Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF56 HP15_56 acyl-CoA dehydrogenase domain protein
Query= reanno::psRCH2:GFF1051 (387 letters) >FitnessBrowser__Marino:GFF56 Length = 374 Score = 250 bits (639), Expect = 4e-71 Identities = 138/371 (37%), Positives = 220/371 (59%), Gaps = 3/371 (0%) Query: 12 ETIDMLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGY 71 E +M REQ + F+ EI P E ++ + P ++WRK GEMGLL TV EEYGGAG + Sbjct: 7 EDHNMFREQARRFIEREICPHLEEWEKSGIVPKEIWRKAGEMGLLCSTVPEEYGGAGGDF 66 Query: 72 LAHVVAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAMS 131 V +EE++R +A+ A+ + HS + I G EQK ++LP+++SGE +G +AMS Sbjct: 67 GHSAVMIEELARVNAT-AIGFTTHSEIVAPYIVAYGTEEQKQKWLPRMVSGEIIGVIAMS 125 Query: 132 EPNAGSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFIV 191 EP GSD+ SM+ + + GD+Y+++G KT+ITNG +A+ ++ T +D + +T V Sbjct: 126 EPGIGSDLRSMRTQLRRDGDQYIISGQKTFITNGGNAD--LVVTATKVDPASKDLTLVCV 183 Query: 192 ERDWKGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENGGVKVLMSGLDYERVVL 251 E D GF++G DK+G++G +T ELFFDDV VP N LG EN G L L +ER+++ Sbjct: 184 ETDRDGFAKGRLLDKIGLKGQDTAELFFDDVRVPVSNRLGEENEGFGYLTHQLAWERLII 243 Query: 252 AGGPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQAC 311 A + S LD+ + Y +RK FG+++ +FQ + K+A++ Q R ++ + Sbjct: 244 AIRAAESIDSFLDMTIGYTKERKVFGKTVFDFQNTRFKLAEIKAQATMLRVFVDNCLERV 303 Query: 312 DRGETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEIGAGTS 371 + AA L +E ++ + +Q+ GG G+++E+ G+ DA++ I GTS Sbjct: 304 MNNDLPADVAAMAKLMGSELQGKLLDEMLQLHGGYGFMSEYRIGQAWIDARVARIYGGTS 363 Query: 372 EIRRMLIGREL 382 EI + +I R+L Sbjct: 364 EIMKEIISRKL 374 Lambda K H 0.318 0.135 0.391 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: 356 Number of extensions: 15 Number of successful extensions: 3 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: 387 Length of database: 374 Length adjustment: 30 Effective length of query: 357 Effective length of database: 344 Effective search space: 122808 Effective search space used: 122808 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