Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_011778671.1 MVAN_RS07115 pyruvate dehydrogenase (acetyl-transferring) E1 component subunit alpha
Query= BRENDA::Q72GU1 (367 letters) >NCBI__GCF_000015305.1:WP_011778671.1 Length = 323 Score = 159 bits (403), Expect = 8e-44 Identities = 99/303 (32%), Positives = 144/303 (47%), Gaps = 3/303 (0%) Query: 33 LEGEKLRRLYRDMLAARMLDERYTILIRTGKT-SFIAPAAGHEAAQVAIAHAIRPGFDWV 91 ++ + R L DM+ R ++E+ L K F+ G EA A+ P D V Sbjct: 1 MDSGQARDLLTDMIRVRRMEEKCAELYSESKIRGFLHLYVGEEAVAAGSLRALGPD-DAV 59 Query: 92 FPYYRDHGLALALGIPLKELFGQMLATKADPNKGRQMPEHPGSKALNFFTVASPIASHVP 151 YR+H AL G+P+ + +M ++GR H F+ + ++ +P Sbjct: 60 VATYREHAHALLRGVPMTSIMAEMFGKVQGCSRGRGGSMHLFDADRRFYGGNAIVSGGLP 119 Query: 152 PAAGAAISMKLLRTGQVAVCTFGDGATSEGDWYAGINFAAVQGAPAVFVCENNFYAISVD 211 AAG A++ +V C FG+GA +EG ++ +N A + P +F CENN YA+ Sbjct: 120 LAAGLALADAHQGRNRVTACYFGEGAVAEGAFHESLNMAVLWRLPVLFCCENNLYAMGTA 179 Query: 212 YRHQTHSPTIADKAHAFGIPGYLVDGMDVLASYYVVKEAVERARRGEGPSLVELRVYRYG 271 R + + KA A+ +P VDGMDV A + +EAVE RRG GP VE R YR+ Sbjct: 180 LRRELSQTDLTVKAAAYNVPTLAVDGMDVAACQFAAQEAVEHIRRGGGPFFVEFRTYRFR 239 Query: 272 PHSSADDDSRYRPKEEVAFWRKKDPIPRFRRFLEARGLWNEEWEEDVREEIRAELERGLK 331 HS D + YR K EV WR++DPI F GL E + E + EL + Sbjct: 240 AHSMFDPE-LYRDKAEVEQWRQRDPIAMFTDRCTGEGLLAPEDVAAIEESVGVELSDAVA 298 Query: 332 EAE 334 AE Sbjct: 299 YAE 301 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: 304 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: 367 Length of database: 323 Length adjustment: 29 Effective length of query: 338 Effective length of database: 294 Effective search space: 99372 Effective search space used: 99372 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