Alignments for a candidate for paaZ1 in Nocardiopsis lucentensis DSM 44048

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ1 in Nocardiopsis lucentensis DSM 44048

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_017601603.1 D471_RS0127555 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_000341125.1:WP_017601603.1
          Length = 677

 Score =  643 bits (1658), Expect = 0.0
 Identities = 338/680 (49%), Positives = 460/680 (67%), Gaps = 19/680 (2%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L S+  G+W +       +  A +GE +  +++ G D+AA   +A   G PALRA+TF +
Sbjct: 5   LESYALGSWFTPEDEGAPLADANTGETVARISANGPDVAAMIDYARRVGGPALRALTFHQ 64

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           RA +LK +A +L   K+ FYALS +TGATR D+ VD++GG GTLF+++S G RELP+ T+
Sbjct: 65  RALILKELATYLTGHKDEFYALSHRTGATRRDTMVDVDGGFGTLFSFSSKGRRELPNSTV 124

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
             +  L PL ++G F  +H+ TS+ GVAV INAFNFP WGMLEKLAP +L GMP+I+KPA
Sbjct: 125 VLDGPLEPLGRKGTFVGQHVYTSRPGVAVQINAFNFPVWGMLEKLAPAFLAGMPSIVKPA 184

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
             T+ LT+A+V+ +V+SGL+PEG++ L+ G+   LLD+L  QD+V FTGSAATG +LR  
Sbjct: 185 GQTSYLTEAVVRRMVESGLLPEGSLQLLVGTHRGLLDNLGPQDIVGFTGSAATGALLREH 244

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           PN+V   +   +EADSLNC +LG DV  + PEF LF+++VV EMT KAGQKCTAIRR+IV
Sbjct: 245 PNVVRGGVQLNVEADSLNCSILGPDVRVEDPEFDLFVKQVVTEMTVKAGQKCTAIRRVIV 304

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIR-- 361
           P+ + +AV++A+  RL  VVVG   +E V+MG L   +QRA+V++ V  LLA+   +   
Sbjct: 305 PEPMADAVTEAISDRLSAVVVGAADREDVRMGPLATLDQRAEVRKAVKALLASADVVHGD 364

Query: 362 ------LGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQL 415
                 +G  A+   AGAF  P LL   +PD     H  EAFGPV+T++       A++L
Sbjct: 365 PDEVEVVGADAE---AGAFMSPILLRA-RPD-AGEPHEVEAFGPVSTVITYDGVAQAVEL 419

Query: 416 ACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGP 475
           A  G GSL G++VT DP +AR+ +   A  HGRI +L+ + AKESTGHGSPLP LVHGGP
Sbjct: 420 AARGTGSLVGSVVTHDPDVAREIVLGLAPWHGRILVLDRDDAKESTGHGSPLPMLVHGGP 479

Query: 476 GRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQ 535
           GRAGGGEE+GG+R VKH+MQRTA+Q SP M  AI+  W  G++ +   +HPFRK   +L+
Sbjct: 480 GRAGGGEEMGGVRGVKHHMQRTAIQASPDMATAITGHWTTGSRRDVGEVHPFRKNLAQLR 539

Query: 536 PGDSLLTPRRTMTEADIVNFACLSGDHFYAHMD-KIAAAESIFGERVVHGYFVLSAAAGL 594
            GD++ +  RT+T  DI +FA  +GD FYAH D + AAA  +FG  V HGY V+S AAGL
Sbjct: 540 IGDTISSADRTVTREDIDHFAEFTGDTFYAHTDEEAAAANPLFGGIVAHGYLVVSLAAGL 599

Query: 595 FVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVE 654
           FVD   GPV+AN+G+++LRF+ PVK G+TI+V+LT K+ T +          G V W   
Sbjct: 600 FVDPDPGPVLANFGVDNLRFLTPVKEGETIRVQLTAKQITPRANAD-----YGEVRWDAL 654

Query: 655 VFNQHQTPVALYSILTLVAR 674
           V N+   PVA Y +LTLVA+
Sbjct: 655 VTNERDEPVATYDVLTLVAK 674


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: 1135
Number of extensions: 51
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: 677
Length adjustment: 39
Effective length of query: 642
Effective length of database: 638
Effective search space:   409596
Effective search space used:   409596
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.

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Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

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About GapMind

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:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

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:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

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:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

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

GapMind for catabolism of small carbon sources