Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate AO353_25680 AO353_25680 acyl-CoA dehydrogenase
Query= reanno::Phaeo:GFF1011 (386 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25680 Length = 375 Score = 281 bits (720), Expect = 2e-80 Identities = 150/367 (40%), Positives = 226/367 (61%), Gaps = 2/367 (0%) Query: 17 LRDMVHRWAQERVRPMAQEIDQKNEFPAELWQEMGELGLLGITVPEEFGGAGMSYLAHTV 76 + D ++AQER++P A E D+++ FP E EM ELG G+ VPE++GG YLA+ + Sbjct: 10 ISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTGYLAYAM 69 Query: 77 AVEEIARASASVSLSYGAHSNL-CVNQIKLNGNAEQKAKYLPRLVSGEHVGALAMSEAGA 135 A+EEIA + S H+++ CV +K GN +QK ++L L SG +GA A++E A Sbjct: 70 ALEEIAAGDGACSTIMSVHNSVGCVPILKF-GNDDQKERFLKPLASGAMLGAFALTEPQA 128 Query: 136 GSDVVSMSLRAEKRNDHYRLNGNKYWITNGPDADTLVVYAKTDPDAGSKGMTAFLIEKEF 195 GSD S+ RA DHY LNG K +IT+G +A ++V+A TDP AG +G++AF++ + Sbjct: 129 GSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFIVPTDS 188 Query: 196 KGFSTSQHFDKLGMRGSNTAELVFEDVEVPFENVLGEEGKGVRVLMSGLDYERVVLAGIG 255 G+ ++ DKLG S+T +++FEDV+VP N LGEEG+G ++ ++ L+ RV +A Sbjct: 189 PGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVGIASQS 248 Query: 256 TGIMAACMDEMMPYMKERKQFGQPIGNFQLMQGKIADMYTAMNTARAYVYEVAKACDKGT 315 G+ A + Y +ER+ FG+PI Q + ++ADM T + AR V+ A D G Sbjct: 249 VGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALRDSGK 308 Query: 316 VTRQDAAACCLYASEVAMTQAHQAVQAFGGAGYLSDNPVGRIFRDAKLMEIGAGTSEIRR 375 +A+ L+ASE+A A+Q GG GYLSD P+ RI+RD ++ +I GTS+I+R Sbjct: 309 PALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGTSDIQR 368 Query: 376 MLIGREL 382 M+I R L Sbjct: 369 MVISRNL 375 Lambda K H 0.318 0.132 0.382 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: 337 Number of extensions: 20 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: 386 Length of database: 375 Length adjustment: 30 Effective length of query: 356 Effective length of database: 345 Effective search space: 122820 Effective search space used: 122820 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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