Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate H281DRAFT_06133 H281DRAFT_06133 hypothetical protein
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_06133 Length = 377 Score = 479 bits (1233), Expect = e-140 Identities = 239/373 (64%), Positives = 295/373 (79%) Query: 1 MLPTDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGC 60 M+ T E I ++ R FA ERL P A++WD+ H FP A+ E+ ELG GM+V E+WGG Sbjct: 1 MILTQEHEMIRESIRTFAAERLAPHASDWDKNHTFPAAALKELGELGALGMVVEEKWGGA 60 Query: 61 DTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGA 120 Y++ +ALEEIAAGDGA STI+SV NS+ C K+G++ QKE++L+PLA G LG Sbjct: 61 GLDYMSLVLALEEIAAGDGATSTIVSVQNSLACGITSKYGSEKQKEQWLRPLAQGQKLGC 120 Query: 121 FALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGIS 180 F LTEP GSDAS+L+T AR +GD +VLNG KQFIT+G+ A V IVFAVTD SA K+GIS Sbjct: 121 FCLTEPHTGSDASALRTTARRDGDEWVLNGVKQFITTGKYADVAIVFAVTDKSADKKGIS 180 Query: 181 AFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGG 240 F++PT +PGY VAR+E+K+GQHASDT QI+FED +V ++ +G+EG+GY+IAL+NLE G Sbjct: 181 CFLIPTATPGYVVARLEEKMGQHASDTAQIIFEDCRVHLSAMMGQEGDGYRIALSNLEAG 240 Query: 241 RVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYA 300 R+GIA+Q+VGMARAAFEAA YA+ERE+FGK +IEHQAV FRLADMATQI AR MV A Sbjct: 241 RIGIAAQAVGMARAAFEAAVKYAKERETFGKLLIEHQAVTFRLADMATQIEAARMMVWRA 300 Query: 301 AALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIY 360 A L+D+GK L EASMAK+FASEMAEKVCS A+Q GG GY+SDFP+ERIYRDVRVCQIY Sbjct: 301 ATLKDAGKACLTEASMAKMFASEMAEKVCSDAIQIHGGCGYVSDFPVERIYRDVRVCQIY 360 Query: 361 EGTSDIQRMVISR 373 EG +DIQRMVI R Sbjct: 361 EGANDIQRMVIGR 373 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: 419 Number of extensions: 13 Number of successful extensions: 1 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: 377 Length adjustment: 30 Effective length of query: 345 Effective length of database: 347 Effective search space: 119715 Effective search space used: 119715 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