Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate CA265_RS22715 CA265_RS22715 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >FitnessBrowser__Pedo557:CA265_RS22715 Length = 379 Score = 293 bits (750), Expect = 6e-84 Identities = 159/382 (41%), Positives = 234/382 (61%), Gaps = 5/382 (1%) Query: 10 LNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYG 69 ++F+L E+ +R A RDFAQ E+ P + D+ +FP + +K+G+LG LG+ V E+Y Sbjct: 1 MHFELSEEQLMIRQAARDFAQQELKPGVIERDEHQKFPAEQVKKLGELGFLGMMVSEKYN 60 Query: 70 GAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHV 129 G+ + +++++ MEE+S+ AS + +++L + G+EAQK KYL L +GE + Sbjct: 61 GSGLDAISYVLVMEELSKIDASASVVVSVNNSLVCYGLEAYGSEAQKEKYLKPLAAGEKI 120 Query: 130 GALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARG 189 GA +SEP AGSD S + AEDKG YYLLNG+K WITNG A T +V A+T PEL +G Sbjct: 121 GAFCLSEPEAGSDATSQRTTAEDKGDYYLLNGTKNWITNGSTASTYLVIAQTHPELRHKG 180 Query: 190 VTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLD 249 + AF++EKGM+GF++ K +KLG+RGS T L+F DV+VP EN +G G K M L+ Sbjct: 181 INAFIVEKGMEGFTVGPKENKLGIRGSDTHSLMFNDVKVPKENRIGEDGFGFKFAMKTLE 240 Query: 250 YERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAY 309 R + LGI Q + Y +RK FG+ I E Q I K+ADM T ++A R Y Sbjct: 241 GGRIGIAAQALGIAQGAFELATQYAKERKSFGKPISEHQAIAFKLADMATQIEAARLLVY 300 Query: 310 TVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRD 369 A D G + + + L+ ++ A + E VQ++GG G++ EY + RL RD Sbjct: 301 KAAWLKDQ-GLPYTQA----GSMAKLYASKVAMDVTIEAVQVHGGYGFVKEYHVERLMRD 355 Query: 370 AKLYEIGAGTSEIRRMLIGREL 391 AK+ +I GTSEI++M+I RE+ Sbjct: 356 AKITQIYEGTSEIQKMVISREV 377 Lambda K H 0.318 0.136 0.400 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: 374 Number of extensions: 12 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: 396 Length of database: 379 Length adjustment: 30 Effective length of query: 366 Effective length of database: 349 Effective search space: 127734 Effective search space used: 127734 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