Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_011382620.1 AMB_RS00880 3,4-dehydroadipyl-CoA semialdehyde dehydrogenase
Query= BRENDA::P77455 (681 letters) >NCBI__GCF_000009985.1:WP_011382620.1 Length = 515 Score = 466 bits (1199), Expect = e-135 Identities = 248/512 (48%), Positives = 329/512 (64%), Gaps = 5/512 (0%) Query: 1 MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60 M +L S+L+G WQ G G + +SGE L + +GLD+A A FA ++G PALRA++ Sbjct: 1 MIRLQSYLAGRWQDGAGSGAQLKDPVSGEVLATASGDGLDIAEALAFARDRGGPALRALS 60 Query: 61 FIERAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELP 119 F RA ++ A+A L +ER+ ++ A +G T D+ +D++GGIGTL YAS+G R+L Sbjct: 61 FAGRAGLINALAGVLAENRERYNTVALANSGNTAVDAGLDVDGGIGTLKYYASIG-RKLG 119 Query: 120 DDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAI 179 + L E L+K+ F RH+ TS GVAVHINAFNFP WG+ EK A + L G+P + Sbjct: 120 EARLLAEATDDQLTKDEAFRGRHIWTSNRGVAVHINAFNFPSWGLWEKAAVSLLAGVPFL 179 Query: 180 IKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQM 239 KPATAT+ L MVK +V +G++PEGA+SL+CG DL+DHL DVV FTGSA T Sbjct: 180 AKPATATSWLAYEMVKDVVAAGVLPEGAMSLLCGGGRDLMDHLKPGDVVAFTGSAETAAQ 239 Query: 240 LRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIR 299 LR PN++A ++ F +EADSLN C LG D PD PEFA FI+EV REMT KAGQKCTAIR Sbjct: 240 LRSNPNVIAANVRFAVEADSLNLCALGPDAAPDAPEFAAFIKEVSREMTVKAGQKCTAIR 299 Query: 300 RIIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCE 359 R++VP++ V+ V AL L K ++GDP EGV+MG LV+ Q + L A Sbjct: 300 RVLVPRSRVDDVVAALKPALAKALMGDPRTEGVRMGPLVSRAQTVAAWAGLEALKAETQV 359 Query: 360 IRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAG 419 + GG D G F P TLL C P AVH E FGPVATLMP + A+ LA G Sbjct: 360 VAGGGNDD---GGCFVPATLLLCNDPLAARAVHEIEVFGPVATLMPYDSVEQAVDLAHKG 416 Query: 420 GGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAG 479 GGSLA ++ + D F+ A +HGR+ +++ A +GHG +P +HGGPGRAG Sbjct: 417 GGSLAASVFSGDAAFLAGFVPAIATSHGRVLVVDSSVAASHSGHGVVMPHCIHGGPGRAG 476 Query: 480 GGEELGGLRAVKHYMQRTAVQGSPTMLAAISK 511 GGEELGGLR ++ YMQR+A+QGS +ML A+++ Sbjct: 477 GGEELGGLRGLRFYMQRSAIQGSRSMLDAMTQ 508 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: 843 Number of extensions: 35 Number of successful extensions: 4 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: 515 Length adjustment: 37 Effective length of query: 644 Effective length of database: 478 Effective search space: 307832 Effective search space used: 307832 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 17 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