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_011384980.1 AMB_RS13080 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000009985.1:WP_011384980.1 Length = 383 Score = 303 bits (776), Expect = 5e-87 Identities = 161/363 (44%), Positives = 226/363 (62%), Gaps = 2/363 (0%) Query: 18 FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77 F + P + E++ P E + +M G+ G+ P+EYGG G ++ E+ + Sbjct: 18 FVRERLVPNEERIAEDDALPAEIIAEMKDLGLFGLSIPEEYGGLGLTMEEEVLCAFEIGQ 77 Query: 78 VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137 I + +GS I G EEQKQK+L LA+GE + +F LTEPNAG+DA+ + Sbjct: 78 TSPAFRSIFGTNNGIGSQGIIIDGTEEQKQKYLPRLATGELIASFALTEPNAGSDAASLR 137 Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTD-KSKGNKGISAFIVEKGTPGFSFGV 196 TTA DGD YI+NG+K FITNA I+ +MA TD +KG GISAFIVE +PG S G Sbjct: 138 TTARKDGDHYIVNGTKRFITNAPEASIFTLMARTDPNNKGAGGISAFIVEADSPGLSLGK 197 Query: 197 KEKKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDGGRIGIAAQALGLAQG 255 +KKMG +G+ T ++IFED R+P N++G EGQGFK AM LD GR+ I+A +G+++ Sbjct: 198 IDKKMGQKGAHTCDVIFEDVRVPAANIIGGIEGQGFKTAMKVLDRGRLHISATCVGVSER 257 Query: 256 ALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVEA 315 + ++VKY ERVQFG+P+ +FQ Q LAD + AAR +V AA KD G EA Sbjct: 258 LIRDSVKYAAERVQFGKPIGEFQLVQAMLADSRTEAYAARCMVLDAARKKDQGINVSTEA 317 Query: 316 AMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGK 375 A K+FA+E + +AVQ+HGG GY DY +ER RD ++ IYEGT+++Q++VI+ Sbjct: 318 ACCKMFASEAVGRIADRAVQVHGGAGYISDYGIERFYRDVRLFRIYEGTTQIQQLVIARN 377 Query: 376 LLK 378 +LK Sbjct: 378 MLK 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: 352 Number of extensions: 16 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: 378 Length of database: 383 Length adjustment: 30 Effective length of query: 348 Effective length of database: 353 Effective search space: 122844 Effective search space used: 122844 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