Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate AO356_17045 AO356_17045 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_17045 Length = 378 Score = 256 bits (655), Expect = 6e-73 Identities = 147/373 (39%), Positives = 212/373 (56%), Gaps = 6/373 (1%) Query: 19 DALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAMGYLAH 78 + RD+VR F + E P + +K LW K G+ G+L +PE YGG +L Sbjct: 12 ELFRDSVRTFLEKEAVPYHSQWEKQGHVDRQLWNKAGEAGMLCSHLPEAYGGLDADFLYS 71 Query: 79 MVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALAMSEPG 138 V +EEI R + G+ + HS++ I G+EA K KYL KL+SGE V A+AM+EPG Sbjct: 72 TVVIEEIGRLGLT-GIGFSLHSDIVAPYILHYGSEALKHKYLPKLVSGEMVTAIAMTEPG 130 Query: 139 AGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAFLIEKG 198 AGSD+ +K A G Y++NGSK +ITNG AD ++V AKT+P+ GA+G + FL+E G Sbjct: 131 AGSDLQGVKTTAVLDGDEYVINGSKTFITNGFLADLVIVVAKTDPKAGAKGTSLFLVEAG 190 Query: 199 MKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERAVLTGG 258 GF ++L+K+GM+ T EL FQDV VP +N+LG G LM L ER + G Sbjct: 191 TPGFEKGKRLEKVGMKAQDTSELFFQDVRVPKDNLLGQAGMGFAYLMQELPQERLTVAIG 250 Query: 259 PLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAKNLDML 318 L ++ + + Y +RK FG++I +FQ + K+A+M T +Q GR F + L + Sbjct: 251 GLASAEAALQWTLDYTRERKAFGKTIADFQNTRFKLAEMATEIQIGRVFVDRCLE-LHLQ 309 Query: 319 GTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEIGAG 378 G V A W + + E VQ++GG G++ EYP+ R W DA++ I AG Sbjct: 310 GKLDV----PTAAMAKYWGTDLQCKVLDECVQLHGGYGFMWEYPIARAWADARVQRIYAG 365 Query: 379 TSEIRRMLIGREL 391 T+EI + +I R L Sbjct: 366 TNEIMKEIIARSL 378 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: 398 Number of extensions: 21 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: 396 Length of database: 378 Length adjustment: 30 Effective length of query: 366 Effective length of database: 348 Effective search space: 127368 Effective search space used: 127368 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 Apr 09 2024. 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