Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF1190 PGA1_c12060 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF1051 (387 letters) >FitnessBrowser__Phaeo:GFF1190 Length = 383 Score = 237 bits (604), Expect = 5e-67 Identities = 134/369 (36%), Positives = 209/369 (56%), Gaps = 3/369 (0%) Query: 16 MLREQVQAFVAAEIAPRAEAIDQENLFPADMWRKFGEMGLLGVTVSEEYGGAGLGYLAHV 75 ML + F+ E AP+ E ++ + W + G +GLL +V EEYGG G + Sbjct: 16 MLADMTAQFITREWAPKFETWRKQGMMDRSTWNEAGALGLLCPSVPEEYGGVGGDFGHEA 75 Query: 76 VAMEEISRGSASVALSYGAHSNLCVNQINRNGNPEQKARYLPKLISGEHVGALAMSEPNA 135 + E SR + + + +G HS + + + G EQK R+LPK+I+GE VGALAM+EP+ Sbjct: 76 AILIEGSRANLA-SWGHGIHSGIVAHYVLSYGTEEQKQRWLPKMITGELVGALAMTEPST 134 Query: 136 GSDVVSMKLRAEKRGDRYVLNGSKTWITNGPDANTYVIYAKTDLDKGAHGITAFIVERDW 195 GSDV +K +A K G+ Y L+G KT+ITNG AN ++ AKTD +G+ GI+ VE D Sbjct: 135 GSDVQRIKTKAVKDGNAYRLSGQKTFITNGQHANLILVAAKTDPSQGSKGISLVAVETDG 194 Query: 196 -KGFSRGNKFDKLGMRGSNTCELFFDDVEVPQENVLGAENG-GVKVLMSGLDYERVVLAG 253 GFSRG DK+G+ ++T ELFFD+VE+ EN+LG G G +M L ER+++A Sbjct: 195 ADGFSRGRNLDKIGLHAADTSELFFDNVEIAPENILGGTEGQGFYQMMQQLPQERLIIAC 254 Query: 254 GPTGIMQSCLDVVVPYIHDRKQFGQSIGEFQFIQGKVADMYTQLNASRAYLYAVAQACDR 313 G G M+ ++ + Y +R+ FG + +FQ + K+ + T+ +RA+L + Sbjct: 255 GAVGAMEGAVERTITYCKEREAFGGPLTQFQNTRFKLVECQTKTKVARAFLDECMVEHLQ 314 Query: 314 GETTRKDAAGVILYTAENATQMALQAIQILGGNGYINEFPTGRLLRDAKLYEIGAGTSEI 373 G+ T + AA + + + + +Q+ GG G++ E+ + DA++ I GT+EI Sbjct: 315 GKLTVEKAAMAKYWITDTQGDVLDECVQLHGGYGFMQEYAVAEMWTDARVQRIYGGTNEI 374 Query: 374 RRMLIGREL 382 + LI R L Sbjct: 375 MKELIARSL 383 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: 380 Number of extensions: 18 Number of successful extensions: 5 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: 383 Length adjustment: 30 Effective length of query: 357 Effective length of database: 353 Effective search space: 126021 Effective search space used: 126021 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