Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_086509502.1 BZY95_RS08430 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_002151265.1:WP_086509502.1 Length = 385 Score = 266 bits (680), Expect = 7e-76 Identities = 148/368 (40%), Positives = 211/368 (57%), Gaps = 1/368 (0%) Query: 12 MIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYIDYVAYA 71 + D R F +E+APH +AWE+AG + +L Q+GE GLLG+ +PE GGS D+ Sbjct: 11 LFHDTIRRFLEQEVAPHYEAWEEAGEMPRSLWQQLGEAGLLGIDLPEALGGSGADFAIVQ 70 Query: 72 LAVEEISA-GDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFALTEPQ 130 LA+EEIS G G + +IH ++ +L+ G+ AQ++ WL +ASG IG A+TEP Sbjct: 71 LALEEISRQGFGGLASAYNIHANIVMPYLLHIGTPAQRERWLPAMASGETIGAIAMTEPG 130 Query: 131 AGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAFLVPTD 190 AGS+ ++TRA + W L+GSK F +N + + L IV A TDP G +G+S FLV T Sbjct: 131 AGSDLAAMKTRASRTESGWRLDGSKLFITNGQIADLVIVCAKTDPAAGARGVSLFLVDTT 190 Query: 191 TPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRIGIGAQ 250 GF+ + K+G ASDT + D R+PE LLGE G G A + L R+G+ AQ Sbjct: 191 LAGFSRGQPIKKIGQHASDTAELFFDDLRLPEEALLGEAGAGFAYLMQELPRERLGVAAQ 250 Query: 251 ALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAARLKSAG 310 ALG A L Y RER FG+ + E Q+ LA+++ Q++ R G Sbjct: 251 ALGAMEGALALTLDYVRERRAFGRAVGEFQNTRFTLAEVRAQIDMGRAYFEQCVAKYRQG 310 Query: 311 LPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEGSSEIQ 370 ++A+ KL SEM + +Q+ GGYGY +YP+ R+Y DAR+ +Y G+SEI Sbjct: 311 EMNGTDAAILKLQLSEMQCRTIDACLQLFGGYGYTREYPISRFYLDARVQTLYAGTSEIM 370 Query: 371 RLLIAREL 378 + +IAR L Sbjct: 371 KEVIARSL 378 Lambda K H 0.318 0.133 0.390 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: 321 Number of extensions: 12 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: 383 Length of database: 385 Length adjustment: 30 Effective length of query: 353 Effective length of database: 355 Effective search space: 125315 Effective search space used: 125315 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 24 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