Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_015929943.1 MNOD_RS15885 phenylacetic acid degradation bifunctional protein PaaZ
Query= BRENDA::P77455 (681 letters) >NCBI__GCF_000022085.1:WP_015929943.1 Length = 685 Score = 657 bits (1696), Expect = 0.0 Identities = 354/660 (53%), Positives = 444/660 (67%), Gaps = 13/660 (1%) Query: 22 IHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIERAAMLKAVAKHLLSEKER 81 I AI G + ++ GLDMAA A G PALRA+TF ERA L+A+A HL + K+ Sbjct: 23 IPSAIDGRIVARSSTRGLDMAAMVHHARTVGGPALRALTFHERADRLRALATHLTAHKDA 82 Query: 82 FYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTLWPEDELIPLSKEGGFAAR 141 L+A TGAT+ D+ DI+GGIGTLF YAS G RELP + PLS+ G F Sbjct: 83 LAELAADTGATKRDNAFDIDGGIGTLFAYASRGRRELPAQRFVVDGGPEPLSRGGSFLGM 142 Query: 142 HLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPATATAQLTQAMVKSIVDSG 201 H++T GVAVH+NAFNFPCWGMLEKLAP+ L G+P I KPATATA + +A+V+ IV++ Sbjct: 143 HVMTPLRGVAVHVNAFNFPCWGMLEKLAPSILAGVPVITKPATATAYVAEAVVRLIVEAD 202 Query: 202 LVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQPNIVAKSIPFTMEADSLN 261 ++P+GA+ L+CGSAGDLLDHL QDV++FTGSAAT Q+LR P + +++ F E DSLN Sbjct: 203 VLPKGALQLLCGSAGDLLDHLAGQDVLSFTGSAATSQVLRDHPAVSRQAVRFIAERDSLN 262 Query: 262 CCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIVPQALVNAVSDALVARLQK 321 VLG D PEF LF++EVVREMT KAGQKCTAIRR+IVP+AL AV AL A+L Sbjct: 263 AAVLGPDAAEGTPEFNLFVKEVVREMTVKAGQKCTAIRRVIVPRALEPAVIGALKAQLAA 322 Query: 322 VVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLGGQADLSA------AGAFF 375 V VGDP +E V+MG L + QRA +E V +A EI G ++A AGAF Sbjct: 323 VPVGDPRREDVRMGPLASLSQRAATREAV-AEIAREAEIVFGDPETVTAIGADPEAGAFM 381 Query: 376 PPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAGGGSLAGTLVTADPQIA 435 P LL CP P A HA EAFGPVAT+M + A+ L G GSL ++VTADP++A Sbjct: 382 APVLLRCPDPLRAVAPHAVEAFGPVATVMAYDDLDDAVALVAKGEGSLVASVVTADPEVA 441 Query: 436 RQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAGGGEELGGLRAVKHYMQ 495 + A HGR+ +L+ + AKESTGHGSPLP LVHGGPGRAGGGEELGGLR V HY+Q Sbjct: 442 ESLVFGIAAHHGRVHVLDRDCAKESTGHGSPLPGLVHGGPGRAGGGEELGGLRGVFHYLQ 501 Query: 496 RTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSLLTPRRTMTEADIVNF 555 RTAVQGSP L+A+++ W+ GA HPFR+ ++ L GD++ TP R +T DI +F Sbjct: 502 RTAVQGSPARLSALTRTWLSGAPAPVTAEHPFRRDYDALAVGDTVETPSRVITLDDIEHF 561 Query: 556 ACLSGDHFYAHMDKIAA-AESIFGERVVHGYFVLSAAAGLFVDAGVGPVIANYGLESLRF 614 A +GD FYAHM++ AA A F RV HGY +LS AAGLFVD GP++ANYGL++LRF Sbjct: 562 ASFTGDTFYAHMNEEAAKANPFFPGRVAHGYLILSFAAGLFVDPAPGPLLANYGLDNLRF 621 Query: 615 IEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQHQTPVALYSILTLVAR 674 ++PV PGD I+VRLT K+K + A + G V W VEVFNQ VA Y +LT+ AR Sbjct: 622 LKPVSPGDAIRVRLTVKQK-----QPARKPEYGEVRWDVEVFNQDGETVARYELLTMSAR 676 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: 1184 Number of extensions: 61 Number of successful extensions: 5 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: 685 Length adjustment: 39 Effective length of query: 642 Effective length of database: 646 Effective search space: 414732 Effective search space used: 414732 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 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