Align isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF1551 PGA1_c15710 acyl-CoA dehydrogenase
Query= BRENDA::Q75N94 (430 letters) >FitnessBrowser__Phaeo:GFF1551 Length = 406 Score = 191 bits (486), Expect = 3e-53 Identities = 122/348 (35%), Positives = 184/348 (52%), Gaps = 11/348 (3%) Query: 78 EFPAEMWKKLGDAGFLGITANEDYGGLGMGYQAHCIVMEELSRASGSIALSYAAHSQLCV 137 E E+++++G+ G LG T E YGGLG GY ++ +V E+ R + S L + Sbjct: 61 ETDPEIFREMGEMGLLGTTIPEQYGGLGAGYVSYGLVAREVERVDSGYRSMMSVQSSLVM 120 Query: 138 NQLSLNGSPEQKERFLPGLLSGDKIGALAMSEHSAGSDVVSMKTTAKEVDGGYVLNGTKM 197 + GS EQ++++LP L SG+ IG ++E AGSD MKT A++ DGGY L G+KM Sbjct: 121 YPIYAYGSEEQRQKYLPKLSSGEWIGCFGLTEPDAGSDPAGMKTRAEKTDGGYRLTGSKM 180 Query: 198 WITNGPDADFIVVYAKTEPQKGSKGITAFVVEKTFDGFSCARKLDKLGMRGSNTGELIFE 257 WI+N P AD VV+AK+E G I FV+EK G S + +K +R S TGE++ + Sbjct: 181 WISNAPIADVFVVWAKSEAHGGK--IRGFVLEKGMKGLSAPKIANKASLRASITGEIVMD 238 Query: 258 DVFVPKENVLGEVNRGVKVLMEGLDLERLVLSAGPLGIMQAALDLVLPYTHVRKQFGTPI 317 V V + +L V G+K L+ R +S G +G +A Y RKQFG P+ Sbjct: 239 GVEVGDDALLPHV-EGLKGPFGCLNRARYGISWGAMGAAEACWHAARQYGLDRKQFGRPL 297 Query: 318 AHNQLIQGKLADMYTKLQASRAYTYSTARHIDNSASLSE-VSIRTQDCAGAILYAAERAT 376 A+ QL Q KLA+M T++ + R +D + + E +SI ++ G +A Sbjct: 298 ANTQLFQLKLANMQTEITLGLQASLRVGRLMDEANAAPEMISIVKRNNCG-------KAL 350 Query: 377 ECALDAIQLMGGNGYINELPAGRLLRDAKLYEIGAGTSEIRRMVIGRA 424 E A A + GGNG E R + + + GT ++ +++GRA Sbjct: 351 EIARHARDMHGGNGISLEFGVIRHMVNLETVNTYEGTHDVHALILGRA 398 Lambda K H 0.317 0.134 0.380 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: 389 Number of extensions: 24 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: 430 Length of database: 406 Length adjustment: 32 Effective length of query: 398 Effective length of database: 374 Effective search space: 148852 Effective search space used: 148852 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 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