Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_012116241.1 XAUT_RS21625 isovaleryl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_000017645.1:WP_012116241.1 Length = 390 Score = 266 bits (681), Expect = 6e-76 Identities = 140/376 (37%), Positives = 217/376 (57%) Query: 3 DLELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGG 62 D +L E M+RD R F+ EIAP A ++ L ++G LGLLG+ EE+GG Sbjct: 10 DFDLGETADMLRDTVRSFSDAEIAPRAAEIDRTNQFPRDLWPKLGALGLLGVTAEEEYGG 69 Query: 63 SYIDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIG 122 S + Y+ + +A+EEIS + G H+++ + G+ QK ++L +L SG +G Sbjct: 70 SGLGYLEHVIAMEEISRASASVGLSYGAHSNLCINQISRNGTAEQKAKYLPKLISGEHVG 129 Query: 123 CFALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGL 182 A++EP AGS+ ++RTRA+ ++LNGSK + +N ++ +V+A TDP G KG+ Sbjct: 130 ALAMSEPGAGSDVVSMRTRADKKGDRYILNGSKMWITNGPIAETLVVYAKTDPAAGPKGM 189 Query: 183 SAFLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEG 242 +AFLV D PGF+ + K+G+R SDT + DC +PE N+LG G+G+ + +S L+ Sbjct: 190 TAFLVERDFPGFSTAQKLDKLGMRGSDTGELVFQDCEVPEENVLGAVGRGVNVLMSGLDY 249 Query: 243 GRIGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILH 302 R + GI +A + L Y ER QFG+PI Q + +ADM +NA + + Sbjct: 250 ERAVLAGGPTGIMQACMDIVLPYVHERKQFGQPIGTFQLMQGKIADMYVTMNATKAYVYA 309 Query: 303 AARLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQI 362 A+ G +A+ A L+A+E A + +A+Q GG GY+ DYP R RDA++ +I Sbjct: 310 VAKACDRGATTREDAAGAILYAAEKATWMALEAIQTLGGNGYINDYPTGRLLRDAKLYEI 369 Query: 363 YEGSSEIQRLLIAREL 378 G+SEI+R+LI R+L Sbjct: 370 GAGTSEIRRMLIGRQL 385 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: 334 Number of extensions: 18 Number of successful extensions: 1 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: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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 Apr 09 2024. 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