Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF2 HP15_2 acyl-CoA dehydrogenase domain protein
Query= reanno::SB2B:6937192 (389 letters) >FitnessBrowser__Marino:GFF2 Length = 389 Score = 616 bits (1589), Expect = 0.0 Identities = 302/386 (78%), Positives = 341/386 (88%), Gaps = 1/386 (0%) Query: 1 MSHLYSTLNFGLGEDVDMLRDAVYEFAKGEIAPLAEKVDRDNAFPNELWAKFGDMGLLGV 60 M YS LNFGLGE +DMLR+ + FA EIAP AE++DR+N FP +LW K GDMGLLG+ Sbjct: 1 MKSQYSELNFGLGETLDMLREQINGFAASEIAPRAEEIDRNNEFPMDLWRKMGDMGLLGI 60 Query: 61 TVAEEYGGVNMGYLAHVVAMEEISRASASIGLSYGAHSNLCVNQIYRNGNEAQRAKYLPK 120 TV+EEYGG +MGYLAHV+AMEEISRASAS+GLSYGAHSNLCVNQI+RNG E Q+ KYLPK Sbjct: 61 TVSEEYGGSDMGYLAHVIAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEEQKQKYLPK 120 Query: 121 LISGEHIGALAMSEPNAGSDVVSMKLHARKEGDRYILNGNKMWITNGPDAHTYVIYAKTD 180 L+SGEHIGALAMSEPNAGSDV+SMKL A+ EGD Y+LNGNKMWITNGPDA+TYVIYAKTD Sbjct: 121 LVSGEHIGALAMSEPNAGSDVISMKLTAKDEGDHYLLNGNKMWITNGPDANTYVIYAKTD 180 Query: 181 LDKGPHGITAFIVERGFKGFSQAQKLDKLGMRGSNTCELVFEDCEVPEENILGGLNNGVK 240 G G+TAFIVER GFS+ QKLDKLGMRGSNTCELVF+DC+VP+EN+LGG+ NG K Sbjct: 181 TSAGSRGVTAFIVERDAPGFSRHQKLDKLGMRGSNTCELVFQDCKVPKENVLGGVGNGAK 240 Query: 241 VLMSGLDYERVVLSGGPLGIMTACMDIVVPYVHERVQFGKSIGEFQLVQGKLADMYTGMN 300 VLMSGLDYER+VLSGGPLGIM A MD+VVPY+ ER QFG++IGEF+LVQGK+ADMYT MN Sbjct: 241 VLMSGLDYERLVLSGGPLGIMQAAMDVVVPYIRERKQFGQAIGEFELVQGKVADMYTWMN 300 Query: 301 AAKSYVYNVARACDRG-ETTRKDAAGVILYAAELATKMALDAIQLLGGNGYVNEYATGRL 359 AKSYVY VA + DRG ETTRKDAAG ILY+AE+ATK+ALDAIQLLGGNGY+NEY TGRL Sbjct: 301 TAKSYVYMVAMSADRGAETTRKDAAGAILYSAEMATKIALDAIQLLGGNGYINEYPTGRL 360 Query: 360 LRDAKLYEIGAGTSEIRRMLIGRELF 385 LRDAKLYEIGAGTSEIRRMLIGREL+ Sbjct: 361 LRDAKLYEIGAGTSEIRRMLIGRELY 386 Lambda K H 0.318 0.137 0.396 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: 575 Number of extensions: 14 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: 389 Length of database: 389 Length adjustment: 30 Effective length of query: 359 Effective length of database: 359 Effective search space: 128881 Effective search space used: 128881 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