GapMind for catabolism of small carbon sources

 

Alignments for a candidate for paaJ2 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_3904 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_3904
          Length = 383

 Score =  298 bits (764), Expect = 1e-85
 Identities = 174/401 (43%), Positives = 243/401 (60%), Gaps = 24/401 (5%)

Query: 6   ICDGIRTPIGRY-GGALSSVRADDLAAIPLRELLVRNPRLDAECIDDVILGCANQAGEDN 64
           I D  RTP+GR  GG   + RA+D++A  + +LL RN ++D   ++DVI GC NQ  E  
Sbjct: 2   IVDFGRTPMGRSKGGMHRNTRAEDMSAHLISKLLERNVKVDPSEVEDVIWGCVNQTLEQG 61

Query: 65  RNVARMATLLAGLPQSVSGTTINRLCGSGLDALGFAARAIKAGDGDLLIAGGVESMSRAP 124
            N+ARMA+L+  +P + +G T++RLCGS + AL  AA+AI  G+GD+ + GGVE M    
Sbjct: 62  WNIARMASLMTQIPHTAAGQTVSRLCGSSMSALHTAAQAIMTGNGDVFVVGGVEHMGHVS 121

Query: 125 FVMGKAASAFSRQAEMFDTTIGWRFVNPLMAQQFGTDS--MPETAENVAELLKISREDQD 182
            + G                      NP M+      S  M  TAE + ++  I+RE QD
Sbjct: 122 MMHGVDP-------------------NPHMSLYAAKASGMMGLTAEMLGKMHGITREQQD 162

Query: 183 SFALRSQQRTAKAQSSGILAEEIVPVVLKNKKGVVTEIQHDEHLRPETTLEQLRGLKAPF 242
           +F +RS Q   KA   G   +EI+P+   ++ G +    +DE +RPETTLE L  LK  F
Sbjct: 163 AFGVRSHQLAHKATLEGKFKDEIIPMQGYDENGFLKLFDYDETIRPETTLESLAALKPAF 222

Query: 243 RANG-VITAGNASGVNDGAAALIIASEQMAAAQGLTPRARIVAMATAGVEPRLMGLGPVP 301
              G  +TAG +S + DGA+ +I+ S Q A   G+ P A I +MA AGV+P +MG GPVP
Sbjct: 223 NPKGGTVTAGTSSQITDGASCMIVMSAQRAQDLGIQPMAVIRSMAVAGVDPAIMGYGPVP 282

Query: 302 ATRRVLERAGLSIHDMDVIELNEAFAAQALGVLRELGLPDDA-PHVNPNGGAIALGHPLG 360
           AT++ L+RAGL I+D+D  ELNEAFAAQAL VL++L + D     VN +GGAIALGHP G
Sbjct: 283 ATQKALKRAGLGINDIDFFELNEAFAAQALPVLKDLKVLDKMNEKVNLHGGAIALGHPFG 342

Query: 361 MSGARLALAASHELHRRNGRYALCTMCIGVGQGIAMILERV 401
            SGAR++    + + +  G + + TMCIG+GQGI+ + ERV
Sbjct: 343 CSGARISGTLLNVMKQNGGTFGVATMCIGLGQGISTVFERV 383


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: 417
Number of extensions: 17
Number of successful extensions: 4
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: 383
Length adjustment: 31
Effective length of query: 370
Effective length of database: 352
Effective search space:   130240
Effective search space used:   130240
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.

Links

Downloads

Related tools

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