Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate H281DRAFT_01346 H281DRAFT_01346 isovaleryl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >FitnessBrowser__Burk376:H281DRAFT_01346 Length = 393 Score = 646 bits (1666), Expect = 0.0 Identities = 316/391 (80%), Positives = 349/391 (89%) Query: 5 ANLPGLNFQLGEDIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITV 64 +NLPGL F LGE+I+ LRD++ FA EIAPRAA+ID++DQFPMDLWRK GDLGVLG+TV Sbjct: 2 SNLPGLQFPLGEEIEMLRDSIAGFAAKEIAPRAAEIDRTDQFPMDLWRKFGDLGVLGMTV 61 Query: 65 PEQYGGAAMGYLAHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLI 124 E+YGGA MGY AHMVAMEEISRASASVGLSYGAHSNLCVNQI+RNG EAQK KYL KL+ Sbjct: 62 SEEYGGANMGYTAHMVAMEEISRASASVGLSYGAHSNLCVNQIHRNGTEAQKQKYLPKLV 121 Query: 125 SGEHVGALAMSEPGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPE 184 SGEHVGALAMSEP AGSDV+SMKL+A+ KG Y+LNG+KMWITNGPD DTLVVYAKT+ E Sbjct: 122 SGEHVGALAMSEPNAGSDVVSMKLRADRKGDRYVLNGTKMWITNGPDCDTLVVYAKTDVE 181 Query: 185 LGARGVTAFLIEKGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVL 244 +RG+TAF++EKGMKGFS+AQKLDKLGMRGSHTGELVFQDVEVP EN+LG LN G KVL Sbjct: 182 ANSRGITAFIVEKGMKGFSVAQKLDKLGMRGSHTGELVFQDVEVPEENILGQLNGGVKVL 241 Query: 245 MSGLDYERAVLTGGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAG 304 MSGLDYERAVL GGP GIM +VMD V+PYIHDRKQFGQSIGEFQLIQGKVAD+YT LQA Sbjct: 242 MSGLDYERAVLAGGPTGIMVAVMDAVVPYIHDRKQFGQSIGEFQLIQGKVADLYTTLQAC 301 Query: 305 RSFAYTVAKNLDMLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLG 364 R++ Y V + LD LGT HVRQVRKDCA VIL+ AEKATWMAGE +QI GGNGYINEYP+G Sbjct: 302 RAYLYAVGRQLDTLGTAHVRQVRKDCAGVILYTAEKATWMAGEAIQILGGNGYINEYPVG 361 Query: 365 RLWRDAKLYEIGAGTSEIRRMLIGRELFAET 395 RLWRDAKLYEIGAGTSEIRRMLIGRELFAET Sbjct: 362 RLWRDAKLYEIGAGTSEIRRMLIGRELFAET 392 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: 607 Number of extensions: 13 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: 396 Length of database: 393 Length adjustment: 31 Effective length of query: 365 Effective length of database: 362 Effective search space: 132130 Effective search space used: 132130 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