Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_043917997.1 jaqu_RS05745 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_000877395.1:WP_043917997.1 Length = 402 Score = 221 bits (562), Expect = 4e-62 Identities = 135/372 (36%), Positives = 193/372 (51%), Gaps = 6/372 (1%) Query: 5 ELSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSY 64 +LSED+RM+RD AR FA E+AP + +D + +MG GLLG+ +PEE+GG Sbjct: 28 QLSEDERMLRDAARAFAEAELAPGVTRAARDEVVDPEVFRRMGAAGLLGVTIPEEYGGLG 87 Query: 65 IDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCF 124 YV Y L EI D ++MS+ +S+ P+ YGS+AQK WL +LASG AIGCF Sbjct: 88 AGYVTYGLVAREIERVDSGYRSMMSVQSSLVMYPIHAYGSEAQKARWLPQLASGEAIGCF 147 Query: 125 ALTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSA 184 LTEP AGS+ ++TRAE + + G+K + SNA + + +V+A D + Sbjct: 148 GLTEPDAGSDPGGMKTRAEKTATGYRITGTKTWISNAPIADVFVVWAKLDGV-----IRG 202 Query: 185 FLVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGR 244 FL+ TPG + + K+ +RAS T + + +PE LL +GL L R Sbjct: 203 FLIERGTPGLSAPKIGGKLSLRASVTGEIVMDGVEVPEEALL-PGVEGLKGPFGCLNRAR 261 Query: 245 IGIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAA 304 GI +G A A + AA Y +R QFG+P+A+ Q LADMQT + L Sbjct: 262 YGISWGVMGAAEACWHAARQYGLDRKQFGRPLAQTQLYQKKLADMQTAIGLGLQGSLRLG 321 Query: 305 RLKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYE 364 R+ AG S K A V QA +HGG G E++ V R+ + YE Sbjct: 322 RMMEAGTASPELVSMMKRNNCGAALDVARQARDMHGGNGISEEFGVMRHMINLETVNTYE 381 Query: 365 GSSEIQRLLIAR 376 G+ ++ L++ R Sbjct: 382 GTHDVHALILGR 393 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: 388 Number of extensions: 17 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: 402 Length adjustment: 31 Effective length of query: 352 Effective length of database: 371 Effective search space: 130592 Effective search space used: 130592 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