Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_041096878.1 SUTH_RS02630 isovaleryl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_000828635.1:WP_041096878.1 Length = 388 Score = 195 bits (496), Expect = 2e-54 Identities = 129/378 (34%), Positives = 196/378 (51%), Gaps = 13/378 (3%) Query: 18 LADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGL 77 L +D M+RDA +AQ ++ PR E R A ++++ G++GLLG T E+YGG + Sbjct: 8 LGEDVDMLRDAVWQFAQKEILPRAAEIDRDNLFPADLWKKFGDMGLLGMTADEEYGGTKM 67 Query: 78 DYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFG 137 Y+++ + E+ R + S+L + I G++AQK KYLPKL +GE +G Sbjct: 68 GYLAHIVAMEEISRASASVGLSYGAHSNLCVNQIRRNGNEAQKAKYLPKLISGEHVGALA 127 Query: 138 LTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLDED-GRDEIRGF 196 ++EP GSD SM RA Y L+GSKMWITN AD VV+AK D G + F Sbjct: 128 MSEPGAGSDVVSMKLRADLKGDRYVLNGSKMWITNGGDADTLVVYAKTSPDAGARGMTAF 187 Query: 197 ILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSARY 255 I+EKG G S K+G+R S T + D+ VP EN++ G R + L+ R Sbjct: 188 IVEKGFAGFSKGQHLDKLGMRGSNTYPLFFDDCEVPAENVMGGEGNGTRVLMSGLDYERA 247 Query: 256 GIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGR 315 ++ G LG +C + ++ +RKQFG+ + QL+Q KLADM + V LG+ Sbjct: 248 VLSGGPLGIMAACMDVVLPFIHERKQFGQSIGEFQLMQGKLADMYSTWQATRAYVYALGK 307 Query: 316 MKDEGTAAVEITSIMKRNSCG-------KALDIARLARDMLGGNGISDEFGVARHLVNLE 368 D G A +++++ G KA +A A LGG G ++E+ R + + Sbjct: 308 ACDRGDHA----RTLRKDAAGAILYSAEKATWMAGEAIQALGGVGYTNEYPAGRLWRDAK 363 Query: 369 VVNTYEGTHDIHALILGR 386 + GT +I +++GR Sbjct: 364 LYEIGAGTSEIRRMLIGR 381 Lambda K H 0.320 0.138 0.414 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: 370 Number of extensions: 18 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: 395 Length of database: 388 Length adjustment: 31 Effective length of query: 364 Effective length of database: 357 Effective search space: 129948 Effective search space used: 129948 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 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