GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Sinorhizobium meliloti 1021

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate SM_b20268 SM_b20268 hydroxyproline-2-epimerase

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__Smeli:SM_b20268
          Length = 333

 Score =  283 bits (724), Expect = 4e-81
 Identities = 141/334 (42%), Positives = 214/334 (64%), Gaps = 5/334 (1%)

Query: 4   SRSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMF 63
           + +   ID HT G   R+V GG P ++G +M EK+ +  +  D++RT +M EPRGH+ M 
Sbjct: 3   THTFSCIDGHTCGNPVRLVSGGGPRLEGANMLEKRAHFLKEFDWIRTGLMFEPRGHDMMS 62

Query: 64  GSVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPA 123
           GS++  P  PD D  ++F++  G L MCGHGTIG +T  IE G++   EP   + ++APA
Sbjct: 63  GSILYPPTRPDCDVAVLFIETSGCLPMCGHGTIGTITMGIENGLITPREP-GKLSIDAPA 121

Query: 124 GIIRGDVTV-VDGK-AKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHAS 181
           G +  D+T   +G+  +EV   NVP+FLY EG+  ++ G+G +  D+++GG+F+AI+   
Sbjct: 122 GKV--DITYRQEGRFVEEVRLTNVPSFLYAEGLAAEVEGLGEIVVDVAYGGNFYAIVEPQ 179

Query: 182 QLGLKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKN 241
           +    +    AG+L   + KLR  +N K E  HP    I+ +  ++   +PT PEA  +N
Sbjct: 180 KNFRDMADHTAGELVGWSPKLRAALNAKYEFVHPEHPEIRGLSHIQWTGKPTQPEAHARN 239

Query: 242 VVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADF 301
            V +G+  +DRSPCGTGTSA++A L AKG+LKVG++FV+ESI+G+LFKG +    KVAD 
Sbjct: 240 AVFYGEKAIDRSPCGTGTSARIAQLAAKGKLKVGDEFVHESIIGSLFKGRVEAAAKVADR 299

Query: 302 NAVVPKITGSAYITGFNHFVIDEEDPLKHGFILK 335
           +A++P I G A +TG N   ID+ DP  HGF+++
Sbjct: 300 DAIIPSIAGWARMTGINTIFIDDRDPFAHGFVVR 333


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: 342
Number of extensions: 12
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: 333
Length adjustment: 28
Effective length of query: 307
Effective length of database: 305
Effective search space:    93635
Effective search space used:    93635
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