Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_055435174.1 ASC41_RS03050 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_001418085.1:WP_055435174.1 Length = 390 Score = 154 bits (390), Expect = 3e-42 Identities = 116/380 (30%), Positives = 189/380 (49%), Gaps = 10/380 (2%) Query: 16 LDSQ-LTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQY 74 +DS+ T+ + R S + Q+ ++P + + + +R I+ + GE+G G PE Y Sbjct: 1 MDSRYFTEEHNLFRQSLADFLQKEVVPHIDKWEKTGHIERFIWEKFGEMGFFGIAYPEAY 60 Query: 75 GGSGMNYVCYGLIAREVERVDSG-YRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGE 133 GG ++ + E+++V+SG + + M + L M +N GSEE KQKYL K TGE Sbjct: 61 GGMDLDLFYTVIFLEELQKVNSGGFAAAMWAHAYLAMTHVNAEGSEEIKQKYLTKSITGE 120 Query: 134 WVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAK--DDAGD 191 ++G +TEP GSD M T A K Y L+G+K +ITN +D VV AK + G+ Sbjct: 121 FIGAMAVTEPFGGSDVAGMRTTAVKEGNTYVLNGSKTFITNGVYSDYIVVAAKTSPELGN 180 Query: 192 --IRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVRGLKGPFTCL 249 I F++++ KG+SA + K+G RAS TGEI D V P + G P+ Sbjct: 181 KGISMFIVDRDTKGVSATKL-DKLGWRASDTGEIAFDNVVIPASHLMGE-EGKGFPYIMQ 238 Query: 250 NSARYGIAWG--ALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQ 307 + A + G A AE E A +Y +R+ FG+ + Q ++ +AD ++ + + Sbjct: 239 HFAFERLIMGVNAHARAEFALEYAVKYMGERQAFGKSIDKFQALRHTMADCYADMEVCKE 298 Query: 308 GCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLE 367 + D+ V+ +I K S + D+ MLGG G +E+ +AR L + Sbjct: 299 FNYTVAARLDKNEYVVKEATISKLRSTKMADDVIYQCLQMLGGYGYMEEYPMARLLRDSR 358 Query: 368 VVNTYEGTHDIHALILGRAI 387 + GT +I I+ + + Sbjct: 359 LGPIGGGTSEILREIIAKMV 378 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: 355 Number of extensions: 17 Number of successful extensions: 4 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: 390 Length adjustment: 31 Effective length of query: 364 Effective length of database: 359 Effective search space: 130676 Effective search space used: 130676 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 24 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