Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate AO353_25680 AO353_25680 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >FitnessBrowser__pseudo3_N2E3:AO353_25680 Length = 375 Score = 207 bits (527), Expect = 4e-58 Identities = 124/370 (33%), Positives = 188/370 (50%), Gaps = 5/370 (1%) Query: 21 TDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMN 80 TD + + D+AR ++QERL P E R + + EM ELG G +PEQ+GG Sbjct: 4 TDEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAELGFFGMLVPEQWGGCDTG 63 Query: 81 YVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGL 140 Y+ Y + E+ D ++MSV +S+ VPI +FG+++ K+++L LA+G +G F L Sbjct: 64 YLAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFAL 123 Query: 141 TEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAG----DIRGFV 196 TEP GSD S+ TRAR Y L+G K +IT+ A V +V+A D I F+ Sbjct: 124 TEPQAGSDASSLKTRARLNGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGISAFI 183 Query: 197 LEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARYG 255 + G + K+G AS T +I+ ++V P N G K L R G Sbjct: 184 VPTDSPGYKVARVEDKLGQHASDTCQILFEDVQVPVANRLGEEGEGYKIALANLEGGRVG 243 Query: 256 IAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRL 315 IA ++G A A +E AR Y +R+ FG+P+ +Q + +LADM T+I + Q L Sbjct: 244 IASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAAL 303 Query: 316 KDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGT 375 +D G + S+ K + + + A LGG G +F + R ++ V YEGT Sbjct: 304 RDSGKPALVEASMAKLFASEMAEKVCSTALQTLGGYGYLSDFPLERIYRDVRVCQIYEGT 363 Query: 376 HDIHALILGR 385 DI +++ R Sbjct: 364 SDIQRMVISR 373 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: 322 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: 375 Length adjustment: 30 Effective length of query: 365 Effective length of database: 345 Effective search space: 125925 Effective search space used: 125925 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