Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_043917695.1 jaqu_RS04205 acyl-CoA dehydrogenase family protein
Query= BRENDA::Q3JP94 (395 letters) >NCBI__GCF_000877395.1:WP_043917695.1 Length = 387 Score = 188 bits (478), Expect = 2e-52 Identities = 118/375 (31%), Positives = 190/375 (50%), Gaps = 2/375 (0%) Query: 18 LADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPGL 77 L +D +R+ H +AQ ++ P +E ++ EMGE+GLLG T+PE+ GG G+ Sbjct: 10 LGEDVEALREMVHRWAQDRVKPMASEIDGSNAFPNDLWSEMGELGLLGITVPEEDGGAGM 69 Query: 78 DYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCFG 137 Y+++ + E+ R + S+L + I G QK +YLP L +G +G Sbjct: 70 GYLAHTVAIEEIARASASVSLSYGAHSNLCVNQIALNGDADQKARYLPDLISGAAVGALA 129 Query: 138 LTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRGF 196 ++E GSD M RA K Y L+G+K WITN P A VV+AK D E G I F Sbjct: 130 MSEAGAGSDVVGMKLRADKRNDRYVLNGTKYWITNGPDASTLVVYAKTDPEAGSRGITAF 189 Query: 197 ILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSARY 255 ++EK KG S K+G+R S T E++ ++ VP EN+L +G++ + L+ R Sbjct: 190 LVEKAMKGFSTSPHFDKLGMRGSNTAELIFEDVEVPFENVLGEEGRGVQVLMSGLDYERV 249 Query: 256 GIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLGR 315 +A LG +C Y+ +R+QFG+P+ + QL+Q K+ADM T + V + Sbjct: 250 VLAGIGLGIMAACLDEIMPYLAERRQFGKPIGSFQLMQGKIADMYTAMNSARAYVYEAAK 309 Query: 316 MKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYEG 375 D G + + + +A+ A A +GG G ++ V+R + +++ G Sbjct: 310 ACDRGEVTRQDAAACCLYASEQAMVQAHQAVQAMGGAGFMNDTPVSRLFRDAKLMEIGAG 369 Query: 376 THDIHALILGRAQTG 390 T +I +++GR G Sbjct: 370 TSEIRRMLVGRELMG 384 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: 335 Number of extensions: 14 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: 395 Length of database: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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