Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate WP_010441027.1 G7G_RS0110000 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >NCBI__GCF_000192475.1:WP_010441027.1 Length = 385 Score = 223 bits (567), Expect = 9e-63 Identities = 129/375 (34%), Positives = 210/375 (56%), Gaps = 6/375 (1%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 TDE ++ A +F + L P +W + ++ + + G + E++GG G Sbjct: 12 TDEHRMFAEMAGRFMDDALVPNTEKWAEDGVVDRDFWLQAGQTGLMAGSIAEEYGGVGGG 71 Query: 64 YLAYAMAL-EEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFA 122 ++ L E+ A GD + S+ I +G++DQK ++L LASG M+GA A Sbjct: 72 MGFDSVTLYEQTARGDAGWGYGIQ---SIVTHYITTYGSEDQKHKWLPKLASGEMIGALA 128 Query: 123 LTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAF 182 +TEP GSD ++KT A +G+ Y L G K FIT+GQ+A +VIV A TD S G +G+S Sbjct: 129 MTEPGTGSDVQAVKTTAEKDGNSYRLKGSKIFITNGQSADLVIVAAKTDKSLGAKGVSLI 188 Query: 183 IVPTD-SPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLG-EEGEGYKIALANLEGG 240 V T+ + G++ R +KLG +DT ++ FEDV+VP+ N LG EEG+G+ + L Sbjct: 189 AVETEGTEGFRRGRNLEKLGMKGNDTAELFFEDVKVPMTNLLGPEEGQGFYQLMKQLPWE 248 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+ I ++G A Y +ER++FG+ +++ Q F+LA+ T+ V R V+ Sbjct: 249 RLTIGIMALGAIDFAISETVKYVQERKAFGQRVMDFQNTRFKLAECKTKAEVLRSFVNDC 308 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 ++G+ ASM K + SE+ ++ LQ GGYG++ ++P+ R+Y D RV IY Sbjct: 309 IGKLEAGELDAATASMVKYWGSEVQNEIMHECLQLFGGYGFMMEYPIARLYADARVQMIY 368 Query: 361 EGTSDIQRMVISRNL 375 GT+++ + +I+R+L Sbjct: 369 GGTNEVMKELIARSL 383 Lambda K H 0.319 0.134 0.389 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: 317 Number of extensions: 15 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: 375 Length of database: 385 Length adjustment: 30 Effective length of query: 345 Effective length of database: 355 Effective search space: 122475 Effective search space used: 122475 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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