Align glutaryl-CoA dehydrogenase (ETF) (EC 1.3.8.6) (characterized)
to candidate WP_085219040.1 B9N75_RS12195 acyl-CoA dehydrogenase
Query= BRENDA::B0EVL5 (395 letters) >NCBI__GCF_900177405.1:WP_085219040.1 Length = 396 Score = 568 bits (1463), Expect = e-166 Identities = 283/396 (71%), Positives = 326/396 (82%), Gaps = 3/396 (0%) Query: 1 MATNRVT-FDWADPLYLDSQLTDTERMVRDSARAYSQERLLPRVQEAFRHEKTDRAIFNE 59 M R+T FDWADP LD+QLTD ERMVRD+A Y+QE+L PRV +A+ +E DR I NE Sbjct: 1 MTEPRITSFDWADPFGLDAQLTDEERMVRDTAEGYAQEKLQPRVTKAYLNEDFDREIMNE 60 Query: 60 MGELGLLGATIPEQYGGSGMNYVCYGLIAREVERVDSGYRSMMSVQSSLVMVPINEFGSE 119 +G LGL+GATI +YGG+G+ YV YGLIAR VERVDSGYRS MSVQSSLVM PIN +G+E Sbjct: 61 LGALGLIGATIAPEYGGAGLGYVSYGLIARAVERVDSGYRSAMSVQSSLVMHPINAYGTE 120 Query: 120 ETKQKYLPKLATGEWVGCFGLTEPNHGSDPGSMVTRARKVDGGYSLSGAKMWITNSPIAD 179 E ++KYLPKLA+GEWVGCFGLTEP+ GSDPGSM TRA+K+DGGY LSGAKMWITNSPIAD Sbjct: 121 EQRKKYLPKLASGEWVGCFGLTEPDAGSDPGSMRTRAQKIDGGYRLSGAKMWITNSPIAD 180 Query: 180 VFVVWAKDDA--GDIRGFVLEKGWKGLSAPAIHGKVGLRASITGEIVMDEVFCPEENAFP 237 VFVVWAK +A G I+GFVLEKG KGL+AP + K+ LRASITGEIVMD V PEEN P Sbjct: 181 VFVVWAKSEAHDGKIKGFVLEKGMKGLTAPKVKEKLSLRASITGEIVMDGVEIPEENLLP 240 Query: 238 TVRGLKGPFTCLNSARYGIAWGALGAAEACYETARQYTMDRKQFGRPLAANQLIQKKLAD 297 V GLKGPF CLN ARYGIAWG++GAAEAC+ AR YT+DRKQFGRPLAA QL+Q KLA+ Sbjct: 241 NVEGLKGPFGCLNRARYGIAWGSMGAAEACFHAARLYTLDRKQFGRPLAATQLVQMKLAN 300 Query: 298 MLTEITLGLQGCLRLGRLKDEGNAPVELTSIMKRNSCGKSLDIARVARDMLGGNGISDEF 357 MLT+I+LGLQ LR+GR DEG E S++KRN+CGK+LDIAR+ARDM GGNGIS EF Sbjct: 301 MLTDISLGLQAALRVGRRMDEGVLIPETISLIKRNNCGKALDIARIARDMHGGNGISAEF 360 Query: 358 CIARHLVNLEVVNTYEGTHDIHALILGRAITGLAAF 393 + RH NLE VNTYEGTHD+H LILGRAITG+AAF Sbjct: 361 QVMRHAANLETVNTYEGTHDVHGLILGRAITGIAAF 396 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: 513 Number of extensions: 16 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: 396 Length adjustment: 31 Effective length of query: 364 Effective length of database: 365 Effective search space: 132860 Effective search space used: 132860 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