Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate 5208388 Shew_0900 acyl-CoA dehydrogenase domain-containing protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__PV4:5208388 Length = 391 Score = 184 bits (468), Expect = 3e-51 Identities = 119/377 (31%), Positives = 182/377 (48%), Gaps = 16/377 (4%) Query: 2 LPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCD 61 L ++++ I D +AQE+L +R F +E + E+ ELG G +PE +G + Sbjct: 17 LLSEDERMIRDMVHDYAQEKLMTRVLMANRNEHFDREIMNELGELGLLGATLPEAYGCAN 76 Query: 62 TGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAF 121 Y++Y + EI D + MSV +S+ PI +GN+ Q++++L LA+G +G F Sbjct: 77 ANYVSYGLVAREIERVDSGYRSAMSVQSSLVMHPIYAYGNEQQRQKYLPKLATGEWVGCF 136 Query: 122 ALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISA 181 LTEP GSD +KTRA Y LNG K +IT+ A V +V+A D I Sbjct: 137 GLTEPDVGSDPGGMKTRAERIDGGYRLNGAKMWITNSPIADVFVVWAKLDGV-----IRG 191 Query: 182 FIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEG-----EGYKIALAN 236 FI+ G ++E K AS T +I+ ++V+V GEE EG K Sbjct: 192 FILEKGMKGLSAPKIEGKFSLRASITGEIVMDNVEV------GEEALLPNVEGLKGPFGC 245 Query: 237 LEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQM 296 L R GIA ++G A + AAR Y+ +R F +P+ Q + +LADM T+I Sbjct: 246 LNKARYGIAWGALGAAEFCWHAARQYSLDRIQFNRPLAATQLIQKKLADMQTEITTGLFA 305 Query: 297 VHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRV 356 A L D + S+ K + A ++ T+ GG G +F + R ++ Sbjct: 306 CLQAGRLMDQDALPVEAISLIKRNSCGKALEIARTSRDMHGGNGISDEFHVIRHVMNLEA 365 Query: 357 CQIYEGTSDIQRMVISR 373 YEGT DI +++ R Sbjct: 366 VNTYEGTHDIHALILGR 382 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: 16 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: 391 Length adjustment: 30 Effective length of query: 345 Effective length of database: 361 Effective search space: 124545 Effective search space used: 124545 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 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