Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_099018480.1 CCS90_RS05525 pyruvate dehydrogenase
Query= reanno::Smeli:SMc03202 (337 letters) >NCBI__GCF_002591915.1:WP_099018480.1 Length = 701 Score = 244 bits (623), Expect = 5e-69 Identities = 134/333 (40%), Positives = 196/333 (58%), Gaps = 17/333 (5%) Query: 3 RMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISESG 62 R+ M+ A+R +D ++ ++ ++VFGEDVG GGV T GLQ K+G+ + FDT +SE G Sbjct: 380 RINMVTAIRKTLDYELSHNNKMLVFGEDVGAKGGVHAVTLGLQEKHGEAQVFDTSLSEEG 439 Query: 63 IVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTGGG 122 I+G +IG+A GL P EIQF Y PA +QL E +R+R+N F P+VVRM G Sbjct: 440 IIGRSIGLALAGLLPVPEIQFRKYADPAEEQLN-ETGSMRWRTNNRFAAPMVVRMAGGYF 498 Query: 123 IFGGQTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGPFD 182 G HSQ E + H G +V +PSN DA GLL A+ + +P +F E +++ + Sbjct: 499 GCGDPWHSQCAEVKWVHAIGWQVAMPSNAEDAVGLLRYALRNNNPTIFFEHRKMLDH--- 555 Query: 183 GHHERPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEETGI 242 AWS+ P Y IP G+ G VTV+++G MVH+ A E+TGI Sbjct: 556 --------AWSRRPY---PGDQYIIPFGQGNKILSGDRVTVVSWGGMVHMCQTAIEQTGI 604 Query: 243 DAEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLESPV 302 A++IDLR+L P D ++QS KKTGRC++VHE +++GFGAE+AA++ + F++L++P+ Sbjct: 605 QADLIDLRTLRPWDKAMVLQSVKKTGRCLIVHEDNMSAGFGAEIAAILAKEAFFYLDAPI 664 Query: 303 VRLTGWDTPYPHAQEW--DYFPGPARVGRALAE 333 RL D PH + P P + + L E Sbjct: 665 ERLATADIGNPHDPKLMEHALPNPDSIAQRLME 697 Lambda K H 0.321 0.138 0.424 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: 592 Number of extensions: 28 Number of successful extensions: 3 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: 337 Length of database: 701 Length adjustment: 34 Effective length of query: 303 Effective length of database: 667 Effective search space: 202101 Effective search space used: 202101 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: 52 (24.6 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