Align branched-chain-2-oxoacid decarboxylase (subunit 2/2) (EC 4.1.1.72) (characterized)
to candidate WP_013074671.1 BTUS_RS03120 alpha-ketoacid dehydrogenase subunit beta
Query= BRENDA::Q9HIA4 (319 letters) >NCBI__GCF_000092905.1:WP_013074671.1 Length = 326 Score = 354 bits (908), Expect = e-102 Identities = 176/323 (54%), Positives = 238/323 (73%), Gaps = 5/323 (1%) Query: 1 MNMVQALNSAMDLKMSEDDSVIILGEDVGRDGGVFRVTDGLQAKYGPQRVIDTPLSELGI 60 M M+QA++ AM + + DD V++LGEDVG++GGVFR T+GLQA +GP RV+DTPL+E I Sbjct: 4 MTMIQAIHEAMKMALESDDRVMVLGEDVGKNGGVFRATEGLQAHFGPDRVVDTPLAESAI 63 Query: 61 VGMAIGMAVNGLKPIPEIQFQDFIYTSMDQIINQMAKIRYRSGGDYTVPLVLRTPVGGGI 120 VG A+G+AV G++PI EIQF FIY +MDQI Q A+IR+RSGG Y+ P+V+R P GGG+ Sbjct: 64 VGAAVGLAVAGMRPIAEIQFLGFIYEAMDQIAAQAARIRFRSGGQYSAPIVIRAPFGGGV 123 Query: 121 KGGLYHSQSGEAYFAHTAGLTVVSPSNPYDAKGLLISAIESPDPVIFLEPKRLYRAQKVE 180 + HS S EA F HT GL VV PSNP DAKGLL++A+ PDPV++LEP +LYRA + E Sbjct: 124 RTPELHSDSLEALFLHTPGLKVVIPSNPRDAKGLLLAAVRDPDPVLYLEPLKLYRAFRGE 183 Query: 181 VPDEKYTIPLRKANVLKQGNDVTIVTYGSMVPTVMSVASKSK----YDVEVIDLRTIAPM 236 VP+E Y +P+ +A V+ G DVT++ +G VP + A ++ Y EVIDLRTIAPM Sbjct: 184 VPEEWYEVPIGRAQVVIPGQDVTVIAWGPTVPVAVQAARSAQEAWGYSCEVIDLRTIAPM 243 Query: 237 DRDTIISSVKKTGRVVIVHEAPRTLGVGAEISAMISERAIEYLYAPIVRVTGPDTPF-PY 295 D +T+++SV+KTGRVV+VHEA R+ GVGAE++A +SE A L AP+VRV G DTP+ P Sbjct: 244 DTETLVASVEKTGRVVVVHEAVRSGGVGAEVAARLSESAFLSLAAPMVRVAGYDTPYPPP 303 Query: 296 RLEEYYLPNEGRINAALDRVMSF 318 +E+ +LP+ R+ A+ RV +F Sbjct: 304 AIEDAWLPSVDRVVEAIHRVAAF 326 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: 351 Number of extensions: 12 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: 326 Length adjustment: 28 Effective length of query: 291 Effective length of database: 298 Effective search space: 86718 Effective search space used: 86718 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