Alignments for a candidate for paaZ2 in Halomonas desiderata SP1

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Halomonas desiderata SP1

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate WP_086509216.1 BZY95_RS06870 phenylacetic acid degradation bifunctional protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>NCBI__GCF_002151265.1:WP_086509216.1
          Length = 680

 Score =  724 bits (1870), Expect = 0.0
 Identities = 378/680 (55%), Positives = 469/680 (68%), Gaps = 6/680 (0%)

Query: 1   MQQLASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMT 60
           M  L S+++  W  G   ++ +  AI+GE +    +E +D +    +    G   L A+ 
Sbjct: 1   MPVLKSYVASQWV-GATAAKALPSAINGETIAHTHAETIDFSQVVDYGRHTGVKNLLAVD 59

Query: 61  FIERAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPD 120
           F +RAA+LKA+A ++   KE  Y +S  TG TRADSW+DIEGG GTLF YAS+G + LP 
Sbjct: 60  FQQRAAILKALAIYIQERKEALYEISHHTGCTRADSWIDIEGGFGTLFAYASIGRKGLPS 119

Query: 121 DTLWPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAII 180
             +  E   I L K+  F   H+L  + GV VHINAFNFP WGMLEK AP +L GMP I+
Sbjct: 120 GNVAHEGPSIQLGKDNHFNGTHILVPRRGVCVHINAFNFPIWGMLEKFAPAFLAGMPCIV 179

Query: 181 KPATATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQML 240
           KPATAT+ L +A V+ I +SGL+P GA+ LI G  GDLLD L+ QD VTFTGSAAT   L
Sbjct: 180 KPATATSYLAEAAVRIIDESGLLPAGALQLIIGGTGDLLDRLEEQDFVTFTGSAATALKL 239

Query: 241 RVQPNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRR 300
           +  PN++A+SIPF  EADSLN  +L  DVTPD  EF +F +EVV+EMT KAGQKCTAIRR
Sbjct: 240 KSHPNVMARSIPFNAEADSLNSAILAPDVTPDDEEFGIFAKEVVKEMTAKAGQKCTAIRR 299

Query: 301 IIVPQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAA---- 356
           ++VP   ++A++D +  RL K+  GDPAQEGV+MGAL + EQ  DV + +  LL      
Sbjct: 300 VLVPAEHLDALADRIKERLGKITFGDPAQEGVRMGALASQEQLRDVTDAIGRLLETSECV 359

Query: 357 -GCEIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQL 415
            G   RL         GAF  P LL   +P +    H  EAFGPVATLMP      AL +
Sbjct: 360 FGKSDRLEPVGKGVENGAFIAPHLLINYRPLQDGGAHDIEAFGPVATLMPYHGIDEALAI 419

Query: 416 ACAGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGP 475
           A  G GSL  TL T DP IA + I   A  HGR+QIL+ E++KESTGHGSPLP L HGGP
Sbjct: 420 AAKGKGSLVTTLTTRDPAIAAEMIPVLAAQHGRLQILDAEASKESTGHGSPLPMLKHGGP 479

Query: 476 GRAGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQ 535
           GRAGGGEELGG+RAV HY+QRTA+QGSPTM+AA+++++VRGAKV E+ +HPFR+YF++LQ
Sbjct: 480 GRAGGGEELGGIRAVHHYLQRTAIQGSPTMVAAVTREYVRGAKVIENDVHPFRRYFDDLQ 539

Query: 536 PGDSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLF 595
            G+SLLT RRT+TEADIVNF CLSGDHFY H D IAA ++ FG+R+ HGYFVLSAAAGLF
Sbjct: 540 VGESLLTHRRTVTEADIVNFGCLSGDHFYMHFDDIAARKTQFGQRIAHGYFVLSAAAGLF 599

Query: 596 VDAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEV 655
           V  G GPV+ANYGL++LRFI PV PGDTI+ RLTCKRK  + + S E  P GVV W V V
Sbjct: 600 VYPGEGPVLANYGLDTLRFITPVAPGDTIRARLTCKRKIDQGRTSPEGYPQGVVMWDVAV 659

Query: 656 FNQHQTPVALYSILTLVARQ 675
            NQ    VA Y ILTLVA++
Sbjct: 660 TNQKDELVASYDILTLVAKR 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: 1125
Number of extensions: 46
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: 680
Length adjustment: 39
Effective length of query: 642
Effective length of database: 641
Effective search space:   411522
Effective search space used:   411522
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