Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate Pf1N1B4_1019 Branched-chain alpha-keto acid dehydrogenase, E1 component, beta subunit (EC 1.2.4.4)
Query= BRENDA::Q9HIA4 (319 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_1019 Length = 329 Score = 297 bits (761), Expect = 2e-85 Identities = 156/320 (48%), Positives = 220/320 (68%), Gaps = 4/320 (1%) Query: 1 MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60 + +++A+N A+ MSED++VI+LGEDVG +GGVFR T GL+ +G +RVID+PL+E + Sbjct: 6 VTLLEAVNLALHRAMSEDENVIVLGEDVGVNGGVFRATLGLRDTFGFKRVIDSPLAETML 65 Query: 61 VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120 G+ +GMA GLKP+ EIQF FIY +M+ +++ +++R R+ G T P+V+R+P+G GI Sbjct: 66 GGLVVGMAAQGLKPVVEIQFMGFIYATMEHLVSHASRMRNRTRGRITCPMVMRSPMGAGI 125 Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQKVE 180 + +HS+S EA FAH GL VV PS+P A GLL++AI+ PDPVIFLEP RLYR Sbjct: 126 RAPEHHSESTEALFAHIPGLRVVIPSSPARAYGLLLAAIDDPDPVIFLEPTRLYRMNPQP 185 Query: 181 VPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASK---SKYDVEVIDLRTIAPMD 237 + D+ +PL L++G+D+T++++G+ V + A+K EVID+ +I P+D Sbjct: 186 LLDDGKRLPLDSCFTLREGSDITLISWGASVMETLQAATKLAEQGVSAEVIDVASIKPLD 245 Query: 238 RDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTPFP-YR 296 DT+ +SV+KTGR VIVHEAPR+ GVGAEI+A + ER L API RVT PD P P YR Sbjct: 246 LDTMEASVRKTGRCVIVHEAPRSCGVGAEIAASLYERVFLELQAPIQRVTAPDIPPPLYR 305 Query: 297 LEEYYLPNEGRINAALDRVM 316 LE Y+P I A + VM Sbjct: 306 LESLYMPGIEDILHACNTVM 325 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: 305 Number of extensions: 15 Number of successful extensions: 2 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: 329 Length adjustment: 28 Effective length of query: 291 Effective length of database: 301 Effective search space: 87591 Effective search space used: 87591 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