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_043918838.1 jaqu_RS10025 acyl-CoA dehydrogenase family protein
Query= BRENDA::Q18AQ1 (378 letters) >NCBI__GCF_000877395.1:WP_043918838.1 Length = 379 Score = 259 bits (662), Expect = 9e-74 Identities = 145/357 (40%), Positives = 212/357 (59%), Gaps = 3/357 (0%) Query: 22 EVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGDTVGYIMAVEELSRVCGT 81 E+ P A + P + K+A+ G+ G+ +E GG G + + E LS C + Sbjct: 23 EIAPHARAWEAAGDIPRDLWPKLAELGLAGLYVSEEAGGTGLTRLDATLVFEALSMACPS 82 Query: 82 TGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGLTEPNAGTDASGQQTTAV 141 LS H I YG++E K + L + E ++ LTEP +G+DA+ +T A Sbjct: 83 VASFLSIHNMCARM-IDAYGSDELKDRMLPKALTCETWLSYCLTEPGSGSDAAALKTRAE 141 Query: 142 LDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFIVEKGTPGFSFGVKEKKM 201 + + L G+K FI+ D Y+VMA + ++ G +GISAF+VE GT G SFG E KM Sbjct: 142 RTNEGWRLTGTKAFISGGGYSDAYIVMARSGEA-GPRGISAFVVEDGTDGLSFGGLEDKM 200 Query: 202 GIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIGIAAQALGLAQGALDETV 261 G R T ++ +D +P NLLG+EG GF+ AM+ LDGGR+ IAA +LG AQ ALD T+ Sbjct: 201 GWRSQPTRQVQLDDAPVPASNLLGEEGHGFRYAMAGLDGGRLNIAACSLGAAQQALDLTL 260 Query: 262 KYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAINKDLGKPYGVE-AAMAKL 320 YV+ER FG+ L+ FQNTQF+LA+ME+++Q+AR + QAA + D G P + AMAK Sbjct: 261 AYVRERKAFGQSLADFQNTQFRLAEMEIELQSARTFLRQAAWHLDQGTPEATKFCAMAKK 320 Query: 321 FAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEGTSEVQRMVISGKLL 377 E V +QLHGGYGY DY +E++ RD ++ +I EGT+E+ R++++ +L Sbjct: 321 MVTEAGSRVVDGCLQLHGGYGYLADYGIEKLSRDLRVHQILEGTNEIMRLIVARNML 377 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: 333 Number of extensions: 12 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: 379 Length adjustment: 30 Effective length of query: 348 Effective length of database: 349 Effective search space: 121452 Effective search space used: 121452 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