Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate GFF2427 Psest_2475 Acyl-CoA dehydrogenases
Query= reanno::psRCH2:GFF2392 (383 letters) >FitnessBrowser__psRCH2:GFF2427 Length = 392 Score = 248 bits (632), Expect = 3e-70 Identities = 139/372 (37%), Positives = 209/372 (56%), Gaps = 1/372 (0%) Query: 8 EDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYIDY 67 +DQ + +D R F ++E+APH + WE + L ++GE GLLG+ +PE+ GG Sbjct: 16 DDQTLFQDSVRRFLQQEVAPHYEQWEADHQLPRALWHRLGEAGLLGVDLPEQLGGCAAGV 75 Query: 68 VAYALAVEEISA-GDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFAL 126 + EEIS G G + +IH ++ + + G+ AQ+ WL +A+G +G A+ Sbjct: 76 ETCLMICEEISRQGFGGLASGYNIHANIVMPYIHHLGNPAQQACWLPRMAAGEVLGAIAM 135 Query: 127 TEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAFL 186 TEP AGS+ +R A+ V G W LNGSK F +N + + IV A TDP +G+S FL Sbjct: 136 TEPGAGSDLAAMRASAQKVPGGWKLNGSKVFITNGLLADMVIVCAKTDPNARARGVSLFL 195 Query: 187 VPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRIG 246 V T PGF+ ++ K+G ASDT + D +PE LLG+ GKG A + L R+G Sbjct: 196 VDTTLPGFSRGKAIRKIGQHASDTAELFFDDLIVPEDALLGDAGKGFAYLMQELPRERLG 255 Query: 247 IGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAARL 306 + AQA+G A + L Y ++R FG+ IA+ Q+ LA+++ L R + Sbjct: 256 VAAQAIGAIDGALQLTLDYVQQRRAFGQRIADFQNTRFTLAEVRAHLEMGRAYFEKCLQR 315 Query: 307 KSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEGS 366 + G ++A+ KL SEM + Q +Q+ GGYGY +YP+ R+Y DARI IY G+ Sbjct: 316 YARGEMSSTDAAALKLMLSEMQCRCVDQCLQLFGGYGYTLEYPISRFYVDARIQTIYAGT 375 Query: 367 SEIQRLLIAREL 378 SEI + +IAR++ Sbjct: 376 SEIMKEVIARDM 387 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: 327 Number of extensions: 16 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: 383 Length of database: 392 Length adjustment: 30 Effective length of query: 353 Effective length of database: 362 Effective search space: 127786 Effective search space used: 127786 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