Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_090448746.1 BLS63_RS26370 acyl-CoA dehydrogenase
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >NCBI__GCF_900100495.1:WP_090448746.1 Length = 378 Score = 256 bits (655), Expect = 6e-73 Identities = 146/375 (38%), Positives = 214/375 (57%), Gaps = 6/375 (1%) Query: 17 DIDALRDAVRDFAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAMGYL 76 D + RD+VR F + E P +K LW K G+ G+L +PE+YGG +L Sbjct: 10 DHELFRDSVRKFLEQEAVPFHQQWEKDGYIDRQLWNKAGEAGMLCSHIPEEYGGMGADFL 69 Query: 77 AHMVAMEEISRASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALAMSE 136 V +EEI R + G+ + HS++ + G+EA K KYL +L+SGE V A+AM+E Sbjct: 70 YSAVVIEEIGRLGLT-GIGFSLHSDIVAPYLLHYGSEALKHKYLPRLVSGEMVTAIAMTE 128 Query: 137 PGAGSDVISMKLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAFLIE 196 PGAGSD+ +K A G Y++NGSK +ITNG AD ++V AKT+P+ GA+G + FL+E Sbjct: 129 PGAGSDLQGVKTTAVLDGDEYVINGSKTFITNGYLADLVIVVAKTDPKAGAKGTSLFLVE 188 Query: 197 KGMKGFSIAQKLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERAVLT 256 GF+ ++L+K+GM+ T EL FQDV VP EN+LG G LM L ER + Sbjct: 189 ADTPGFAKGKRLEKVGMKAQDTSELFFQDVRVPKENLLGQAGMGFAYLMQELPQERLTVG 248 Query: 257 GGPLGIMQSVMDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAKNLD 316 G L ++ + + Y +RK FG++I +FQ + K+A+M T +Q GR F + L Sbjct: 249 VGALASAEAALKWTLDYTRERKAFGKAIADFQNTRFKLAEMATEIQVGRVFVDRCLE-LH 307 Query: 317 MLGTDHVRQVRKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEIG 376 + G V A + W + + E VQ++GG G++ EYP+ R W DA++ I Sbjct: 308 LQGKLDV----PTAAMLKYWGTDLQCKVLDECVQLHGGYGFMWEYPVARAWADARVQRIY 363 Query: 377 AGTSEIRRMLIGREL 391 AGT+EI + +I R L Sbjct: 364 AGTNEIMKEIIARSL 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: 406 Number of extensions: 19 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 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