Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_057509244.1 ABB28_RS14005 acyl-CoA dehydrogenase
Query= reanno::WCS417:GFF3325 (387 letters) >NCBI__GCF_001431535.1:WP_057509244.1 Length = 387 Score = 195 bits (495), Expect = 2e-54 Identities = 117/366 (31%), Positives = 190/366 (51%), Gaps = 6/366 (1%) Query: 17 LRDQVQSFVSKEIAPRAAQIDRDNLFPADLWQKFGDMGLLGITVPEEYGGAGLGYLAHVV 76 ++D V FV + + P FPA+L + +GLLG T+P YGG G+ +A+ + Sbjct: 22 VQDSVARFVDQRVLPVIGDCFDQARFPAELVPEIAALGLLGATLPPAYGGGGMDAVAYGL 81 Query: 77 AMEEISRGSASVALSYGAHSNLCVNQINRNGNHSQKLKYLPKLISGEHVGALAMSEPNAG 136 +E+ RG + + S+LC++ I G+ +Q+L++LP + GE +G ++E + G Sbjct: 82 ICQELERGDSGLRSFVSVQSSLCMHPIFAYGSEAQRLRWLPAMARGERIGCFGLTEAHGG 141 Query: 137 SDVVSMKLRADKRGDHYVLNGSKTWITNGPDASTYVIYAKTDLEKGPHGITAFIVERDWK 196 SD SMK RA + GD + L+GSK WITN P A +++A+T+ G+ FI+ER Sbjct: 142 SDPSSMKTRAVREGDQWRLDGSKMWITNAPIADLAIVWAQTE-----DGVQGFILERGMA 196 Query: 197 GFSRSNKFDKLGMRGSNTCELFFDDVEVPEENILGTLNGGVKVLMSGLDYERVVLSGGPT 256 GFS K+ +R S+T LFFD V+VPE N L + G+K + L+ R +S GP Sbjct: 197 GFSVQEIGRKMSLRASSTGALFFDQVQVPEANRLAGV-VGMKGPLGCLNQARFGISWGPI 255 Query: 257 GIMQACMDLIVPYIHDRKQFGQSIGEFQLIQGKVADMYTQLNASRAYLYAVAQACERGET 316 G AC+ ++ Y R+ FG+ + Q Q K+ADM ++ ++ + + E G Sbjct: 256 GAAIACLREVLAYAGQRELFGRPLAATQSAQIKLADMARRITGAQLLALQLGRLKEAGRL 315 Query: 317 TRKDAAGVILYSAERATQMALDAIQILGGNGYINEFPAGRLLRDAKLYEIGAGTSEIRRM 376 + + + A +A + +LG G E A R + + GT + ++ Sbjct: 316 QPQQVSLAKWNNCRMAIDIARECRDLLGAAGITTEHAAIRHALNLESVITYEGTETVHQL 375 Query: 377 LIGREL 382 +IGREL Sbjct: 376 VIGREL 381 Lambda K H 0.318 0.136 0.396 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: 330 Number of extensions: 17 Number of successful extensions: 4 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: 387 Length adjustment: 30 Effective length of query: 357 Effective length of database: 357 Effective search space: 127449 Effective search space used: 127449 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