Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_058931418.1 AU252_RS15050 phenylacetic acid degradation bifunctional protein PaaZ
Query= BRENDA::P77455 (681 letters) >NCBI__GCF_001484605.1:WP_058931418.1 Length = 700 Score = 599 bits (1544), Expect = e-175 Identities = 333/695 (47%), Positives = 445/695 (64%), Gaps = 27/695 (3%) Query: 1 MQQLASFLSGTW---QSGRGRSRL-IHHAISGEALWEVTSEGLDMAAARQFAIEKGAPAL 56 +Q + SF+ +W +G S + + A +GE L +V+++GLD+AA + G L Sbjct: 12 VQTVPSFVQDSWWTPDAGSAASAVPVRDASTGEVLAKVSTDGLDLAAVVDYGRTTGQTEL 71 Query: 57 RAMTFIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSR 116 +TF +RA LK +A++L + +E FY SAQTGAT+ DS +DI+GGIG LFT+ S G R Sbjct: 72 GKLTFHQRALKLKELAQYLNARREHFYTFSAQTGATKIDSMIDIDGGIGVLFTFGSKGRR 131 Query: 117 ELPDDTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGM 176 ELP+ + + + LSK+G F A H+ T GVAV INAFNFP WGMLEKLAP ++ G+ Sbjct: 132 ELPNSQVVVDGPMEVLSKDGSFVAEHIYTRIPGVAVQINAFNFPVWGMLEKLAPAFIAGV 191 Query: 177 PAIIKPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAAT 236 P I+KPAT T + A+VK+I++S ++P+G++ LI GS LLD LD +D+V FTGSA+T Sbjct: 192 PIIVKPATPTGYVAAAVVKAIIESNILPKGSLQLISGSVRGLLDVLDYRDLVAFTGSAST 251 Query: 237 GQMLRVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCT 296 L+ PN+V + FT E DSLN +LG D PEF FI+ VV EMT KAGQKCT Sbjct: 252 ALSLKSHPNVVQGGVRFTSETDSLNAAILGPDAVEGTPEFDAFIKSVVTEMTVKAGQKCT 311 Query: 297 AIRRIIVPQALVNAVSDALVARL-QKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLA 355 +IRR IVP LV AV A+ R+ ++VV+GDP +GV MGAL + EQ DV+ V +L Sbjct: 312 SIRRAIVPDELVPAVIAAVGRRVDERVVLGDPRADGVTMGALASLEQLTDVRAAVQSMLD 371 Query: 356 AGCEI-----------RLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLM 404 AG E+ GG + AGAF P +L ET A+H+ EAFGPVA+++ Sbjct: 372 AGGELAYGTLDSPSVTSAGGATGVVDAGAFMSPVVLSWADA-ETDAIHSLEAFGPVASVI 430 Query: 405 PAQNQRHALQLACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHG 464 ++ A++LA GGGSL ++ T DP +AR+ + A HGR+ +LN E A+ STGHG Sbjct: 431 GYKDLPDAVRLAARGGGSLVASVCTNDPAVARELVTGIAAHHGRVLMLNREDARSSTGHG 490 Query: 465 SPLPQLVHGGPGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGA----KVE 520 SP+P LVHGGPGRAGGGEELGG+R+V H+MQRTA+QGSP ML A++ W GA VE Sbjct: 491 SPVPHLVHGGPGRAGGGEELGGIRSVMHHMQRTAIQGSPNMLTAVTGLWHAGADRNFTVE 550 Query: 521 EDRIHPFRKYFEELQPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAA-AESIFGE 579 + HPFRK L+ GD++ + R ++ ADI FA +GD FYAH ++ AA A F Sbjct: 551 TEGTHPFRKSLASLRIGDAVRSDLRQVSLADISAFANSTGDTFYAHTNQEAAEANPFFPG 610 Query: 580 RVVHGYFVLSAAAGLFVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQR 639 V HGY +LS AAGLFV+ GPV+ANYGLE+LRFI PV GD+I+V LT K+ T + Sbjct: 611 IVAHGYLLLSWAAGLFVEPAPGPVLANYGLENLRFITPVAAGDSIRVTLTAKKITPR--- 667 Query: 640 SAEEKPTGVVEWAVEVFNQHQTPVALYSILTLVAR 674 E G V W + NQ+ VA Y +LTLV + Sbjct: 668 --ETDEYGEVAWDALLTNQNDDIVATYDVLTLVEK 700 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: 1075 Number of extensions: 39 Number of successful extensions: 6 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: 700 Length adjustment: 39 Effective length of query: 642 Effective length of database: 661 Effective search space: 424362 Effective search space used: 424362 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 Apr 09 2024. 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