Alignments for a candidate for paaZ2 in Dinoroseobacter shibae DFL-12

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Dinoroseobacter shibae DFL-12

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate 3610446 Dshi_3827 phenylacetic acid degradation protein paaN (RefSeq)

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__Dino:3610446
          Length = 678

 Score =  656 bits (1692), Expect = 0.0
 Identities = 348/676 (51%), Positives = 447/676 (66%), Gaps = 16/676 (2%)

Query: 6   SFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIERA 65
           SF +G W +    +R+I HA++G  L    +  LD+ A   +A + G PALRA+TF +RA
Sbjct: 8   SFAAGHWIAPDADARMIAHAVTGAPLARAGNGALDVQAMLDYARDTGGPALRALTFHDRA 67

Query: 66  AMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTLWP 125
            MLKA+A HL + K+  Y LS  TGAT+AD  +DI+GGIGT+F +AS G RE+PD  ++ 
Sbjct: 68  RMLKALALHLGAHKQALYDLSFATGATQADHLIDIDGGIGTVFVFASKGRREMPDAHVYL 127

Query: 126 EDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPATA 185
           + E+  LS+ G F  +H+ T   GVAVHINAFNFP WGMLEKLAPT L GMPAI+KPATA
Sbjct: 128 DGEVEQLSRTGTFLGQHIATPLQGVAVHINAFNFPVWGMLEKLAPTLLAGMPAIVKPATA 187

Query: 186 TAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQPN 245
           +  +T+  V+ I+DSG++P GA+ L+ G  GD+LD L  QDVV+FTGSA T   LR  P+
Sbjct: 188 SCYVTEKAVRIILDSGILPAGALQLVTGGLGDMLDRLTCQDVVSFTGSADTALRLRAAPH 247

Query: 246 IVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIVPQ 305
           ++  ++ F  E DSLN  +LG D  P  PEF LFIREV REMT KAGQKCTAIRRI+ PQ
Sbjct: 248 LLRNAVRFVAEQDSLNASILGPDAVPGTPEFDLFIREVAREMTAKAGQKCTAIRRILAPQ 307

Query: 306 ALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLGGQ 365
           A V+ V  AL ARL K V+GDP      MGALV+  Q+ DV  K  + +A   E R+ G 
Sbjct: 308 AQVDGVIAALGARLAKTVIGDPRDTATTMGALVSNGQKRDVLAKARV-IATEAE-RVFGD 365

Query: 366 ADL-------SAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418
            +        +  GAF PP LL+C  PD    +H TEAFGPV+T+M  ++  HA+ L   
Sbjct: 366 PEAFTVHGADARTGAFLPPMLLHCADPDAAQRLHDTEAFGPVSTVMGYRDLDHAVALVNR 425

Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478
           G GSL  +L+T DP++ARQ    A   HGR+ I + +S  E+TGHG+PLP ++HGGPGRA
Sbjct: 426 GAGSLVASLITHDPEVARQVALGAGAFHGRLYINDRDSMGEATGHGAPLPHMIHGGPGRA 485

Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGD 538
           GGGEELGG+R V HYMQRTA+QGSP ML AI  +WV GA       HPF + F+ L+ G+
Sbjct: 486 GGGEELGGVRGVMHYMQRTAIQGSPDMLTAIGGKWVPGATETPAPAHPFTRGFDALRIGE 545

Query: 539 SLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAES-IFGERVVHGYFVLSAAAGLFVD 597
           +L TP R +T ADI +FA  +GD FYAHMD  AAA +  F  RV HGY +LS AAGLFVD
Sbjct: 546 TLHTPARQVTLADIEHFAAFTGDTFYAHMDDAAAARNPFFPGRVAHGYLLLSFAAGLFVD 605

Query: 598 AGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFN 657
              GPV+AN GL+SLRF++PV PGD+++ RLT K KT +     E      V W V + N
Sbjct: 606 PDEGPVLANTGLDSLRFLKPVAPGDSLKARLTVKHKTPRNDAYGE------VRWHVSLTN 659

Query: 658 QHQTPVALYSILTLVA 673
           Q    VA Y +LT++A
Sbjct: 660 QEDDLVAEYELLTMIA 675


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: 1176
Number of extensions: 65
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: 678
Length adjustment: 39
Effective length of query: 642
Effective length of database: 639
Effective search space:   410238
Effective search space used:   410238
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 17 2021. The underlying query database was built on Sep 17 2021.

Downloads

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

Related tools

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