Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate AZOBR_RS22300 AZOBR_RS22300 acyl-CoA dehydrogenase
Query= BRENDA::Q3JP94 (395 letters) >FitnessBrowser__azobra:AZOBR_RS22300 Length = 377 Score = 211 bits (536), Expect = 4e-59 Identities = 127/373 (34%), Positives = 200/373 (53%), Gaps = 2/373 (0%) Query: 17 QLADDERMVRDAAHAYAQGKLAPRVTEAFRHETTDAAIFREMGEIGLLGPTIPEQYGGPG 76 +L +++RMVRD A +A +LAP E R EMG +GL+G +PE++ G G Sbjct: 2 RLTEEQRMVRDMARDFAAERLAPTAAERDRTGAFPKEELAEMGRLGLMGMLVPEEFDGAG 61 Query: 77 LDYVSYGLIAREVERVDSGYRSMMSVQSSLVMVPIFEFGSDAQKEKYLPKLATGEWIGCF 136 D+++Y L E+ D ++MSV +S+ +PI +FGS QKE++L +A GE +GCF Sbjct: 62 TDHIAYALAIEEIAAGDGAISTIMSVHNSVGCMPILKFGSAEQKERFLKPMARGEQLGCF 121 Query: 137 GLTEPNHGSDPGSMVTRARKVPGGYSLSGSKMWITNSPIADVFVVWAKLD-EDGRDEIRG 195 LTEP GSD ++ TRAR+ + L+G+K +IT+ ADV +V+A D E G+ I Sbjct: 122 CLTEPQAGSDAAAIKTRARRDGNHWVLNGTKQFITSGKNADVAIVFAVSDPEAGKKGITA 181 Query: 196 FILEKGCKGLSAPAIHGKVGLRASITGEIVLDEAFVPEENIL-PHVKGLRGPFTCLNSAR 254 F++ G + K+G S T +IVL++ +P + +L G R L R Sbjct: 182 FVVPTDTPGFQVARVEEKLGQSCSDTCQIVLEDCRIPADLMLGAEGGGYRVALANLEGGR 241 Query: 255 YGIAWGALGAAESCWHIARQYVLDRKQFGRPLAANQLIQKKLADMQTEITLGLQGVLRLG 314 GIA ++G A + A +Y +R+ G P+ +Q + +LADM T++ Q VL Sbjct: 242 IGIASQSVGMARAALDHATRYAQERQSMGLPIIQHQAVAFRLADMATKVEAARQLVLHAA 301 Query: 315 RMKDEGTAAVEITSIMKRNSCGKALDIARLARDMLGGNGISDEFGVARHLVNLEVVNTYE 374 ++D G ++ ++ K + A + A + GG G ++F V R ++ V YE Sbjct: 302 SLRDAGEPCLKEAAMAKLFASEIAERVCSDAIQIHGGYGYLNDFPVERIYRDVRVCQIYE 361 Query: 375 GTHDIHALILGRA 387 GT DI L++ RA Sbjct: 362 GTSDIQRLVISRA 374 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: 327 Number of extensions: 17 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: 377 Length adjustment: 30 Effective length of query: 365 Effective length of database: 347 Effective search space: 126655 Effective search space used: 126655 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 17 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