Align Isovaleryl-CoA dehydrogenase (EC 1.3.8.4) (characterized)
to candidate WP_041096163.1 SUTH_RS00215 acyl-CoA dehydrogenase family protein
Query= reanno::acidovorax_3H11:Ac3H11_2991 (396 letters) >NCBI__GCF_000828635.1:WP_041096163.1 Length = 388 Score = 322 bits (826), Expect = 9e-93 Identities = 167/365 (45%), Positives = 237/365 (64%), Gaps = 3/365 (0%) Query: 28 FAQAEIAPRAADIDKSDQFPMDLWRKMGDLGVLGITVPEQYGGAAMGYLAHMVAMEEISR 87 +AQ P +D D FP D +R+MG++G+LG TVPE GG + ++ E +S Sbjct: 23 YAQERHHPLLRRMDDDDWFPADEYRRMGEVGLLGTTVPESLGGPGLDLVSQFFIGEALSY 82 Query: 88 ASASVGLSYGAHSNLCVNQINRNGNEAQKAKYLSKLISGEHVGALAMSEPGAGSDVI-SM 146 + +G S+GA NLCVN + RN + Q+A++L +++SG +GAL ++EPGAGSD + SM Sbjct: 83 WNNMLGASWGASENLCVNNLVRNASAEQQARFLPRMLSG--IGALGLTEPGAGSDALGSM 140 Query: 147 KLKAEDKGGYYLLNGSKMWITNGPDADTLVVYAKTEPELGARGVTAFLIEKGMKGFSIAQ 206 K A G +Y+LNG KM+ITNGP AD L+VYAKT PE G G++AF++EKGM GFS+AQ Sbjct: 141 KTSARRDGDHYVLNGRKMFITNGPVADLLLVYAKTTPERGQHGISAFVVEKGMPGFSVAQ 200 Query: 207 KLDKLGMRGSHTGELVFQDVEVPAENVLGGLNQGAKVLMSGLDYERAVLTGGPLGIMQSV 266 L K+G RGS TGEL+F D VPA N++GG ++G KV+MSGLD ER +G +GI Q Sbjct: 201 SLKKMGWRGSPTGELLFDDCRVPAANLIGGEDKGVKVVMSGLDIERVFFSGHVIGIAQRA 260 Query: 267 MDNVIPYIHDRKQFGQSIGEFQLIQGKVADMYTVLQAGRSFAYTVAKNLDMLGTDHVRQV 326 +D + Y R QFGQ I FQL+QG +ADMY L++ R+F+Y + K + G ++ Sbjct: 261 LDLSLDYAKTRVQFGQPIAGFQLVQGMLADMYAALESVRAFSYQLLKEITAAGEAGRGEI 320 Query: 327 RKDCASVILWCAEKATWMAGEGVQIYGGNGYINEYPLGRLWRDAKLYEIGAGTSEIRRML 386 K A+ +L + VQI+GGNG++ E + L+R KL EIGAGT+++R+++ Sbjct: 321 HKRSAAAVLHAGYMLKTVLDHAVQIHGGNGFMWETEVNCLYRAGKLIEIGAGTTQVRQLI 380 Query: 387 IGREL 391 I EL Sbjct: 381 IAGEL 385 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: 458 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: 388 Length adjustment: 31 Effective length of query: 365 Effective length of database: 357 Effective search space: 130305 Effective search space used: 130305 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