GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Pseudomonas fluorescens GW456-L13

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate PfGW456L13_3147 4-hydroxyproline epimerase (EC 5.1.1.8)

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3147
          Length = 332

 Score =  236 bits (601), Expect = 8e-67
 Identities = 127/330 (38%), Positives = 185/330 (56%), Gaps = 1/330 (0%)

Query: 5   RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64
           RS   +DSH  G   R+V GG P +   SM E++E      D++RTA+M EPRGH+ M G
Sbjct: 3   RSFFCVDSHACGNPVRVVTGGGPLLPSVSMAERREIFVREHDWVRTALMFEPRGHDIMSG 62

Query: 65  SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124
            ++      D DFG +F++  G L MCG GTIG  T  IE G+V   EP   + +E PAG
Sbjct: 63  VIIYPSSREDCDFGALFIEVSGCLPMCGAGTIGLSTVVIEEGLVTPREP-GRLAIETPAG 121

Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184
            +  D T+       +   NV ++L+   V VD+PGVG +  DI++GG+F+A++   +  
Sbjct: 122 RVDVDYTMNGEYVDSIRLFNVASYLHSADVVVDVPGVGELVVDIAYGGNFYAVVEPQENW 181

Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVI 244
             +       +  L+ KLR  + E  +  HP  + I  V  V   DE     A  +  V 
Sbjct: 182 PGLNGLTTADIVSLSQKLRAALAEVSDPVHPENSRISGVHHVIWSDEEHSTAADGRGAVF 241

Query: 245 FGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAV 304
           +G   +DRSP GTGTSA++A L  KG LK+G+ +  ES++GT+F+G++    KV  F+ +
Sbjct: 242 YGDKAIDRSPGGTGTSARMAQLFGKGRLKIGDTYRNESLIGTIFEGKVEASVKVGTFDGI 301

Query: 305 VPKITGSAYITGFNHFVIDEEDPLKHGFIL 334
            P I G A ITG N   +D++DPL+HGF L
Sbjct: 302 RPSIGGWAQITGHNTIFVDDKDPLRHGFQL 331


Lambda     K      H
   0.319    0.139    0.403 

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: 319
Number of extensions: 14
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: 335
Length of database: 332
Length adjustment: 28
Effective length of query: 307
Effective length of database: 304
Effective search space:    93328
Effective search space used:    93328
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 (21.7 bits)
S2: 49 (23.5 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