Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate AO356_26365 AO356_26365 acyl-CoA dehydrogenase
Query= BRENDA::Q60759 (438 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_26365 Length = 383 Score = 163 bits (413), Expect = 8e-45 Identities = 113/376 (30%), Positives = 175/376 (46%), Gaps = 8/376 (2%) Query: 59 QLTADEKLIRDTFRNYCQERLMSRILLANRNEVFHRDIVYEMGELGVLGPTI-KGYGCAG 117 +LT ++ +IRD R++ + + + +V MGELG+LG + + +G Sbjct: 5 ELTEEQVMIRDMARDFARGEIAPHAQAWEKAGWIDDGLVANMGELGLLGMVVPEEWGGTY 64 Query: 118 VSSVAYGLLTRELERVDSGYRSMMSVQSSLVMHPIYTYGSEEQRQKYLPGLAKGELLGCF 177 V VAY L E+ D ++MS+ +S+ P+ +G++EQ+Q +L LA G+ +GCF Sbjct: 65 VDYVAYALAVEEISAGDGATGALMSIHNSVGCGPVLNFGTDEQKQTWLAELASGQAIGCF 124 Query: 178 GLTEPNHGSDPGGMETRARHNPSNQSYTLSGTKTWITNSPVADLFIVWARCEDNC----I 233 LTEP GS+ + TRA + + ++G K +++N A L IV+A + I Sbjct: 125 CLTEPQAGSEAHNLRTRAELR--DGQWVINGAKQFVSNGKRAKLAIVFAVTDPELGKKGI 182 Query: 234 RGFILEKGMRGLSAPRIEGKFSLRASATGMIIMDSVEVPEENVL-PNVSSLAGPFGCLNT 292 F++ G R E K +RAS T + + + VPE N+L LA L Sbjct: 183 SAFLVPTDTPGFIVDRTEHKMGIRASDTCAVTLSNCTVPEANLLGARGKGLAIALSNLEG 242 Query: 293 ARYGITWGVLGAAEFCLHTARQYALDRIQFGVPLARNQLVQKKLADMLTEITLGLHACLQ 352 R GI LG A A YA DR+QF P+ +Q + LADM T I L Sbjct: 243 GRIGIAAQALGIARAAFEAALAYARDRVQFDKPIIEHQSIANLLADMHTRINATRLLILH 302 Query: 353 LGRLKDQDKATPEMVSMLKRNNCGKALDIARQARDILGGNGISDEYHVIRHAMNLEAVNT 412 RL+ K S K A + A I GG G ++Y V R+ + Sbjct: 303 AARLRSAGKPCLSEASQAKLFASEMAEKVCSSAIQIHGGYGYLEDYPVERYYRDARITQI 362 Query: 413 YEGTHDIHALILGRAI 428 YEG+ +I +++ R + Sbjct: 363 YEGSSEIQRMVIAREL 378 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: 349 Number of extensions: 21 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: 438 Length of database: 383 Length adjustment: 31 Effective length of query: 407 Effective length of database: 352 Effective search space: 143264 Effective search space used: 143264 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