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 CCNA_01412 CCNA_01412 acyl-CoA dehydrogenase, short-chain specific
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Caulo:CCNA_01412 Length = 381 Score = 301 bits (770), Expect = 3e-86 Identities = 156/363 (42%), Positives = 235/363 (64%), Gaps = 3/363 (0%) Query: 17 SFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELS 76 +FAE ++ P + + DE + FP + + + A+ G GI ++ GG G + + E LS Sbjct: 20 AFAEGQLAPHSADWDENKHFPVDVLRQAAELGFAGIYVNEDVGGSGLSRLDASIIFEALS 79 Query: 77 RVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQ 136 L+ H ++ SW I ++G+++ +Q++L L + E + ++ LTEP +G+DA+ Sbjct: 80 YGDVPVAAYLTIH-NMASWMIDRFGSDDLRQRYLPRLTTMELIASYCLTEPGSGSDAAAM 138 Query: 137 QTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGV 196 +TTA LDGD Y+LNG K FI+ DIYVVMA T +G KG+SAF+VEKG G SFG Sbjct: 139 RTTAKLDGDHYVLNGGKAFISGGGVSDIYVVMARTG-GEGAKGVSAFVVEKGMEGLSFGA 197 Query: 197 KEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGA 256 E+KMG T+++ F++CR+P N +G+EG+GF+ AM LDGGR+ IA+ +LG AQ A Sbjct: 198 NERKMGWNAQPTAQVNFDNCRVPVANRIGQEGEGFRFAMMGLDGGRLNIASCSLGGAQFA 257 Query: 257 LDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVE-A 315 LD Y++ R QFGRPL FQ QF+LADM +++AAR +V +AA D P + Sbjct: 258 LDTAKAYLETRNQFGRPLKDFQALQFKLADMATELEAARLMVRRAAHALDSKHPEATKLC 317 Query: 316 AMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGK 375 AMAK FA + +V A+QLHGGYGY +DYP+ER++RD ++ +I EGT+E+ R++I+ + Sbjct: 318 AMAKRFATDAGFQVANDALQLHGGYGYLQDYPLERLVRDLRVHQILEGTNEIMRVIIARE 377 Query: 376 LLK 378 + + Sbjct: 378 MFR 380 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: 348 Number of extensions: 15 Number of successful extensions: 4 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 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