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 CA265_RS02820 CA265_RS02820 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Pedo557:CA265_RS02820 Length = 384 Score = 372 bits (954), Expect = e-107 Identities = 187/370 (50%), Positives = 261/370 (70%) Query: 9 QMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGY 68 Q +K + FAE ++P E DE + FP E +++ + G+MG+ P+EYGG G Y Sbjct: 14 QSVKAMVRDFAEKNIRPHIMEWDEAQHFPVELFKQLGELGLMGVLVPEEYGGSGLGYQEY 73 Query: 69 IMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPN 128 + + E++RVCG+ G+ L+AH SL + I + N EQKQ++L LA+ E +GA+GLTE N Sbjct: 74 VDVIVEVARVCGSIGLSLAAHNSLCTGHILAFANPEQKQRWLPKLATAEWIGAWGLTEAN 133 Query: 129 AGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKG 188 G+DA TTAV DGD+YI+NG+K +IT+ +GDI VVM T + +KGISA +VE+G Sbjct: 134 TGSDALRMMTTAVEDGDDYIINGAKNWITHGKSGDIAVVMVRTGEQGSSKGISAIVVERG 193 Query: 189 TPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQ 248 TPGF+ G KE K+G+R S T+E+IF++CR+PK NLLG G+GFK AM LDGGRI IAA Sbjct: 194 TPGFTAGKKENKLGMRASETTEMIFDNCRVPKANLLGNVGEGFKQAMKVLDGGRISIAAL 253 Query: 249 ALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLG 308 ALG+A+GA D V Y K+R QFG+P+S FQ F+LADM +++AA L+ QAA K+ Sbjct: 254 ALGIAKGAFDAAVAYSKQRQQFGQPISSFQAISFKLADMATEIEAAELLIRQAADLKNRH 313 Query: 309 KPYGVEAAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQ 368 P E+AMAK FA+E ++ V T AVQ+ GGYGYT+D+PVE+ RD+K+ I EGTSE+Q Sbjct: 314 LPMTKESAMAKYFASEVSVRVATDAVQIFGGYGYTKDFPVEKFYRDSKLCTIGEGTSEIQ 373 Query: 369 RMVISGKLLK 378 ++VI+ ++L+ Sbjct: 374 KIVIAREVLQ 383 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: 362 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: 378 Length of database: 384 Length adjustment: 30 Effective length of query: 348 Effective length of database: 354 Effective search space: 123192 Effective search space used: 123192 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 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