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 SM_b20753 SM_b20753 acyl-CoA dehydrogenase
Query= BRENDA::Q18AQ1 (378 letters) >FitnessBrowser__Smeli:SM_b20753 Length = 380 Score = 290 bits (743), Expect = 3e-83 Identities = 152/374 (40%), Positives = 231/374 (61%), Gaps = 3/374 (0%) Query: 5 SKKYQMLKELYVSFAENEVKPLATELDEEERFPYETVEKMAKAGMMGIPYPKEYGGEGGD 64 S++ + ++ + + FA +E+ P A + D+++ FP ET+ A GM GI + GG G Sbjct: 6 SEEQEAIRTMALDFARDEIAPHAVDWDQQKHFPVETLRAAAALGMAGIYIRDDVGGTGLT 65 Query: 65 TVGYIMAVEELSRVCGTTGVILSAHTSLGSWPIYQYGNEEQKQKFLRPLASGEKLGAFGL 124 + M +E L+ C +S H I +YG +EQ+++ L PL + + L ++ L Sbjct: 66 RLDAAMIIEALATGCPAIASFVSIHNMCAGM-IDRYGTDEQRRRLLPPLLTMDVLASYCL 124 Query: 125 TEPNAGTDASGQQTTAVLDGDEYILNGSKIFITNAIAGDIYVVMAMTDKSKGNKGISAFI 184 TEP +G+DA+ +T AV +GD Y+L G K FI+ A +Y+VMA T + +G KGISAF+ Sbjct: 125 TEPGSGSDAAALKTRAVREGDAYLLTGQKQFISGAGESGLYIVMARTGE-EGPKGISAFV 183 Query: 185 VEKGTPGFSFGVKEKKMGIRGSATSELIFEDCRIPKENLLGKEGQGFKIAMSTLDGGRIG 244 VEK PG +FG EKKMG T ++ ++ R+ EN LG EG+GF+IAM+ LDGGR+ Sbjct: 184 VEKDAPGLTFGANEKKMGWHAQPTRAVMLDNVRVSVENRLGAEGEGFRIAMAGLDGGRLS 243 Query: 245 IAAQALGLAQGALDETVKYVKERVQFGRPLSKFQNTQFQLADMEVKVQAARHLVYQAAIN 304 IAA +LG AQ A D+ + YV+ER FG+ + +FQ QF+LADM ++ AR +++AA Sbjct: 244 IAAASLGGAQSAFDKALAYVQERRAFGKAIGEFQALQFRLADMATDLEIARTFLWRAACA 303 Query: 305 KDLGKPYGVE-AAMAKLFAAETAMEVTTKAVQLHGGYGYTRDYPVERMMRDAKITEIYEG 363 D P + AMAK F + V A+QLHGGYGY DY VE+++RD ++ +I EG Sbjct: 304 LDAADPEATKLCAMAKRFVTDRCFSVANDALQLHGGYGYLADYGVEKIVRDLRVHQILEG 363 Query: 364 TSEVQRMVISGKLL 377 T+E+ R+++S ++ Sbjct: 364 TNEIMRLIVSRAIM 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: 308 Number of extensions: 16 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: 380 Length adjustment: 30 Effective length of query: 348 Effective length of database: 350 Effective search space: 121800 Effective search space used: 121800 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