Align 2-methylbutanoyl-CoA dehydrogenase / butanoyl-CoA dehydrogenase / isobutyryl-CoA dehydrogenase (EC 1.3.8.1; EC 1.3.8.5) (characterized)
to candidate SMc01639 SMc01639 acyl-CoA dehydrogenase
Query= reanno::pseudo3_N2E3:AO353_25680 (375 letters) >FitnessBrowser__Smeli:SMc01639 Length = 386 Score = 243 bits (619), Expect = 8e-69 Identities = 146/380 (38%), Positives = 208/380 (54%), Gaps = 13/380 (3%) Query: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMA----ELGFFGMLVPEQWGG 59 T+EQ I D R F + + P E +R P+E E+A ELGFF PE+ GG Sbjct: 6 TEEQQMIVDTVRTFVETEIYPHENEVERTGVVPRELGLEIARKCKELGFFACNFPEEVGG 65 Query: 60 CDTGYLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLG 119 +L + + E+ G + + IL N+DQ+ER+L P G Sbjct: 66 AGLDHLTFTLVERELGRGSMGLTVFFGRPSG-----ILMACNEDQRERYLLPAVRGDKFD 120 Query: 120 AFALTEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTD----PSAG 175 A A+TEP AGSD +K AR +GD +++NG K FI+ A VIVF T P Sbjct: 121 ALAMTEPDAGSDVRGMKCFARPDGDDWIVNGTKHFISHADIADFVIVFIATGEEQTPRGP 180 Query: 176 KRGISAFIVPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALA 235 K+ I+ F+V +PG+++ + + C + F+D ++P A LGE +G+ IA Sbjct: 181 KKKITCFLVDRGTPGFEIREGYNSVSHRGYKNCILTFDDCRLPSAQILGEVHKGFDIAND 240 Query: 236 NLEGGRVGIASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQ 295 L R+ +A+ SVG AR AF+ A YA ER+ FGKPI +Q V+F+LADM T+I A Sbjct: 241 WLYATRLTVAATSVGRARRAFDYALSYAAERKQFGKPISANQGVSFKLADMITEIDAADL 300 Query: 296 MVHYAAALRDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVR 355 + AA D G P+ E + AK+FA+EM +V A+Q GG G + D PL R +RD R Sbjct: 301 LTLSAAWRLDQGLPSNREIASAKVFATEMLARVTDEAIQIYGGMGLMDDLPLARFWRDAR 360 Query: 356 VCQIYEGTSDIQRMVISRNL 375 V +I++GTS+IQR +ISR+L Sbjct: 361 VERIWDGTSEIQRHIISRDL 380 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: 322 Number of extensions: 14 Number of successful extensions: 4 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: 386 Length adjustment: 30 Effective length of query: 345 Effective length of database: 356 Effective search space: 122820 Effective search space used: 122820 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