Align 2-methylbutanoyl-CoA dehydrogenase (EC 1.3.8.5) (characterized)
to candidate WP_073037063.1 BUB04_RS03730 acyl-CoA dehydrogenase
Query= reanno::pseudo6_N2E2:Pf6N2E2_1146 (375 letters) >NCBI__GCF_900129305.1:WP_073037063.1 Length = 382 Score = 355 bits (912), Expect = e-103 Identities = 178/373 (47%), Positives = 255/373 (68%), Gaps = 1/373 (0%) Query: 4 TEEQTQIRDMARQFAEERLKPFAAEWDREHRFPREAIDEMAELGFFGMLVPEQWGGCDTG 63 TEEQ I+DMAR+FAE + P AAE DR H+ P E + +M ELG G+ +P ++GG Sbjct: 6 TEEQRMIQDMARKFAEREIAPVAAELDRTHKHPEEIVKKMGELGLMGITIPPEYGGAGMD 65 Query: 64 YLAYAMTLEEIAAGDGACSTIMSVHNSVGCVPILKFGNDEQKAKFLTPLASGAMLGAFAL 123 Y++Y + + EI+ +C IMSV NS+ P+ +G +EQK +FLTP+ASG LG + L Sbjct: 66 YVSYVLAMIEISKACASCGVIMSVCNSLYNFPVYTYGTEEQKQQFLTPVASGEYLGCYGL 125 Query: 124 TEPQAGSDASSLKTRARLEGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 TE AGSD + ++T A L+G+ +V+NG K+FIT+G A ++ AVTD G +GIS+F+ Sbjct: 126 TEAGAGSDPAKMRTTAVLDGNEWVINGEKKFITNGNVARYCVLAAVTDKEKGYKGISSFL 185 Query: 184 VPT-DSPGYSVARVEDKLGQHASDTCQILFEDLKVPVGNRLGEEGEGYKIALANLEGGRV 242 V ++PG+ V RVE+KLG +AS T +++FED ++P N LG+EGEG+K L L+GGR+ Sbjct: 186 VDLHNTPGFKVGRVEEKLGINASGTAELIFEDARIPKENLLGKEGEGFKQMLTTLDGGRI 245 Query: 243 GIAAQAVGMARAAFEAARDYARERSSFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAA 302 GIA+QA+G+ RA E A +YA+ R FG+PI QA+ ++LAD+ATQ+ A + AA Sbjct: 246 GIASQAIGIGRAVLEEAIEYAKTREQFGRPIASFQAIQWKLADIATQLDAAELLTLRAAW 305 Query: 303 LRDSGQPALVEASMAKLFASEMAEKVCSMALQTLGGYGYLNDFPLERIYRDVRVCQIYEG 362 L +G+ EA+MAKLFAS+ A +Q LGGYGY ++P+ER RD ++ QIYEG Sbjct: 306 LEQNGRGYEKEAAMAKLFASDTAMWAAVEGVQILGGYGYCKEYPMERHMRDAKITQIYEG 365 Query: 363 TSDIQRMVISRNL 375 T++I R+VISRN+ Sbjct: 366 TNEIMRLVISRNI 378 Lambda K H 0.320 0.134 0.388 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: 382 Number of extensions: 15 Number of successful extensions: 2 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: 382 Length adjustment: 30 Effective length of query: 345 Effective length of database: 352 Effective search space: 121440 Effective search space used: 121440 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 Apr 09 2024. 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