Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate PP_3270 PP_3270 oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Putida:PP_3270 Length = 684 Score = 755 bits (1949), Expect = 0.0 Identities = 397/678 (58%), Positives = 483/678 (71%), Gaps = 8/678 (1%) Query: 4 LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63 L SF++G W G ++ + A+ G L E D A A +A +G +L M F + Sbjct: 7 LQSFIAGRWLGQHG-AQALRSALDGHVLAYSHEERPDFAEAVDYARARGLASLMGMDFQQ 65 Query: 64 RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123 RA LKA+A +L KE+ YALS +GATRADSW+DIEGG TLF+YA +GSRELP L Sbjct: 66 RAQRLKALALYLAECKEQLYALSHHSGATRADSWIDIEGGNATLFSYAGIGSRELPSGNL 125 Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183 E IPL K+G FA H+L ++GVAVHINAFNFP WGMLEK APT+L GMP I+KPA Sbjct: 126 VHEGPAIPLGKQGHFAGSHILVPRAGVAVHINAFNFPIWGMLEKFAPTFLAGMPCIVKPA 185 Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243 T+T+ LT+A+V+ + SGL+PEG++ L+ GS GDLLD L QDVVTFTGSA T LRV Sbjct: 186 TSTSYLTEAVVRLMNASGLLPEGSLQLVIGSTGDLLDRLQGQDVVTFTGSADTAAKLRVT 245 Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303 PN++ S+PFT EADSLNC +LG DV+PD EF L+I+EVVREMTTKAGQKCTAIRR IV Sbjct: 246 PNLIRNSVPFTAEADSLNCAILGPDVSPDSEEFDLYIKEVVREMTTKAGQKCTAIRRAIV 305 Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLG 363 P ++AV+ L RL KVVVGDP+ EGV+MGAL + +Q+ DV E+V LL + C+ G Sbjct: 306 PARHLDAVATRLRERLSKVVVGDPSLEGVRMGALASHDQQRDVGERVRSLLQS-CDQLFG 364 Query: 364 GQADLS------AAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLAC 417 + A GAFF PTLL P H EAFGPV+TLM + AL LA Sbjct: 365 ASDGFAPRGEGVAEGAFFAPTLLQARDPHAEGGAHDIEAFGPVSTLMAYDDLDEALALAA 424 Query: 418 AGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGR 477 G GSL TLVTAD +A + I AA HGR+ +L+ ++AKESTGHGSPLPQL HGGPGR Sbjct: 425 RGKGSLVATLVTADRSVAAKAIPVAAAWHGRLLVLDSQAAKESTGHGSPLPQLKHGGPGR 484 Query: 478 AGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPG 537 AGGGEELGGLRAVKHY+QR AVQGSP+ML A++ ++VRG +V E +HPFR+YFE+L+ G Sbjct: 485 AGGGEELGGLRAVKHYLQRAAVQGSPSMLTAVTGEYVRGGEVIETEVHPFRRYFEQLRVG 544 Query: 538 DSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVD 597 +SLLT RRT+TEAD+VNF CLSGDHFY H D+IAA S FG+R+ HGYFVLSAAAGLFV Sbjct: 545 ESLLTHRRTVTEADLVNFGCLSGDHFYMHFDEIAAKASQFGKRIAHGYFVLSAAAGLFVS 604 Query: 598 AGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFN 657 G GPV+ANYGL++LRFI PV GDTIQ RLTCKRK + + S +P GVV W VEV N Sbjct: 605 PGAGPVLANYGLDTLRFINPVGIGDTIQARLTCKRKIDQGKTSPLGQPQGVVAWDVEVTN 664 Query: 658 QHQTPVALYSILTLVARQ 675 Q VA Y ILTLV ++ Sbjct: 665 QLGELVASYDILTLVLKK 682 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: 1140 Number of extensions: 32 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: 681 Length of database: 684 Length adjustment: 39 Effective length of query: 642 Effective length of database: 645 Effective search space: 414090 Effective search space used: 414090 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: 54 (25.4 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