Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_041096163.1 SUTH_RS00215 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q60759 (438 letters) >NCBI__GCF_000828635.1:WP_041096163.1 Length = 388 Score = 127 bits (320), Expect = 5e-34 Identities = 93/280 (33%), Positives = 140/280 (50%), Gaps = 11/280 (3%) Query: 67 IRDTFRNYCQERLMSRILLANRNEVFHRDIVYEMGELGVLGPTI-KGYGCAGVSSVAYGL 125 I D Y QER + + ++ F D MGE+G+LG T+ + G G+ V+ Sbjct: 16 IYDMAWRYAQERHHPLLRRMDDDDWFPADEYRRMGEVGLLGTTVPESLGGPGLDLVSQFF 75 Query: 126 LTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGELLGCFGLTEPNHG 185 + L ++ + +L ++ + S EQ+ ++LP + G +G GLTEP G Sbjct: 76 IGEALSYWNNMLGASWGASENLCVNNLVRNASAEQQARFLPRMLSG--IGALGLTEPGAG 133 Query: 186 SDP-GGMETRARHNPSNQSYTLSGTKTWITNSPVADLFIVWARCE----DNCIRGFILEK 240 SD G M+T AR + + Y L+G K +ITN PVADL +V+A+ + I F++EK Sbjct: 134 SDALGSMKTSARRDGDH--YVLNGRKMFITNGPVADLLLVYAKTTPERGQHGISAFVVEK 191 Query: 241 GMRGLSAPRIEGKFSLRASATGMIIMDSVEVPEENVLPNVSS-LAGPFGCLNTARYGITW 299 GM G S + K R S TG ++ D VP N++ + L+ R + Sbjct: 192 GMPGFSVAQSLKKMGWRGSPTGELLFDDCRVPAANLIGGEDKGVKVVMSGLDIERVFFSG 251 Query: 300 GVLGAAEFCLHTARQYALDRIQFGVPLARNQLVQKKLADM 339 V+G A+ L + YA R+QFG P+A QLVQ LADM Sbjct: 252 HVIGIAQRALDLSLDYAKTRVQFGQPIAGFQLVQGMLADM 291 Lambda K H 0.320 0.136 0.408 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: 353 Number of extensions: 15 Number of successful extensions: 4 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: 438 Length of database: 388 Length adjustment: 31 Effective length of query: 407 Effective length of database: 357 Effective search space: 145299 Effective search space used: 145299 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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