GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pcaF in Pseudomonas fluorescens FW300-N2C3

Align 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase; EC 2.3.1.174; EC 2.3.1.223 (characterized)
to candidate AO356_02325 AO356_02325 3-ketoacyl-CoA thiolase

Query= SwissProt::P0C7L2
         (401 letters)



>FitnessBrowser__pseudo5_N2C3_1:AO356_02325
          Length = 391

 Score =  301 bits (772), Expect = 2e-86
 Identities = 177/405 (43%), Positives = 244/405 (60%), Gaps = 24/405 (5%)

Query: 2   REAFICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQA 60
           R+  I D  RTP+GR  GG   + RA+D++A  + +LL RN ++D   ++DVI GC NQ 
Sbjct: 6   RDVVIVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPNEVEDVIWGCVNQT 65

Query: 61  GEDNRNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESM 120
            E   N+ARMA+L+  +P + +G T++RLCGS + AL  AA+AI  G+GD+ + GGVE M
Sbjct: 66  LEQGWNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHM 125

Query: 121 SRAPFVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKISR 178
                + G                      NP M+      S  M  TAE + ++  ISR
Sbjct: 126 GHVSMMHGVDP-------------------NPHMSLYAAKASGMMGLTAEMLGKMHGISR 166

Query: 179 EDQDSFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGL 238
           E QD+F +RS Q   KA   G   +EI+P+   ++ G +    +DE +RPETTLE L  L
Sbjct: 167 EQQDAFGVRSHQLAHKATVEGKFKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAAL 226

Query: 239 KAPFRANG-VITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGL 297
           K  F   G  +TAG +S + DGA+ +I+ S Q A   G+ P A I +MA AGV+P +MG 
Sbjct: 227 KPAFNPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGY 286

Query: 298 GPVPATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDA-PHVNPNGGAIALG 356
           GPVPAT++ L+RAGL I D+D  ELNEAFAAQAL VL++L + D     VN +GGAIALG
Sbjct: 287 GPVPATQKALKRAGLGIADIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALG 346

Query: 357 HPLGMSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
           HP G SGAR++    + + +  G + + TMCIG+GQGIA + ERV
Sbjct: 347 HPFGCSGARISGTLLNVMKQNGGTFGVSTMCIGLGQGIATVFERV 391


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: 433
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: 391
Length adjustment: 31
Effective length of query: 370
Effective length of database: 360
Effective search space:   133200
Effective search space used:   133200
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