Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_034411531.1 H566_RS0112825 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Query= BRENDA::P77455 (681 letters) >NCBI__GCF_000482785.1:WP_034411531.1 Length = 522 Score = 394 bits (1012), Expect = e-114 Identities = 223/512 (43%), Positives = 310/512 (60%), Gaps = 6/512 (1%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L +FL G W +G+G S+ + ++GEAL V+S GLD+ A FA E+G ALRAM++ + Sbjct: 6 LPNFLGGEWVAGQGESQTLTDPVTGEALVRVSSAGLDLKAGFAFARERGGAALRAMSYGQ 65 Query: 64 RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122 RAAML AV K L + ++ + A+S A +G T+AD+ VD++G + TL +A G+ L + Sbjct: 66 RAAMLGAVLKVLQANRDSYEAISTANSGTTKADTAVDVDGAMFTLGWFAKAGAA-LGEAR 124 Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182 + L+K+ F ++HLL G+A+ INAFNFP WG+ EK AP L G+P ++KP Sbjct: 125 ALLDGPAARLAKDDVFRSQHLLLPARGLALFINAFNFPAWGLWEKAAPALLSGVPVVVKP 184 Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242 ATATA LTQ MV +V +G++P GA+S++CG +G LLD L +DVV+FTGSAAT +R Sbjct: 185 ATATAWLTQKMVADVVAAGVLPAGALSIVCGGSGGLLDALAGEDVVSFTGSAATAATIRG 244 Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302 S+ +EADSLN +L D P F LF+REVVREMT K+GQKCTAIRR+ Sbjct: 245 HAAFREHSVRLNVEADSLNSALLLPDAAPGSDAFNLFVREVVREMTVKSGQKCTAIRRVF 304 Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362 VP +AV++A+ A+L + VG+P E V+MG+LV+ +Q V++ + L + Sbjct: 305 VPAERYDAVAEAIGAKLAGIRVGNPRDESVRMGSLVSRDQYRTVRDGIAALRGVAEVLHD 364 Query: 363 GGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418 G L A A PTLL VH E FGPVATL+P + A L Sbjct: 365 GDSHALVGADPAVAACVGPTLLGARDAAAATLVHDLEVFGPVATLLPYASLDEAHALVRR 424 Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478 G GSL +L AD HGR+ +++ + TGHG+ +PQ +HGGPGRA Sbjct: 425 GQGSLVASLYGADHAALAASCLALGDLHGRLHVVSPDCGAAHTGHGNVMPQSLHGGPGRA 484 Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAIS 510 GGGEELGGLR + Y +R AVQ +P +L A++ Sbjct: 485 GGGEELGGLRGLGFYHRRCAVQAAPAVLEALA 516 Lambda K H 0.319 0.134 0.395 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: 848 Number of extensions: 45 Number of successful extensions: 6 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: 681 Length of database: 522 Length adjustment: 37 Effective length of query: 644 Effective length of database: 485 Effective search space: 312340 Effective search space used: 312340 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: 53 (25.0 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