) Query: 15 MSEDDSVIILGEDVGR-DGGVFRVTDGLQAKYGPQRVIDTPLSELGIVGMAIGMAVNGLK 73 M +D +II+GEDV R GGV T G ++ P+RV+ P++E G VG+A+G A+ GL+ Sbjct: 414 MEQDPRIIIMGEDVHRLRGGVSGATKGALERW-PERVLAMPIAENGFVGVALGAALCGLR 472 Query: 74 PIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGIKGGLYHSQSGEAY 133 PI EI F DF + DQ+ N ++K+R+ GG + VP+V+R V G HS Sbjct: 473 PIVEIMFGDFCLVAADQLFNAVSKVRHMFGGGFPVPIVIRVRVSPHTGYGSQHSGDPSGL 532 Query: 134 FAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQ-KVEVPDEKYTIPLRK 192 FA G +V+P+ P+D GL+ SA++ DPV+ +E L+ ++ V D Y + L K Sbjct: 533 FALFPGWRIVAPTTPFDYIGLMNSALKCDDPVVVIEHVELFPSEGPVPADDRDYCVRLGK 592 Query: 193 ANVLKQGNDVTIVTYGSMVPTVMSVASKSKYDVEVIDLRTIAP--MDRDTIISSVKKTGR 250 A ++ G+ T++T SMV V ++ D E+IDLR++ P +D + +S++KT R Sbjct: 593 AKTVRPGSACTLLTSASMVAVAKQVVEETGVDAEIIDLRSLDPTGLDWPMVEASIRKTNR 652 Query: 251 VVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTG 288 V +V + R L +G ++ I +R +YL I+ VTG Sbjct: 653 VAVVEQVQRGLSLGGRLTQEIQDRVFDYLDHEILHVTG 690 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: 532 Number of extensions: 26 Number of successful extensions: 4 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: 724 Length adjustment: 34 Effective length of query: 285 Effective length of database: 690 Effective search space: 196650 Effective search space used: 196650 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: 51 (24.3 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