Align Putative branched-chain alpha keto acid dehydrogenase E1 subunit beta (characterized, see rationale)
to candidate SMc03202 SMc03202 2-oxoisovalerate dehydrogenase subunit beta
Query= uniprot:G1UHX5 (328 letters) >FitnessBrowser__Smeli:SMc03202 Length = 337 Score = 295 bits (755), Expect = 1e-84 Identities = 163/336 (48%), Positives = 212/336 (63%), Gaps = 21/336 (6%) Query: 1 MSEITMAKALNTALRDALRDDPRTILFGEDIGALGGVFRITDGLAAEFGDERCFDTPLAE 60 M+ +TM +A+ +A+ ++ D ++FGED+G GGVFR T GL A++G RCFDTP++E Sbjct: 1 MARMTMIEAVRSAMDVSMARDDNVVVFGEDVGYFGGVFRCTQGLQAKYGKTRCFDTPISE 60 Query: 61 SAILGTAVGMAMYGYRPVVEMQFDAFAYPAFEQLVSHVAKLRNRTRGAIGLPLTIRIPYG 120 S I+GTA+GMA YG +P VE+QF + YPA++QL A++R R+ G P+ +R+P G Sbjct: 61 SGIVGTAIGMAAYGLKPCVEIQFADYMYPAYDQLTQEAARIRYRSNGDFTCPIVVRMPTG 120 Query: 121 GGIGGVEHHSDSSEIYYMATPGLTVVTPATAADAYSLLRRSIASPDPVVFLEPKRLY--- 177 GGI G + HS S E + GL VV P+ DA LL +I PDPV+FLEPKRLY Sbjct: 121 GGIFGGQTHSQSPEALFTHVCGLKVVVPSNPYDAKGLLISAIEDPDPVMFLEPKRLYNGP 180 Query: 178 -----------WRKEALGLPVD---TGPLGSAVIRRHGTHATLIAYGPAVTTALEAAEAA 223 W K LG D T P+G A IRR G+ T+IAYG V AL AAE Sbjct: 181 FDGHHERPVTAWSKHELGDVPDGHYTIPIGKAEIRRKGSGVTVIAYGTMVHVALAAAE-- 238 Query: 224 AEHGWDLEVIDLRTLMPLDDATVCASVRRTGRAVVVHEAHGFAGPGAEIAARITERCFYH 283 E G D EVIDLR+L+PLD T+ S ++TGR VVVHEA +G GAE+AA + E CFYH Sbjct: 239 -ETGIDAEVIDLRSLLPLDLETIVQSAKKTGRCVVVHEATLTSGFGAELAALVQEHCFYH 297 Query: 284 LEAPVRRVTGFDVPYPPPLLERHYLPGVDRILDAVA 319 LE+PV R+TG+D PY P E Y PG R+ A+A Sbjct: 298 LESPVVRLTGWDTPY-PHAQEWDYFPGPARVGRALA 332 Lambda K H 0.322 0.138 0.418 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: 352 Number of extensions: 15 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: 328 Length of database: 337 Length adjustment: 28 Effective length of query: 300 Effective length of database: 309 Effective search space: 92700 Effective search space used: 92700 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 (21.9 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