Aligments for a candidate for paaZ2 in Pseudomonas fluorescens GW456-L13

GapMind for catabolism of small carbon sources

Aligments for a candidate for paaZ2 in Pseudomonas fluorescens GW456-L13

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate PfGW456L13_2419 Aldehyde dehydrogenase (EC 1.2.1.3), PaaZ

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_2419
          Length = 689

 Score =  748 bits (1931), Expect = 0.0
 Identities = 394/677 (58%), Positives = 479/677 (70%), Gaps = 6/677 (0%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L SF++G W    G ++++  AI G  +     E  D A A +    +G   L A+ F +
Sbjct: 12  LQSFIAGRWIGQHG-AQVLRSAIDGHEIARTHEERPDFAEAIEHGRRQGISGLMALDFQQ 70

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           RA  LKA+A +L   KE+ YA+S  +GATRADSW+DIEGG  TLFTYASLGSRELP   +
Sbjct: 71  RAQRLKALALYLSERKEQLYAISHHSGATRADSWIDIEGGNSTLFTYASLGSRELPSGNI 130

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
             E   + LSK G FA  H+L  + G+AVHINAFNFP WGMLEK AP++L GMP I+KPA
Sbjct: 131 VHEGPAMQLSKMGTFAGTHILVPRGGLAVHINAFNFPIWGMLEKFAPSFLAGMPCIVKPA 190

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
           +AT+ LT+A+V+ + +SGL+P G++ LI GS GDLLD L  QDVVTFTGSA T   LRV 
Sbjct: 191 SATSYLTEAVVRLMDESGLLPAGSLQLIIGSTGDLLDRLQGQDVVTFTGSADTAAKLRVN 250

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           PN++  S+PF  EADSLNC +L  DVTPD  EF LFI+EV REMTTKAGQKCTAIRR IV
Sbjct: 251 PNLIRNSVPFNAEADSLNCAILAPDVTPDDEEFELFIKEVAREMTTKAGQKCTAIRRAIV 310

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAA-----GC 358
           P   ++AV+  L  RL KVVVGDP+ EGV+MGAL + +Q+ DV E++  LL +     G 
Sbjct: 311 PAKHIDAVATRLRDRLAKVVVGDPSVEGVRMGALASHDQQKDVAERLESLLQSSDMLFGA 370

Query: 359 EIRLGGQADLSAAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLACA 418
                 + +    GAFF PTLL    P      H  EAFGPV+TLM   +   AL LA  
Sbjct: 371 RDGFEPRGENVDKGAFFAPTLLQARDPHAEGGAHDIEAFGPVSTLMAYDDLDEALALAAR 430

Query: 419 GGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGRA 478
           G GSL  +LVT DPQIA + I  AA  HGR+ +L+  SA ESTGHGSPLPQL HGGPGRA
Sbjct: 431 GKGSLVASLVTKDPQIAAKAIPVAAAWHGRLLVLDRHSAGESTGHGSPLPQLKHGGPGRA 490

Query: 479 GGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPGD 538
           GGGEELGGLRAVKHY+QR AVQGSPTMLAA++ ++VRGAKV E  +HPFR++F++LQ G+
Sbjct: 491 GGGEELGGLRAVKHYLQRAAVQGSPTMLAAVTGEYVRGAKVIETDVHPFRRHFQDLQIGE 550

Query: 539 SLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVDA 598
           SLLT RRT+TEAD+VNF CLSGDHFY H D+IAA ES FG+R+ HGYFVLSAAAGLFV  
Sbjct: 551 SLLTHRRTVTEADLVNFGCLSGDHFYMHFDEIAAKESQFGKRIAHGYFVLSAAAGLFVSP 610

Query: 599 GVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFNQ 658
             GPV+ANYGL++LRFI PV  GDTIQ RLTCKRK  + ++S +  P GVV W VEV NQ
Sbjct: 611 APGPVLANYGLDTLRFINPVGIGDTIQARLTCKRKIDQGKKSPQGIPQGVVAWDVEVTNQ 670

Query: 659 HQTPVALYSILTLVARQ 675
               VA Y ILTLV ++
Sbjct: 671 LGELVASYDILTLVVKR 687


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: 1188
Number of extensions: 36
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: 689
Length adjustment: 39
Effective length of query: 642
Effective length of database: 650
Effective search space:   417300
Effective search space used:   417300
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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Protein sequences (fasta format)
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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, 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

GapMind for catabolism of small carbon sources