Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_004321123.1 C665_RS15135 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_000310185.1:WP_004321123.1 Length = 395 Score = 729 bits (1881), Expect = 0.0 Identities = 354/395 (89%), Positives = 379/395 (95%) Query: 1 MATNRVTFDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNEM 60 MA+N+ +F+W DPL LD QLT+TERMVRD+ARAYSQ++LLPRVQEAFRHEKTD AIF EM Sbjct: 1 MASNKASFNWEDPLLLDLQLTETERMVRDTARAYSQDKLLPRVQEAFRHEKTDAAIFREM 60 Query: 61 GELGLLGATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSEE 120 GELGLLGATIPEQYGGSG+NYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFG+E Sbjct: 61 GELGLLGATIPEQYGGSGLNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGTEA 120 Query: 121 TKQKYLPKLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIADV 180 KQKYLPKLATGEW+GCFGLTEPNHGSDPGSM+TRARKVDGG+SLSG+KMWITNSPIADV Sbjct: 121 QKQKYLPKLATGEWIGCFGLTEPNHGSDPGSMITRARKVDGGFSLSGSKMWITNSPIADV 180 Query: 181 FVVWAKDDAGDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFPTVR 240 FVVWAKDD G IRGF+LEKGWKGLSAPAIHGKVGLRASITGEIVMDEVF PEENAFPTVR Sbjct: 181 FVVWAKDDEGQIRGFILEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFVPEENAFPTVR 240 Query: 241 GLKGPFTCLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLADMLT 300 GLKGPFTCLNSAR+GIAWGALGAAEACYETARQYTMDR QFGRPLAANQLIQKKLADMLT Sbjct: 241 GLKGPFTCLNSARFGIAWGALGAAEACYETARQYTMDRNQFGRPLAANQLIQKKLADMLT 300 Query: 301 EITLGLQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEFCIA 360 EITLGLQ LR+GR+KDEG APVE+TSI+KRNSCGK+LDIAR+ARDMLGGNGISDE+ +A Sbjct: 301 EITLGLQAVLRVGRMKDEGIAPVEITSIIKRNSCGKALDIARMARDMLGGNGISDEYPVA 360 Query: 361 RHLVNLEVVNTYEGTHDIHALILGRAITGLAAFSN 395 RHLVNLEVVNTYEGTHD+HALILGRAITGLAAFSN Sbjct: 361 RHLVNLEVVNTYEGTHDVHALILGRAITGLAAFSN 395 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: 602 Number of extensions: 16 Number of successful extensions: 1 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: 395 Length adjustment: 31 Effective length of query: 364 Effective length of database: 364 Effective search space: 132496 Effective search space used: 132496 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