Alignments for a candidate for paaZ1 in Marinomonas arctica 328

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ1 in Marinomonas arctica 328

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_111606228.1 DK187_RS04910 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_003259225.1:WP_111606228.1
          Length = 694

 Score =  761 bits (1964), Expect = 0.0
 Identities = 391/681 (57%), Positives = 483/681 (70%), Gaps = 14/681 (2%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L SF++G W  G    + +   ++GE ++   +E +D A + +FA  KG  +L AM F  
Sbjct: 17  LQSFIAGEWL-GNQAGQALASPVNGETIYHTHAETIDFARSLEFARTKGRASLMAMDFQS 75

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           RA+ L+ + KHLL  KE  YA+S  TGATR DSWVDIEGG GTLF YAS+G RELP   L
Sbjct: 76  RASCLRDLGKHLLEYKESLYAISLLTGATRNDSWVDIEGGAGTLFAYASVGRRELPSGNL 135

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
             ED+  PL ++G F   H+L  + GVAVHINAFNFP WGMLEK A  +L GMP I+KPA
Sbjct: 136 IHEDDAFPLGRDGQFFGSHILVPRQGVAVHINAFNFPIWGMLEKFAANFLAGMPCIVKPA 195

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
           T+T+ LT+A V+ + +SGL+PEG++ LI G  GDLLD LD QDVVTFTGSA+T   L+V 
Sbjct: 196 TSTSYLTEACVRLMHESGLLPEGSLQLIIGRTGDLLDRLDGQDVVTFTGSASTAAKLKVT 255

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           PNI+  SIPF  EADSLNC +L  DV+ D PEF LFI+EV REMT KAGQKCTAIRR+++
Sbjct: 256 PNIINNSIPFNAEADSLNCAILAPDVSVDSPEFELFIKEVAREMTVKAGQKCTAIRRVLI 315

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAA------- 356
           P+  V AVS+ L ARL K+ +GDP  + V+MGAL + EQ+ADV  ++  LL +       
Sbjct: 316 PENQVQAVSERLTARLAKMSIGDPHLDTVRMGALASFEQKADVLAQLEQLLKSSQLVCGH 375

Query: 357 --GCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQ 414
             G E+   G    S  GAF  PTLL    PD     H  EAFGP++TLMP +N  HA+ 
Sbjct: 376 DEGFELLGKG----SEKGAFIQPTLLLSNDPDADGGAHDIEAFGPISTLMPYKNIDHAIA 431

Query: 415 LACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGG 474
           LA  G GSL  TLVT DP+IAR+ +   A  HGR+ ILNE S+KESTGHGSPLP L HGG
Sbjct: 432 LAARGKGSLVTTLVTQDPEIARKVVPALAAWHGRVHILNEASSKESTGHGSPLPMLKHGG 491

Query: 475 PGRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEEL 534
           PGRAGGGEELGG+R VKHYMQR A+QGSPTML+A++ ++VRG +  E  +HPFR+YFE+L
Sbjct: 492 PGRAGGGEELGGIRGVKHYMQRAAIQGSPTMLSAVTGEYVRGGETYESDVHPFRRYFEDL 551

Query: 535 QPGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGL 594
           + G+SLLT RRT+TE DIVNF CLSGDHFY H D IAA +S F +R+ HGYFVLSAAAGL
Sbjct: 552 RIGESLLTHRRTVTETDIVNFGCLSGDHFYMHFDDIAARDSQFEQRIAHGYFVLSAAAGL 611

Query: 595 FVDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVE 654
           FV  G GPV+ANYGL++LRFI PV  GDTI+ RLTCKRK  + + S + +P GVV W V+
Sbjct: 612 FVSPGEGPVLANYGLDTLRFITPVPIGDTIRARLTCKRKIDQGKLSPKGEPQGVVVWDVQ 671

Query: 655 VFNQHQTPVALYSILTLVARQ 675
           V NQH+  VA Y ILTLV +Q
Sbjct: 672 VTNQHEELVASYDILTLVKKQ 692


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: 1186
Number of extensions: 34
Number of successful extensions: 2
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: 694
Length adjustment: 39
Effective length of query: 642
Effective length of database: 655
Effective search space:   420510
Effective search space used:   420510
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