Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate WP_052300733.1 BTUS_RS07880 alpha-ketoacid dehydrogenase subunit beta
Query= BRENDA::Q9HIA4 (319 letters) >NCBI__GCF_000092905.1:WP_052300733.1 Length = 323 Score = 348 bits (893), Expect = e-100 Identities = 173/322 (53%), Positives = 230/322 (71%), Gaps = 5/322 (1%) Query: 1 MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60 M ++QA+ + ++EDD V++ GEDVG++GGVFR TDGLQ +GP+RV DTPLSE GI Sbjct: 1 MTIIQAIQDGLYTALAEDDRVLVFGEDVGQNGGVFRATDGLQDAFGPRRVFDTPLSESGI 60 Query: 61 VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120 VG A+GMA GL+P+ EIQF FIY + +QII+ A++R R+ G ++ LV+R P GGGI Sbjct: 61 VGTAVGMAAAGLRPVVEIQFMGFIYPAFEQIISHAARVRTRTRGRHSASLVIRAPYGGGI 120 Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQKVE 180 + HS S EA+F H GL VV+PS PYDAKGLL++AI+ PDPV+FLEP RLYRA K E Sbjct: 121 RAPELHSDSSEAFFVHQPGLKVVAPSGPYDAKGLLLAAIDDPDPVVFLEPIRLYRAFKEE 180 Query: 181 VPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASKSK----YDVEVIDLRTIAPM 236 VP YT+P+ KA V+++G D+ I +G+MVP M A K+ + V+DLRT+ P+ Sbjct: 181 VPLGYYTVPIGKAKVVREGGDLAIFVWGAMVPRAMEAAEKAAREDGIETRVVDLRTLFPL 240 Query: 237 DRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTPFP-Y 295 D TI+ SV+KTGR +IVHEAPRT GVGAE++ +I ERA L AP+VRVTG D PFP + Sbjct: 241 DVATIVESVEKTGRAMIVHEAPRTAGVGAEVATLIQERAFYSLEAPVVRVTGLDVPFPLF 300 Query: 296 RLEEYYLPNEGRINAALDRVMS 317 LE+ YLP RI + + R ++ Sbjct: 301 SLEDLYLPGVARILSGIRRAVA 322 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: 334 Number of extensions: 14 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: 323 Length adjustment: 28 Effective length of query: 291 Effective length of database: 295 Effective search space: 85845 Effective search space used: 85845 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