Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate GFF2397 Psest_2445 Acyl-CoA dehydrogenases
Query= BRENDA::B0EVL5 (395 letters) >FitnessBrowser__psRCH2:GFF2397 Length = 379 Score = 204 bits (519), Expect = 3e-57 Identities = 124/373 (33%), Positives = 186/373 (49%), Gaps = 5/373 (1%) Query: 22 DTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMNY 81 + + + + AR ++QERL P ++ R + EM LG G +PEQ+GGS Y Sbjct: 5 EDQNAIAEMARQFAQERLKPFAEQWSREHRYPAEAIGEMAALGFFGMLVPEQWGGSDTGY 64 Query: 82 VCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGLT 141 + Y + E+ D ++MSV +S+ VPI FG+E+ K +L LA GE +G F LT Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILRFGNEQQKSDFLTPLARGEQIGAFALT 124 Query: 142 EPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDD----AGDIRGFVL 197 EP GSD S+ TRAR+ Y L+GAK +IT+ A +V+A D G I F++ Sbjct: 125 EPQAGSDASSLRTRARRDGDHYVLNGAKQFITSGKHAGTVIVFAVTDPDAGKGGISAFIV 184 Query: 198 EKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARYGI 256 G + K+G AS T +I +++ P N G + L R GI Sbjct: 185 PTDSPGYQVVRVEDKLGQHASDTCQIAFEDLRVPVANRLGEEGEGYRIALANLEGGRIGI 244 Query: 257 AWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLK 316 A A+G A A +E AR Y DR+ FG+P+ +Q + +LADM T+I + Q L+ Sbjct: 245 AAQAVGMARAAFEAARDYARDRETFGKPIIEHQAVAFRLADMATQIAVARQMVHHAAALR 304 Query: 317 DEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTH 376 + G + S+ K + + + A LGG G +F + R ++ V YEGT Sbjct: 305 EVGRPALVEASMAKLFASEMAEKVCSAAIQTLGGYGYLADFPVERIYRDVRVCQIYEGTS 364 Query: 377 DIHALILGRAITG 389 DI L++ R + G Sbjct: 365 DIQRLVISRNLGG 377 Lambda K H 0.319 0.136 0.409 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: 319 Number of extensions: 10 Number of successful extensions: 2 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: 379 Length adjustment: 30 Effective length of query: 365 Effective length of database: 349 Effective search space: 127385 Effective search space used: 127385 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