Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_012968367.1 KVAR_RS14390 phenylacetic acid degradation bifunctional protein PaaZ
Query= BRENDA::P77455 (681 letters) >NCBI__GCF_000025465.1:WP_012968367.1 Length = 681 Score = 1187 bits (3070), Expect = 0.0 Identities = 586/679 (86%), Positives = 631/679 (92%) Query: 1 MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60 MQQLAS+LSG WQ+GRGR+R IHHAI+G ALWEVTSEGLDMA AR+FAIE+G AL+AMT Sbjct: 1 MQQLASYLSGAWQTGRGRARTIHHAITGAALWEVTSEGLDMAQARRFAIERGGKALQAMT 60 Query: 61 FIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD 120 FIER+AMLKAVAK LL +K+ FY +SAQTGATRADSWVDIEGGIGTLFTYA LGSRELPD Sbjct: 61 FIERSAMLKAVAKRLLEQKDEFYTISAQTGATRADSWVDIEGGIGTLFTYAGLGSRELPD 120 Query: 121 DTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAII 180 D LWPEDELIPLSK+GGFAARH+LTSKSGVAVHINAFNFPCWGMLEKLAPTWL GMPAII Sbjct: 121 DILWPEDELIPLSKQGGFAARHVLTSKSGVAVHINAFNFPCWGMLEKLAPTWLAGMPAII 180 Query: 181 KPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQML 240 KPATATAQLTQAMVK+IVDSGLVPEGAISLICG AGDLLDHLDSQDVVTFTGSAATGQ L Sbjct: 181 KPATATAQLTQAMVKAIVDSGLVPEGAISLICGGAGDLLDHLDSQDVVTFTGSAATGQQL 240 Query: 241 RVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRR 300 R PN+VAKSIPFTMEADSLNCCVLGEDVTP+QPEFALFI EVVREMT KAGQKCTAIRR Sbjct: 241 RTHPNLVAKSIPFTMEADSLNCCVLGEDVTPEQPEFALFIWEVVREMTAKAGQKCTAIRR 300 Query: 301 IIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEI 360 IIVP A +NAVSDAL++RL KV VGDPAQEG+KMGALVN EQR DVQ+ VN L+A+GCE Sbjct: 301 IIVPLAQINAVSDALISRLHKVTVGDPAQEGIKMGALVNREQRQDVQDNVNKLIASGCEA 360 Query: 361 RLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACAGG 420 LGGQADL+A GAFFPPTLLYCPQPDETP VHA EAFGPVATLMP ++++HAL LA AGG Sbjct: 361 LLGGQADLNADGAFFPPTLLYCPQPDETPEVHAIEAFGPVATLMPYRDRQHALTLARAGG 420 Query: 421 GSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRAGG 480 GSLAGTLVTA ++AR+FI AAR HGRIQILNEES+ ESTGHGSPLPQLVHGGPGRAGG Sbjct: 421 GSLAGTLVTASGELAREFILGAARAHGRIQILNEESSAESTGHGSPLPQLVHGGPGRAGG 480 Query: 481 GEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGDSL 540 GEELGGLR+VKHYMQRTAVQGSPTMLA I +QWVRGA+V EDRIHPFRKYFEE+QPGDSL Sbjct: 481 GEELGGLRSVKHYMQRTAVQGSPTMLATIGQQWVRGAQVSEDRIHPFRKYFEEIQPGDSL 540 Query: 541 LTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDAGV 600 LTPRRT+TEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYF++SAAAGLFVDAGV Sbjct: 541 LTPRRTLTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFLISAAAGLFVDAGV 600 Query: 601 GPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQHQ 660 GPVIANYG+E+LRFIEPVKPGDTIQVRLTCKRKT+K+QRSA+EK TGVVEWAVE+FNQHQ Sbjct: 601 GPVIANYGMENLRFIEPVKPGDTIQVRLTCKRKTVKRQRSADEKATGVVEWAVEIFNQHQ 660 Query: 661 TPVALYSILTLVARQHGDF 679 VALYSILTLVARQ GDF Sbjct: 661 QAVALYSILTLVARQQGDF 679 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: 1387 Number of extensions: 32 Number of successful extensions: 1 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: 681 Length adjustment: 39 Effective length of query: 642 Effective length of database: 642 Effective search space: 412164 Effective search space used: 412164 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