Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate CA265_RS19580 CA265_RS19580 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::Q72GU1 (367 letters) >FitnessBrowser__Pedo557:CA265_RS19580 Length = 331 Score = 164 bits (415), Expect = 3e-45 Identities = 100/314 (31%), Positives = 158/314 (50%), Gaps = 3/314 (0%) Query: 42 YRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWVFPYYRDHGL 100 + ML R +E+ L K F G EA A++ G D + YRDH Sbjct: 15 FESMLLMRKFEEKTGQLYGQQKIRGFCHLYIGQEAVVAGAISAMQKG-DSMITTYRDHAH 73 Query: 101 ALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVPPAAGAAISM 160 ALALG+ + +M +KG+ H SK NF+ + + +P AG A + Sbjct: 74 ALALGVSADSIMAEMYGKATGCSKGKGGSMHMFSKEHNFYGGHAIVGGQIPLGAGVAFAE 133 Query: 161 KLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVDYRHQTHSPT 220 K T V +C GDGA +G N A + P +FVCENN YA+ + T+ Sbjct: 134 KYKGTDNVNICYMGDGAVRQGALNETFNMAMLWKLPVIFVCENNGYAMGTSVQRTTNMTD 193 Query: 221 IADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYGPHSSADDDS 280 I F +P VDGMD +A + + EA++RAR+GEGP+ +E+R YRY HS + D + Sbjct: 194 IYKIGLGFDMPCAPVDGMDPVAVHNAMDEAIQRARKGEGPTFLEMRTYRYRGHSMS-DPA 252 Query: 281 RYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLKEAEEAGPVP 340 +YR KEE+ ++ KDP+ R + ++ W E+V +++A +++ +K AEE+ Sbjct: 253 KYRTKEELEDYKAKDPVEHARETILKEKYADQAWIEEVEAKVKAIVDQAVKFAEESPWPD 312 Query: 341 PEWMFADVFAEKPW 354 ++ DV+ ++ + Sbjct: 313 ASELYKDVYMQQDY 326 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: 329 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: 367 Length of database: 331 Length adjustment: 29 Effective length of query: 338 Effective length of database: 302 Effective search space: 102076 Effective search space used: 102076 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 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