Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_025764976.1 X939_RS0119550 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_000566685.1:WP_025764976.1 Length = 387 Score = 192 bits (487), Expect = 2e-53 Identities = 118/368 (32%), Positives = 194/368 (52%), Gaps = 5/368 (1%) Query: 25 RMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGMNYVCY 84 R+++++ R ++ + + P + E + +F+ +GELGL+G +PEQYGG+G+ Y Y Sbjct: 18 RLIQETVRDFALKNIQPHIMEWDESQHFPTEVFHSLGELGLMGMLVPEQYGGAGLGYQEY 77 Query: 85 GLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFGLTEPN 144 + +VD M+ +SL I FG+E+ K KYLPKLA+GEW+G +GLTEPN Sbjct: 78 ITAIIALSKVDPSIGLSMAAHNSLCTNHILMFGNEDQKNKYLPKLASGEWIGAWGLTEPN 137 Query: 145 HGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWAK-DDAGDIRG---FVLEKG 200 GSD G+M T A + + L+GAK +ITN V VV + + GD G F++E G Sbjct: 138 TGSDAGNMKTTAVRDGEDWILNGAKNFITNGQSGRVAVVITRTGEPGDKHGATAFIVEHG 197 Query: 201 WKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTV-RGLKGPFTCLNSARYGIAWG 259 G ++ K+G+RAS T E++ ++ + + G L+ R IA Sbjct: 198 THGFTSGRKENKLGMRASETVELLFEDCRISDSQRLGQIGEGFIQSLKILDGGRISIAAL 257 Query: 260 ALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGRLKDEG 319 +G A YE A Y+ +R QFG+ +++ Q I KLADM T+I + G+ KD G Sbjct: 258 GVGTALGAYEAALAYSKERHQFGKAISSFQGIAFKLADMYTDIQASTLLTFQAGKEKDLG 317 Query: 320 NAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEGTHDIH 379 ++ K +S ++ +A A + GG G + ++ + + ++ EGT +I Sbjct: 318 QKVSLSGAVAKYHSSETAVRVATEAVQIYGGYGFTKDYPAEKFYRDSKLCTIGEGTSEIQ 377 Query: 380 ALILGRAI 387 +++ + I Sbjct: 378 KMVISKEI 385 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: 333 Number of extensions: 14 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: 395 Length of database: 387 Length adjustment: 31 Effective length of query: 364 Effective length of database: 356 Effective search space: 129584 Effective search space used: 129584 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