GapMind for catabolism of small carbon sources

 

Aligments for a candidate for paaZ1 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)



>lcl|FitnessBrowser__Phaeo:GFF2643 PGA1_c26830 phenylacetic acid
           degradation protein PaaZ
          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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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

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:

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. Gaps may be due to:

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 preprint on GapMind for carbon sources, or view the source code.

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