GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ1 in Pseudomonas fluorescens FW300-N1B4

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate Pf1N1B4_5133 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9)

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__pseudo1_N1B4:Pf1N1B4_5133
          Length = 394

 Score =  322 bits (825), Expect = 1e-92
 Identities = 186/400 (46%), Positives = 248/400 (62%), Gaps = 11/400 (2%)

Query: 3   EAFICDGIRTPIGRYGGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGE 62
           + F+   +R+ IG +GG+L  V    LA    R  + R+  L  E I   ++G       
Sbjct: 5   DIFVVSAVRSAIGSFGGSLKDVPPIQLATDVCRAAIERSG-LAPEHIGHAVMGHVIPTEA 63

Query: 63  DNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSR 122
            +  ++R   + AGL +      +NRLCGSGL A+  AA+++  GD    +AGGVESMSR
Sbjct: 64  RDAYISRAVAINAGLTKETPAFNVNRLCGSGLQAIVSAAQSLMLGDAGAALAGGVESMSR 123

Query: 123 APFVMGKAA-SAFSRQAEMFDTTIGWRFVNPLMAQQFGTDSMPETAENVAELLKISREDQ 181
             +++ +A   A     +  D  +G      ++   F    M  TAEN+AE   I+R+ Q
Sbjct: 124 GAYLLPQARWGARMGDMQAIDYMLG------VLQDPFAGFHMGITAENIAEHYGITRQAQ 177

Query: 182 DSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAP 241
           D  AL SQQR A+A + G  A +IVP+ ++ +KG VT    DEH+R E   EQL  +K  
Sbjct: 178 DELALLSQQRAARAIAEGRFAGQIVPIEIETRKGTVT-FATDEHVRAEVNAEQLSRMKPA 236

Query: 242 FRANGVITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVP 301
           F+ +G +TAGNASG+NDGA ALI+A+ Q+   QGL P AR+V  A AGVEP +MGLGP+P
Sbjct: 237 FKKDGSVTAGNASGLNDGAGALIMATGQVVQEQGLKPMARLVGYAHAGVEPSMMGLGPIP 296

Query: 302 ATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDAPHVNPNGGAIALGHPLGM 361
           ATR VL+RAGL++ D+DVIE NEAFAAQA  V +ELG   D   VNPNG  I+LGHP+G 
Sbjct: 297 ATRLVLKRAGLTVADLDVIESNEAFAAQACAVAQELGF--DPQKVNPNGSGISLGHPVGA 354

Query: 362 SGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           +GA +A  A HELHR  GRYAL TMCIG GQGIA++ ERV
Sbjct: 355 TGAIIATKAIHELHRCQGRYALATMCIGGGQGIAVLFERV 394


Lambda     K      H
   0.319    0.135    0.384 

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: 414
Number of extensions: 17
Number of successful extensions: 5
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: 401
Length of database: 394
Length adjustment: 31
Effective length of query: 370
Effective length of database: 363
Effective search space:   134310
Effective search space used:   134310
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: 50 (23.9 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