Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate Pf1N1B4_4787 Butyryl-CoA dehydrogenase (EC 1.3.99.2)
Query= BRENDA::B0EVL5 (395 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4787 Length = 375 Score = 200 bits (508), Expect = 6e-56 Identities = 121/369 (32%), Positives = 186/369 (50%), Gaps = 5/369 (1%) Query: 22 DTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMNY 81 D + + D+AR ++QERL P E R + + EM LG G +PEQ+GG Y Sbjct: 5 DEQLQISDAARQFAQERLKPFAAEWDREHRFPKEAIGEMAGLGFFGMLVPEQWGGCDTGY 64 Query: 82 VCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGLT 141 + Y + E+ D ++MSV +S+ VPI +FG+++ K+++L LA+G +G F LT Sbjct: 65 LAYAMALEEIAAGDGACSTIMSVHNSVGCVPILKFGNDDQKERFLKPLASGAMLGAFALT 124 Query: 142 EPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAKDDAG----DIRGFVL 197 EP GSD S+ TRAR Y L+G K +IT+ A V +V+A D I ++ Sbjct: 125 EPQAGSDASSLKTRARLDGDHYVLNGCKQFITSGQNAGVVIVFAVTDPSAGKRGITALIV 184 Query: 198 EKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARYGI 256 G + K+G AS T +I+ ++V P N G K L R GI Sbjct: 185 PTDSPGYKVARVEDKLGQHASDTCQILFEDVKVPVANRLGEEGEGYKIALANLEGGRVGI 244 Query: 257 AWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLK 316 A ++G A A +E AR Y +R+ FG+P+ +Q + +LADM T+I + Q L+ Sbjct: 245 ASQSVGMARAAFEAARDYARERESFGKPIIEHQAVAFRLADMATQIAVARQMVHYAAALR 304 Query: 317 DEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTH 376 D G + S+ K + + + A LGG G ++F + R ++ V YEGT Sbjct: 305 DSGKPALVEASMAKLFASEMAEKVCSSALQTLGGYGYLNDFPLERIYRDVRVCQIYEGTS 364 Query: 377 DIHALILGR 385 DI +++ R Sbjct: 365 DIQRMVISR 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: 318 Number of extensions: 9 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 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