Alignments for a candidate for paaZ2 in Phaeobacter inhibens BS107

GapMind for catabolism of small carbon sources

Alignments for a candidate for paaZ2 in Phaeobacter inhibens BS107

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate GFF2643 PGA1_c26830 phenylacetic acid degradation protein PaaZ

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__Phaeo:GFF2643
          Length = 676

 Score =  644 bits (1662), Expect = 0.0
 Identities = 343/677 (50%), Positives = 445/677 (65%), Gaps = 14/677 (2%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           ++SF +G W +    +R I  AI+G  L +  ++ LD+     +A   G P+LR +TF +
Sbjct: 6   VSSFAAGQWIAPGAGARSIASAITGAPLAQAGNDALDVQGMLDYARTVGGPSLRKLTFHD 65

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           RA MLKA+A HL   K+  Y LS  TGAT++D  +DI+GGIGT+F +AS G RE+PD  +
Sbjct: 66  RARMLKALAGHLNQHKQALYDLSFNTGATQSDHMIDIDGGIGTMFVFASKGRREMPDAHV 125

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
           + + ++  LS+ G F  +H+ T   GVAVHINAFNFP WGMLEKLAPT L G+PAI+KPA
Sbjct: 126 YLDGDIEQLSRNGTFLGQHICTPLQGVAVHINAFNFPVWGMLEKLAPTLLAGVPAIVKPA 185

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
           TAT  +T+  V+ +++SG++PEGA+ L+ G  GD+LDHL  QDVV+FTGSA T   LR  
Sbjct: 186 TATCYVTELAVRLMLESGILPEGALQLVSGGLGDMLDHLTMQDVVSFTGSAQTALKLRAN 245

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           P I+  SI F  E DSLN  +LG D  P  PEF LF++EV REMTTKAGQKCTAIRRII 
Sbjct: 246 PVILENSIRFVAEQDSLNASILGPDAGPGTPEFDLFVKEVSREMTTKAGQKCTAIRRIIA 305

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLG 363
           P A V AV +AL ARL K  +GDP  E  +MGALV+  Q+ DV EK  I +    E   G
Sbjct: 306 PDAQVEAVIEALSARLAKTRIGDPRLETTRMGALVSNSQKRDVLEKAAI-IGQEAERVFG 364

Query: 364 GQADLSA------AGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLAC 417
              + S        GAF PP L +C  PD+   VH TEAFGPV+T+M   +  HA+ LA 
Sbjct: 365 DPENFSVDGADAEKGAFVPPMLFHCADPDKAQRVHDTEAFGPVSTIMGYHDLDHAITLAN 424

Query: 418 AGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGR 477
            G GSL  +++T D ++AR+    A   HGR+   N +S KESTGHGSPLP +VHGGPGR
Sbjct: 425 RGEGSLVASVITHDTEVAREVALGAGAYHGRLYFNNRDSMKESTGHGSPLPHMVHGGPGR 484

Query: 478 AGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPG 537
           AGGGEELGG+R VKHYMQRTA+QGSP +L+AI +QWV G      ++HPF + F +L+ G
Sbjct: 485 AGGGEELGGVRGVKHYMQRTAIQGSPDILSAIGEQWVPGGTEIAAKVHPFTRKFGDLELG 544

Query: 538 DSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAES-IFGERVVHGYFVLSAAAGLFV 596
           ++L +  R +T  DI  FA  +GD FYAHMD  AAA +  F  RV HGY ++S AAGLFV
Sbjct: 545 ETLHSAARQITLEDIETFAHFTGDTFYAHMDDEAAARNPFFPGRVAHGYLLISFAAGLFV 604

Query: 597 DAGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVF 656
               GPV+AN GL++LRF++PV  GD+I+VRLT K+KT + +        G V W V + 
Sbjct: 605 QPDEGPVLANTGLDNLRFMKPVSAGDSIKVRLTVKKKTPRNE------DYGQVRWHVTLT 658

Query: 657 NQHQTPVALYSILTLVA 673
           NQ     A Y +LT+ A
Sbjct: 659 NQDDEIAAEYELLTMNA 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: 1118
Number of extensions: 48
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: 676
Length adjustment: 39
Effective length of query: 642
Effective length of database: 637
Effective search space:   408954
Effective search space used:   408954
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.

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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