Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate 3610446 Dshi_3827 phenylacetic acid degradation protein paaN (RefSeq)
Query= BRENDA::P77455 (681 letters) >FitnessBrowser__Dino:3610446 Length = 678 Score = 656 bits (1692), Expect = 0.0 Identities = 348/676 (51%), Positives = 447/676 (66%), Gaps = 16/676 (2%) Query: 6 SFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIERA 65 SF +G W + +R+I HA++G L + LD+ A +A + G PALRA+TF +RA Sbjct: 8 SFAAGHWIAPDADARMIAHAVTGAPLARAGNGALDVQAMLDYARDTGGPALRALTFHDRA 67 Query: 66 AMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTLWP 125 MLKA+A HL + K+ Y LS TGAT+AD +DI+GGIGT+F +AS G RE+PD ++ Sbjct: 68 RMLKALALHLGAHKQALYDLSFATGATQADHLIDIDGGIGTVFVFASKGRREMPDAHVYL 127 Query: 126 EDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPATA 185 + E+ LS+ G F +H+ T GVAVHINAFNFP WGMLEKLAPT L GMPAI+KPATA Sbjct: 128 DGEVEQLSRTGTFLGQHIATPLQGVAVHINAFNFPVWGMLEKLAPTLLAGMPAIVKPATA 187 Query: 186 TAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQPN 245 + +T+ V+ I+DSG++P GA+ L+ G GD+LD L QDVV+FTGSA T LR P+ Sbjct: 188 SCYVTEKAVRIILDSGILPAGALQLVTGGLGDMLDRLTCQDVVSFTGSADTALRLRAAPH 247 Query: 246 IVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIVPQ 305 ++ ++ F E DSLN +LG D P PEF LFIREV REMT KAGQKCTAIRRI+ PQ Sbjct: 248 LLRNAVRFVAEQDSLNASILGPDAVPGTPEFDLFIREVAREMTAKAGQKCTAIRRILAPQ 307 Query: 306 ALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLGGQ 365 A V+ V AL ARL K V+GDP MGALV+ Q+ DV K + +A E R+ G Sbjct: 308 AQVDGVIAALGARLAKTVIGDPRDTATTMGALVSNGQKRDVLAKARV-IATEAE-RVFGD 365 Query: 366 ADL-------SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418 + + GAF PP LL+C PD +H TEAFGPV+T+M ++ HA+ L Sbjct: 366 PEAFTVHGADARTGAFLPPMLLHCADPDAAQRLHDTEAFGPVSTVMGYRDLDHAVALVNR 425 Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478 G GSL +L+T DP++ARQ A HGR+ I + +S E+TGHG+PLP ++HGGPGRA Sbjct: 426 GAGSLVASLITHDPEVARQVALGAGAFHGRLYINDRDSMGEATGHGAPLPHMIHGGPGRA 485 Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGD 538 GGGEELGG+R V HYMQRTA+QGSP ML AI +WV GA HPF + F+ L+ G+ Sbjct: 486 GGGEELGGVRGVMHYMQRTAIQGSPDMLTAIGGKWVPGATETPAPAHPFTRGFDALRIGE 545 Query: 539 SLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAES-IFGERVVHGYFVLSAAAGLFVD 597 +L TP R +T ADI +FA +GD FYAHMD AAA + F RV HGY +LS AAGLFVD Sbjct: 546 TLHTPARQVTLADIEHFAAFTGDTFYAHMDDAAAARNPFFPGRVAHGYLLLSFAAGLFVD 605 Query: 598 AGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFN 657 GPV+AN GL+SLRF++PV PGD+++ RLT K KT + E V W V + N Sbjct: 606 PDEGPVLANTGLDSLRFLKPVAPGDSLKARLTVKHKTPRNDAYGE------VRWHVSLTN 659 Query: 658 QHQTPVALYSILTLVA 673 Q VA Y +LT++A Sbjct: 660 QEDDLVAEYELLTMIA 675 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: 1176 Number of extensions: 65 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: 678 Length adjustment: 39 Effective length of query: 642 Effective length of database: 639 Effective search space: 410238 Effective search space used: 410238 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