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_011513566.1 PCRYO_RS06325 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000013905.1:WP_011513566.1 Length = 384 Score = 291 bits (745), Expect = 2e-83 Identities = 152/363 (41%), Positives = 230/363 (63%), Gaps = 2/363 (0%) Query: 18 FAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSR 77 F N++ P+ + E +R P + + +M + G+ G+ P+EYGG G + EL R Sbjct: 18 FVNNQLIPMEHWVAENDRLPDDIINQMRELGLFGLTIPEEYGGLGVTMEEEVTLAFELGR 77 Query: 78 VCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQ 137 ++ + +GS + G E QKQK+L LASGE +G+F LTEP++G+DA+ + Sbjct: 78 TSPAFRSLIGTNNGIGSSGLVIDGTEAQKQKYLPRLASGEIIGSFCLTEPDSGSDAASLK 137 Query: 138 TTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTD-KSKGNKGISAFIVEKGTPGFSFGV 196 TTA+ DGD YI+NG+K +ITNA ++ VMA TD ++K + GISAFIVE TPG + G Sbjct: 138 TTAIKDGDTYIINGTKRYITNAPEAGVFTVMARTDPQNKRSGGISAFIVESDTPGITLGK 197 Query: 197 KEKKMGIRGSATSELIFEDCRIPKENLLGK-EGQGFKIAMSTLDGGRIGIAAQALGLAQG 255 +KKMG +G+ T ++IF++C +P + L+G EG GFK AM LD GR+ IAA + G A Sbjct: 198 IDKKMGQKGAHTCDVIFDNCIVPADALIGGVEGVGFKTAMKVLDKGRLHIAAASTGAATR 257 Query: 256 ALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVEA 315 LD+ + Y ER QFG+P++ FQ Q LAD + ++ AA+ +V A+ +D GK E+ Sbjct: 258 MLDDALHYAVERKQFGQPIANFQLIQAMLADSKAEIYAAKSMVLDASRLRDEGKDVVTES 317 Query: 316 AMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGK 375 + AK+FA E V +AVQ+HGG GY DY +ER RD ++ +YEGT+++Q+++I+ Sbjct: 318 SCAKMFATEMCGRVADRAVQIHGGAGYIADYGIERFYRDVRLYRLYEGTTQIQQIIIARN 377 Query: 376 LLK 378 ++K Sbjct: 378 MIK 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: 332 Number of extensions: 12 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: 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 24 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