Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate GFF2427 Psest_2475 Acyl-CoA dehydrogenases
Query= reanno::Smeli:SM_b21121 (387 letters) >FitnessBrowser__psRCH2:GFF2427 Length = 392 Score = 263 bits (672), Expect = 6e-75 Identities = 147/380 (38%), Positives = 219/380 (57%), Gaps = 2/380 (0%) Query: 5 GLNFALGEEIDAL-RASVRRFASERIAPLADDADRSNAFPMSLWREMGELGLLGITADEA 63 G + A E+ L + SVRRF + +AP + + + P +LW +GE GLLG+ E Sbjct: 8 GADCATSEDDQTLFQDSVRRFLQQEVAPHYEQWEADHQLPRALWHRLGEAGLLGVDLPEQ 67 Query: 64 HGGAGLGYLAHCVAMEEISRAS-ASVGLSYGAHSNLCVNQINRNGKPAQKSRYLPKLISG 122 GG G + EEISR + Y H+N+ + I+ G PAQ++ +LP++ +G Sbjct: 68 LGGCAAGVETCLMICEEISRQGFGGLASGYNIHANIVMPYIHHLGNPAQQACWLPRMAAG 127 Query: 123 EHVGALAMSEPGAGSDVVSMKLKADKRGDRYVLNGSKMWITNGPDADVLVVYAKTDPAAG 182 E +GA+AM+EPGAGSD+ +M+ A K + LNGSK++ITNG AD+++V AKTDP A Sbjct: 128 EVLGAIAMTEPGAGSDLAAMRASAQKVPGGWKLNGSKVFITNGLLADMVIVCAKTDPNAR 187 Query: 183 PRGITAFLVEKAFPGFSAGQKLDKLGMRGSNTSELIFTDCEVPEENVLGGVGEGVKVLMS 242 RG++ FLV+ PGFS G+ + K+G S+T+EL F D VPE+ +LG G+G LM Sbjct: 188 ARGVSLFLVDTTLPGFSRGKAIRKIGQHASDTAELFFDDLIVPEDALLGDAGKGFAYLMQ 247 Query: 243 GLDYERVVLSAGPLGIMAACLDVVVPYLHERKQFGQPIGEFQLMQGKLADMYVTMNAARA 302 L ER+ ++A +G + L + + Y+ +R+ FGQ I +FQ + LA++ + RA Sbjct: 248 ELPRERLGVAAQAIGAIDGALQLTLDYVQQRRAFGQRIADFQNTRFTLAEVRAHLEMGRA 307 Query: 303 YVYAVAAACDRGETARKDAAGCILYAAEKATAMALEAIQALGGNGYTNDYPAGRLLRDAK 362 Y RGE + DAA L +E + +Q GG GYT +YP R DA+ Sbjct: 308 YFEKCLQRYARGEMSSTDAAALKLMLSEMQCRCVDQCLQLFGGYGYTLEYPISRFYVDAR 367 Query: 363 LYEIGAGTSEIRRMLIGREL 382 + I AGTSEI + +I R++ Sbjct: 368 IQTIYAGTSEIMKEVIARDM 387 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: 328 Number of extensions: 11 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: 387 Length of database: 392 Length adjustment: 30 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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