Align isobutyryl-CoA dehydrogenase (EC 1.3.8.1) (characterized)
to candidate WP_057509244.1 ABB28_RS14005 acyl-CoA dehydrogenase
Query= reanno::psRCH2:GFF2392 (383 letters) >NCBI__GCF_001431535.1:WP_057509244.1 Length = 387 Score = 199 bits (507), Expect = 8e-56 Identities = 125/373 (33%), Positives = 187/373 (50%), Gaps = 6/373 (1%) Query: 6 LSEDQRMIRDMARDFARREIAPHAQAWEKAGWIDDTLVAQMGELGLLGMVVPEEWGGSYI 65 LS+++R ++D F + + P LV ++ LGLLG +P +GG + Sbjct: 15 LSDEERAVQDSVARFVDQRVLPVIGDCFDQARFPAELVPEIAALGLLGATLPPAYGGGGM 74 Query: 66 DYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNYGSQAQKDEWLTELASGRAIGCFA 125 D VAY L +E+ GD + +S+ +S+ P+ YGS+AQ+ WL +A G IGCF Sbjct: 75 DAVAYGLICQELERGDSGLRSFVSVQSSLCMHPIFAYGSEAQRLRWLPAMARGERIGCFG 134 Query: 126 LTEPQAGSEAHNLRTRAELVDGHWVLNGSKQFCSNAKRSKLAIVFAVTDPELGKKGLSAF 185 LTE GS+ +++TRA W L+GSK + +NA + LAIV+A T+ G+ F Sbjct: 135 LTEAHGGSDPSSMKTRAVREGDQWRLDGSKMWITNAPIADLAIVWAQTE-----DGVQGF 189 Query: 186 LVPTDTPGFAVERSEHKMGIRASDTCGVSLSDCRIPEANLLGERGKGLAIALSNLEGGRI 245 ++ GF+V+ KM +RAS T + ++PEAN L G+ L L R Sbjct: 190 ILERGMAGFSVQEIGRKMSLRASSTGALFFDQVQVPEANRLA-GVVGMKGPLGCLNQARF 248 Query: 246 GIGAQALGIARAAFEAALLYARERVQFGKPIAEHQSIANMLADMQTQLNAARLLILHAAR 305 GI +G A A L YA +R FG+P+A QS LADM ++ A+LL L R Sbjct: 249 GISWGPIGAAIACLREVLAYAGQRELFGRPLAATQSAQIKLADMARRITGAQLLALQLGR 308 Query: 306 LKSAGLPCLSEASQAKLFASEMAEKVCSQAVQIHGGYGYLEDYPVERYYRDARITQIYEG 365 LK AG + S AK MA + + + G G ++ R+ + YEG Sbjct: 309 LKEAGRLQPQQVSLAKWNNCRMAIDIARECRDLLGAAGITTEHAAIRHALNLESVITYEG 368 Query: 366 SSEIQRLLIAREL 378 + + +L+I REL Sbjct: 369 TETVHQLVIGREL 381 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: 333 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: 387 Length adjustment: 30 Effective length of query: 353 Effective length of database: 357 Effective search space: 126021 Effective search space used: 126021 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