Align butanoyl-CoA dehydrogenase (NAD+, ferredoxin) (subunit 3/3) (EC 1.3.1.109); short-chain acyl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_012760746.1 RLEG_RS35160 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000023185.1:WP_012760746.1 Length = 381 Score = 302 bits (774), Expect = 9e-87 Identities = 157/367 (42%), Positives = 234/367 (63%) Query: 11 LKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIM 70 ++E FA + + PLA E+DE FP + +M G+ GI +E+GG G + +++ Sbjct: 13 IRETTARFAADHIAPLAVEIDESNTFPRQLWPEMGALGLHGITVEEEFGGAGLGYLDHVV 72 Query: 71 AVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAG 130 A+EE+SR + G+ AH++L I ++ + EQK+++L L SGE +G+ ++E AG Sbjct: 73 AMEEVSRASASVGLSYGAHSNLCVNQIRRWASPEQKRRYLPKLISGEHVGSLAMSEVGAG 132 Query: 131 TDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTP 190 +D + A GD Y+LNG+K +ITNA D+ VV A TD + G KGISA I+EKG P Sbjct: 133 SDVVSMRLRAEKKGDRYVLNGTKFWITNAPHADVLVVYAKTDPAAGPKGISALIIEKGLP 192 Query: 191 GFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQAL 250 GF K K+G+RGS T+EL+FEDC +P E L+G+EG+G KI MS LD R +A L Sbjct: 193 GFGVSKKLSKLGMRGSDTAELVFEDCAVPAEALMGREGEGVKILMSGLDYERAVLAGGPL 252 Query: 251 GLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKP 310 G+ Q LD + YV++R QFG+ + FQ Q ++ADM V + +AR VY A D G+ Sbjct: 253 GIMQACLDVVLPYVRDRKQFGKAIGDFQLMQGKIADMYVALNSARAYVYSVARACDAGRA 312 Query: 311 YGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRM 370 +AA A LFA+E A++V+ +A+Q GG GYT+++PVER +RDAK+ +I GT+E++R Sbjct: 313 TRTDAAAAILFASENAVKVSLEAIQALGGAGYTKEWPVERFLRDAKLYDIGAGTNEIRRY 372 Query: 371 VISGKLL 377 +I +L+ Sbjct: 373 LIGRELI 379 Lambda K H 0.315 0.133 0.373 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: 353 Number of extensions: 13 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: 378 Length of database: 381 Length adjustment: 30 Effective length of query: 348 Effective length of database: 351 Effective search space: 122148 Effective search space used: 122148 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (22.0 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Apr 09 2024. 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