Align 3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) (EC 1.2.4.4) (characterized)
to candidate WP_011654333.1 RL_RS28920 alpha-ketoacid dehydrogenase subunit beta
Query= reanno::Smeli:SMc03202 (337 letters) >NCBI__GCF_000009265.1:WP_011654333.1 Length = 337 Score = 654 bits (1688), Expect = 0.0 Identities = 313/336 (93%), Positives = 325/336 (96%) Query: 1 MARMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISE 60 MARMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFR TQGLQAKYG+TRCFDTPISE Sbjct: 1 MARMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRSTQGLQAKYGRTRCFDTPISE 60 Query: 61 SGIVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTG 120 SGIVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTG Sbjct: 61 SGIVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTG 120 Query: 121 GGIFGGQTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGP 180 GGIFGGQTHSQSPEALFTHVCGLKV+VPSNPYDAKGLLI+AIEDPDPVMFLEPKRLYNGP Sbjct: 121 GGIFGGQTHSQSPEALFTHVCGLKVIVPSNPYDAKGLLIAAIEDPDPVMFLEPKRLYNGP 180 Query: 181 FDGHHERPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAEET 240 FDGHHERPVT WSKH+LG+VPDGHYTIPIGKAE+RR GS VTVIAYGTMVHVALAAAE+ Sbjct: 181 FDGHHERPVTPWSKHDLGEVPDGHYTIPIGKAEVRRAGSAVTVIAYGTMVHVALAAAEDA 240 Query: 241 GIDAEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYHLES 300 GIDAEVIDLRSLLPLDL+TIV+S KTGRCVVVHEATLTSGFGAE+ ALVQEHCFYHLE+ Sbjct: 241 GIDAEVIDLRSLLPLDLDTIVKSVSKTGRCVVVHEATLTSGFGAEVVALVQEHCFYHLEA 300 Query: 301 PVVRLTGWDTPYPHAQEWDYFPGPARVGRALAEAME 336 PVVR+ GWDTPYPHAQEWDYFPGP RVGRALAE ME Sbjct: 301 PVVRVAGWDTPYPHAQEWDYFPGPGRVGRALAEVME 336 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: 564 Number of extensions: 10 Number of successful extensions: 1 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: 337 Length adjustment: 28 Effective length of query: 309 Effective length of database: 309 Effective search space: 95481 Effective search space used: 95481 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