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_043745120.1 AMB_RS18150 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000009985.1:WP_043745120.1 Length = 378 Score = 312 bits (800), Expect = 9e-90 Identities = 162/360 (45%), Positives = 230/360 (63%), Gaps = 3/360 (0%) Query: 18 FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77 FA E+ P A DEE FP +T+ K A+ G GI ++ GG + + EEL+ Sbjct: 19 FAVGEMAPHAAHWDEEGIFPEDTLRKAAELGFAGIYVGEDVGGSALSRLDAALIFEELAA 78 Query: 78 VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137 C +T +S H ++ +W I +G++EQ+++FL L S K ++ LTEPNAG+DA+ + Sbjct: 79 ACPSTAAYISIH-NMAAWMIDSFGDQEQRRRFLPDLCSMRKFASYCLTEPNAGSDAASLR 137 Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGVK 197 T A DGD Y+LNG+K FI+ D+YVVM T + G KGIS +VE GTPG SFG + Sbjct: 138 TKAERDGDHYVLNGTKAFISGGGRSDVYVVMVRTG-APGPKGISCLVVEAGTPGLSFGKQ 196 Query: 198 EKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGAL 257 EKK+G + T+ +IFEDCR+P N +G EG GFKIAM LDGGRI I A +LG A+ L Sbjct: 197 EKKLGWKTQPTASVIFEDCRVPVANRIGAEGDGFKIAMKGLDGGRINIGACSLGGARACL 256 Query: 258 DETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYG-VEAA 316 + ++Y +R QFG+ +S FQ TQF+LADM +++AAR ++++AA + D P V A Sbjct: 257 EHAIEYTGQRQQFGQAISAFQATQFKLADMATELEAARLMIHRAAHSLDSKSPQATVHCA 316 Query: 317 MAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGKL 376 MAK A + VT A+QLHGGYGY ++YP+ER RD ++ +I EG++E+ R++I L Sbjct: 317 MAKRMATDVGFAVTDAALQLHGGYGYIKEYPIERYFRDLRVHQILEGSNEIMRVIIGRAL 376 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: 326 Number of extensions: 17 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: 378 Length adjustment: 30 Effective length of query: 348 Effective length of database: 348 Effective search space: 121104 Effective search space used: 121104 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