Aligments for a candidate for paaZ1 in Pseudomonas putida KT2440

GapMind for catabolism of small carbon sources

Aligments for a candidate for paaZ1 in Pseudomonas putida KT2440

Align oxepin-CoA hydrolase (EC 3.3.2.12) (characterized)
to candidate PP_3270 PP_3270 oxepin-CoA hydrolase/3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase

Query= BRENDA::P77455
         (681 letters)



>FitnessBrowser__Putida:PP_3270
          Length = 684

 Score =  755 bits (1949), Expect = 0.0
 Identities = 397/678 (58%), Positives = 483/678 (71%), Gaps = 8/678 (1%)

Query: 4   LASFLSGTWQSGRGRSRLIHHAISGEALWEVTSEGLDMAAARQFAIEKGAPALRAMTFIE 63
           L SF++G W    G ++ +  A+ G  L     E  D A A  +A  +G  +L  M F +
Sbjct: 7   LQSFIAGRWLGQHG-AQALRSALDGHVLAYSHEERPDFAEAVDYARARGLASLMGMDFQQ 65

Query: 64  RAAMLKAVAKHLLSEKERFYALSAQTGATRADSWVDIEGGIGTLFTYASLGSRELPDDTL 123
           RA  LKA+A +L   KE+ YALS  +GATRADSW+DIEGG  TLF+YA +GSRELP   L
Sbjct: 66  RAQRLKALALYLAECKEQLYALSHHSGATRADSWIDIEGGNATLFSYAGIGSRELPSGNL 125

Query: 124 WPEDELIPLSKEGGFAARHLLTSKSGVAVHINAFNFPCWGMLEKLAPTWLGGMPAIIKPA 183
             E   IPL K+G FA  H+L  ++GVAVHINAFNFP WGMLEK APT+L GMP I+KPA
Sbjct: 126 VHEGPAIPLGKQGHFAGSHILVPRAGVAVHINAFNFPIWGMLEKFAPTFLAGMPCIVKPA 185

Query: 184 TATAQLTQAMVKSIVDSGLVPEGAISLICGSAGDLLDHLDSQDVVTFTGSAATGQMLRVQ 243
           T+T+ LT+A+V+ +  SGL+PEG++ L+ GS GDLLD L  QDVVTFTGSA T   LRV 
Sbjct: 186 TSTSYLTEAVVRLMNASGLLPEGSLQLVIGSTGDLLDRLQGQDVVTFTGSADTAAKLRVT 245

Query: 244 PNIVAKSIPFTMEADSLNCCVLGEDVTPDQPEFALFIREVVREMTTKAGQKCTAIRRIIV 303
           PN++  S+PFT EADSLNC +LG DV+PD  EF L+I+EVVREMTTKAGQKCTAIRR IV
Sbjct: 246 PNLIRNSVPFTAEADSLNCAILGPDVSPDSEEFDLYIKEVVREMTTKAGQKCTAIRRAIV 305

Query: 304 PQALVNAVSDALVARLQKVVVGDPAQEGVKMGALVNAEQRADVQEKVNILLAAGCEIRLG 363
           P   ++AV+  L  RL KVVVGDP+ EGV+MGAL + +Q+ DV E+V  LL + C+   G
Sbjct: 306 PARHLDAVATRLRERLSKVVVGDPSLEGVRMGALASHDQQRDVGERVRSLLQS-CDQLFG 364

Query: 364 GQADLS------AAGAFFPPTLLYCPQPDETPAVHATEAFGPVATLMPAQNQRHALQLAC 417
                +      A GAFF PTLL    P      H  EAFGPV+TLM   +   AL LA 
Sbjct: 365 ASDGFAPRGEGVAEGAFFAPTLLQARDPHAEGGAHDIEAFGPVSTLMAYDDLDEALALAA 424

Query: 418 AGGGSLAGTLVTADPQIARQFIADAARTHGRIQILNEESAKESTGHGSPLPQLVHGGPGR 477
            G GSL  TLVTAD  +A + I  AA  HGR+ +L+ ++AKESTGHGSPLPQL HGGPGR
Sbjct: 425 RGKGSLVATLVTADRSVAAKAIPVAAAWHGRLLVLDSQAAKESTGHGSPLPQLKHGGPGR 484

Query: 478 AGGGEELGGLRAVKHYMQRTAVQGSPTMLAAISKQWVRGAKVEEDRIHPFRKYFEELQPG 537
           AGGGEELGGLRAVKHY+QR AVQGSP+ML A++ ++VRG +V E  +HPFR+YFE+L+ G
Sbjct: 485 AGGGEELGGLRAVKHYLQRAAVQGSPSMLTAVTGEYVRGGEVIETEVHPFRRYFEQLRVG 544

Query: 538 DSLLTPRRTMTEADIVNFACLSGDHFYAHMDKIAAAESIFGERVVHGYFVLSAAAGLFVD 597
           +SLLT RRT+TEAD+VNF CLSGDHFY H D+IAA  S FG+R+ HGYFVLSAAAGLFV 
Sbjct: 545 ESLLTHRRTVTEADLVNFGCLSGDHFYMHFDEIAAKASQFGKRIAHGYFVLSAAAGLFVS 604

Query: 598 AGVGPVIANYGLESLRFIEPVKPGDTIQVRLTCKRKTLKKQRSAEEKPTGVVEWAVEVFN 657
            G GPV+ANYGL++LRFI PV  GDTIQ RLTCKRK  + + S   +P GVV W VEV N
Sbjct: 605 PGAGPVLANYGLDTLRFINPVGIGDTIQARLTCKRKIDQGKTSPLGQPQGVVAWDVEVTN 664

Query: 658 QHQTPVALYSILTLVARQ 675
           Q    VA Y ILTLV ++
Sbjct: 665 QLGELVASYDILTLVLKK 682


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: 1140
Number of extensions: 32
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: 684
Length adjustment: 39
Effective length of query: 642
Effective length of database: 645
Effective search space:   414090
Effective search space used:   414090
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, 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