GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaZ2 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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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