Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_089303319.1 CHB84_RS20615 thiamine pyrophosphate-dependent dehydrogenase E1 component subunit alpha
Query= BRENDA::Q72GU1 (367 letters) >NCBI__GCF_900188115.1:WP_089303319.1 Length = 341 Score = 155 bits (391), Expect = 2e-42 Identities = 99/316 (31%), Positives = 160/316 (50%), Gaps = 3/316 (0%) Query: 38 LRRLYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWVFPYYR 96 L ++YR M E ++ G+ S P G E A A+ A+ D + YR Sbjct: 22 LTQMYRTMRLITSTGEHAVGEVKAGRLKSAFYPVRGLEGACAAMGVAMLTE-DQLVSNYR 80 Query: 97 DHGLALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAAGA 156 G ALA G L+ + ++ +KG+ H +++ F T + S +P AAG Sbjct: 81 SLGDALAKGASLRSIVAEIYGRADGTSKGKGGAMHIHDQSVGFVTSTGVVGSGIPIAAGL 140 Query: 157 AISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRHQT 216 ++ +L + V FGDG TS G ++ +N A++ P VFVC+NN +A Sbjct: 141 GLAAQLDGAARAVVSVFGDGTTSIGAYHESMNLASLWNLPMVFVCQNNQWAEHTPIAEYA 200 Query: 217 HSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHSSA 276 S +A +A A+ +P VDG D +A+ ++ A+ RAR G GP+ VE++ YR HS + Sbjct: 201 ASTDLAARAEAYAMPSLAVDGFDPIATAQQLRTALGRARNGGGPTFVEIKTYRLTGHSGS 260 Query: 277 DDDSRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEAEEA 336 D S Y P +E+A ++DP P FRR+L G+ +E+ +V +E+ AE+E A+++ Sbjct: 261 SDYS-YMPTDELAAATERDPAPTFRRWLLDEGVLDEQALAEVDKEVIAEVEDAFAFAQDS 319 Query: 337 GPVPPEWMFADVFAEK 352 + DVFA++ Sbjct: 320 PQPAASERYTDVFADE 335 Lambda K H 0.320 0.138 0.426 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: 278 Number of extensions: 8 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: 367 Length of database: 341 Length adjustment: 29 Effective length of query: 338 Effective length of database: 312 Effective search space: 105456 Effective search space used: 105456 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 49 (23.5 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