Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate Ac3H11_3089 Benzaldehyde dehydrogenase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_3089 Length = 520 Score = 405 bits (1042), Expect = e-117 Identities = 230/511 (45%), Positives = 308/511 (60%), Gaps = 6/511 (1%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L +F +G WQ G G + + G AL V + GLD+A A FA + G ALRA T+ E Sbjct: 5 LPNFAAGRWQHGTGPGTALWDPVLGTALVRVDAAGLDLAEAFAFARDMGGAALRAATYRE 64 Query: 64 RAAMLKAVAKHLLSEKERFYALS-AQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDT 122 RAAML AV K L + ++ +Y ++ A G + DS VDI+G I TL YA G L D Sbjct: 65 RAAMLAAVVKVLQTHRDSYYDIATANAGTVKNDSAVDIDGAIFTLGQYARWGDA-LGDVR 123 Query: 123 LWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKP 182 + + L KE F ++HL + GVA+ INAFNFP WG+ EK AP L GMP I+KP Sbjct: 124 ALRDGGAVKLGKEPVFLSQHLQVPRQGVALFINAFNFPAWGLWEKAAPALLSGMPVIVKP 183 Query: 183 ATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRV 242 ATATA LTQ MV+ +VD+G++P GA+S+I GS+ L+D L DVV+FTGSA T ++R Sbjct: 184 ATATAWLTQRMVQDVVDAGVLPVGALSVIAGSSAGLMDQLQPFDVVSFTGSAETAGVIRA 243 Query: 243 QPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRII 302 + +S+ +EADSLN +L P F L +REVVREMT K+GQKCTAIRRI+ Sbjct: 244 HAAVAQRSVRANIEADSLNSALLLPGEAPGSEAFNLLVREVVREMTVKSGQKCTAIRRIL 303 Query: 303 VPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRL 362 VP + +A ++A+ A+L + VG+P +GV+MG+LV+ Q A V+E + L A + Sbjct: 304 VPADVYDAAAEAIGAKLAGITVGNPRNDGVRMGSLVSRAQLASVREGLVTLQAHATVLHD 363 Query: 363 GGQADL----SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418 G L A A P LL D VH E FGPVATL+P ++ HA+ LA Sbjct: 364 GRHQPLVDADPAVAACMGPVLLGARDADAAQPVHDVEVFGPVATLLPYRDSAHAIALAQR 423 Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478 G GSL +L +D A +HGR+ ++ + A+ +GHG+ +P HGGPGRA Sbjct: 424 GQGSLVTSLYGSDEAALAHTALAVAASHGRVHVVTPDVAQTHSGHGNVMPMSQHGGPGRA 483 Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAI 509 GGG ELGGLRA+ Y QR+AVQ SP +LAA+ Sbjct: 484 GGGAELGGLRALDFYHQRSAVQASPAVLAAL 514 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: 826 Number of extensions: 34 Number of successful extensions: 3 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: 520 Length adjustment: 37 Effective length of query: 644 Effective length of database: 483 Effective search space: 311052 Effective search space used: 311052 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