Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate WP_011951687.1 SWIT_RS04275 alpha-ketoacid dehydrogenase subunit beta
Query= BRENDA::Q9HIA4 (319 letters) >NCBI__GCF_000016765.1:WP_011951687.1 Length = 327 Score = 265 bits (677), Expect = 1e-75 Identities = 148/324 (45%), Positives = 208/324 (64%), Gaps = 10/324 (3%) Query: 1 MNMVQALNSAMDLKMSEDDSVIILGEDVG--RDGGVFRVTDGLQAKYGPQRVIDTPLSEL 58 M M+ A+N A+ M E+ +++LGEDV DGGVF T GL ++G RV TP+SE Sbjct: 7 MTMIDAINRALHDAMEENGKILLLGEDVADPEDGGVFGATRGLSTRFGEDRVKSTPISEQ 66 Query: 59 GIVGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGG 118 IVG AIG ++ G +P+ E+ +F+ +MD ++N AK+R+ SGG +VP+ +RT G Sbjct: 67 AIVGAAIGASLVGYRPVAEVMLMNFMTVAMDMLVNHAAKLRFMSGGQTSVPITVRTMTGS 126 Query: 119 GIKGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQK 178 G+ G HS EA+FAHTAG+ VV PS+ DA GLL SAI+ DPVIF+E +Y AQ Sbjct: 127 GLSLGGQHSDFVEAWFAHTAGMKVVIPSSANDAYGLLRSAIDDADPVIFVETLPIYWAQG 186 Query: 179 VEVPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVA---SKSKYDVEVIDLRTIAP 235 EV E+ IP+ KA V ++G+D+TI+ YG MV ++VA +K VEVIDLRT++P Sbjct: 187 -EVSFER--IPIGKARVCREGSDLTIIAYGQMVSHSLTVATELAKQGKSVEVIDLRTVSP 243 Query: 236 MDRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTPFPY 295 DR+T+++SV KTGR +IVHEA + GVGAEI+++I E L AP+ R+ P P+ Sbjct: 244 WDRETVLASVAKTGRALIVHEAVKEYGVGAEIASVIGEALFGRLVAPVQRLGAAYCPVPF 303 Query: 296 R--LEEYYLPNEGRINAALDRVMS 317 LE+ + PN I AA ++S Sbjct: 304 SKPLEQAFAPNAESIGAAAAALLS 327 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: 282 Number of extensions: 14 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: 327 Length adjustment: 28 Effective length of query: 291 Effective length of database: 299 Effective search space: 87009 Effective search space used: 87009 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