GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ1 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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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:

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. 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:

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:

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