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_01346 H281DRAFT_01346 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Burk376:H281DRAFT_01346 Length = 393 Score = 246 bits (627), Expect = 1e-69 Identities = 136/379 (35%), Positives = 219/379 (57%), Gaps = 6/379 (1%) Query: 3 PTDEQLQ-ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCD 61 P E+++ + D+ FA + + P AAE DR +FP + + +LG GM V E++GG + Sbjct: 10 PLGEEIEMLRDSIAGFAAKEIAPRAAEIDRTDQFPMDLWRKFGDLGVLGMTVSEEYGGAN 69 Query: 62 TGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAF 121 GY A+ +A+EEI+ + H+++ I + G + QK+++L L SG +GA Sbjct: 70 MGYTAHMVAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLVSGEHVGAL 129 Query: 122 ALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISA 181 A++EP AGSD S+K RA GD YVLNG K +IT+G + ++V+A TD A RGI+A Sbjct: 130 AMSEPNAGSDVVSMKLRADRKGDRYVLNGTKMWITNGPDCDTLVVYAKTDVEANSRGITA 189 Query: 182 FIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGR 241 FIV G+ VA+ DKLG S T +++F+DV+VP N LG+ G K+ ++ L+ R Sbjct: 190 FIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGVKVLMSGLDYER 249 Query: 242 VGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAA 301 +A G+ A +A Y +R+ FG+ I E Q + ++AD+ T + R ++ Sbjct: 250 AVLAGGPTGIMVAVMDAVVPYIHDRKQFGQSIGEFQLIQGKVADLYTTLQACRAYLYAVG 309 Query: 302 ALRDSGKPALV-----EASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRV 356 D+ A V + + L+ +E A + A+Q LGG GY++++P+ R++RD ++ Sbjct: 310 RQLDTLGTAHVRQVRKDCAGVILYTAEKATWMAGEAIQILGGNGYINEYPVGRLWRDAKL 369 Query: 357 CQIYEGTSDIQRMVISRNL 375 +I GTS+I+RM+I R L Sbjct: 370 YEIGAGTSEIRRMLIGREL 388 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: 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: 393 Length adjustment: 30 Effective length of query: 345 Effective length of database: 363 Effective search space: 125235 Effective search space used: 125235 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