Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_090271903.1 BLU11_RS02525 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_900105005.1:WP_090271903.1 Length = 378 Score = 208 bits (530), Expect = 2e-58 Identities = 133/371 (35%), Positives = 187/371 (50%), Gaps = 5/371 (1%) Query: 20 LTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEMGELGLLGATIPEQYGGSGM 79 + D +R + + AR ++QERLLP E R + EMG+LG LG +PEQ+GG Sbjct: 3 INDEQREITNVARQFAQERLLPFAAEWDREHRFPTEALAEMGQLGFLGMLVPEQWGGCDT 62 Query: 80 NYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEETKQKYLPKLATGEWVGCFG 139 Y+ Y L E+ D ++MSV +S+ PI FGSEE K ++LP LA GE +G F Sbjct: 63 GYLTYALALEEIAAGDGACSTIMSVHNSVGCAPILRFGSEEQKDRFLPPLARGEQIGGFA 122 Query: 140 LTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADVFVVWA--KDDAG--DIRGF 195 LTEP+ GSD GS+ TRAR+ Y L GAK +IT+ A +V+A DAG I F Sbjct: 123 LTEPHAGSDAGSLRTRARRDGDSYVLDGAKQFITSGREAGTVIVFAVTDPDAGKRGITAF 182 Query: 196 VLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAF-PTVRGLKGPFTCLNSARY 254 ++ G + K+G AS T +I D + N G + L R Sbjct: 183 IVPTDSPGYEVVRVEEKLGQHASDTCQIAFDGLRLSAANRLGGEGEGYRIALANLEGGRI 242 Query: 255 GIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLTEITLGLQGCLRLGR 314 GIA A+G A A +E AR Y +R+ FG+ L +Q + +LADM T+I + Q Sbjct: 243 GIAAQAVGMARAAFEVARDYARERQAFGKALTEHQAVAFRLADMATQIAVARQMVHHAAA 302 Query: 315 LKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIARHLVNLEVVNTYEG 374 L+D G + S+ K + + A LGG G +F + R ++ V YEG Sbjct: 303 LRDAGQPALVEASMAKLFASEMAEKACSAAIQTLGGYGYLKDFPLERIYRDVRVCQIYEG 362 Query: 375 THDIHALILGR 385 T DI L++ R Sbjct: 363 TSDIQRLVIAR 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: 343 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: 378 Length adjustment: 30 Effective length of query: 365 Effective length of database: 348 Effective search space: 127020 Effective search space used: 127020 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