Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate AO356_01580 AO356_01580 isovaleryl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_01580 Length = 387 Score = 262 bits (670), Expect = 1e-74 Identities = 136/366 (37%), Positives = 219/366 (59%) Query: 10 ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 + D + F + L P AA+ D ++ FP + + ++G G+ VPE++GG GYLA+ + Sbjct: 17 LRDQVQAFVKAELAPRAAQIDIDNLFPADMWRKFGDMGLLGITVPEEYGGAGLGYLAHVV 76 Query: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALTEPQAG 129 A+EEI+ G + + H+++ I + GN +QK ++L L SG +GA A++EP AG Sbjct: 77 AMEEISRGSASVALSYGAHSNLCVNQINRNGNHEQKTKYLPKLISGEHIGALAMSEPNAG 136 Query: 130 SDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDSP 189 SD S+K RA GDHYVLNG K +IT+G +A +++A TD G GI+AFIV D Sbjct: 137 SDVVSMKLRADKRGDHYVLNGSKTWITNGPDANTYVIYAKTDLEKGPHGITAFIVERDWK 196 Query: 190 GYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQSV 249 G+ + DKLG S+TC++ F+DV+VP N LG G K+ ++ L+ RV ++ Sbjct: 197 GFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGALNGGVKVLMSGLDYERVVLSGGPT 256 Query: 250 GMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGKP 309 G+ +A + Y +R+ FG+ I E Q + ++ADM TQ+ +R ++ A + G+ Sbjct: 257 GIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLYAVAQACERGET 316 Query: 310 ALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQRM 369 +A+ L+++E A ++ A+Q LGG GY+++FP R+ RD ++ +I GTS+I+RM Sbjct: 317 TRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRDAKLYEIGAGTSEIRRM 376 Query: 370 VISRNL 375 +I R L Sbjct: 377 LIGREL 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: 319 Number of extensions: 14 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: 387 Length adjustment: 30 Effective length of query: 345 Effective length of database: 357 Effective search space: 123165 Effective search space used: 123165 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