GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Shewanella loihica PV-4

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate 5209915 Shew_2363 proline racemase (RefSeq)

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__PV4:5209915
          Length = 333

 Score =  246 bits (628), Expect = 6e-70
 Identities = 124/323 (38%), Positives = 193/323 (59%), Gaps = 1/323 (0%)

Query: 10  IDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVMTQ 69
           +D+HT G   R+V  G P++KG +M EK++      D++R A+M EPRGH+ M G+ +  
Sbjct: 9   VDAHTCGNPVRLVTSGHPDLKGRTMSEKRQDFLAQYDWIRKALMFEPRGHDMMSGAFLYP 68

Query: 70  PCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGIIRGD 129
           PC  +AD  I+F++  G L MCGHGTIG +TAA+E+G++    P   + ++ PAG I+  
Sbjct: 69  PCSDNADAAILFIETSGCLPMCGHGTIGTITAALESGLLTPKMP-GQLTIDVPAGQIKVQ 127

Query: 130 VTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKIEP 189
                 K   V   NVPA+L  + V +D+PG+G +K D+S+GG+++AI+        +  
Sbjct: 128 YQQTGAKVDWVKIFNVPAYLAHKDVVLDIPGLGPLKIDVSYGGNYYAIVDPQANFPGLRH 187

Query: 190 QNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIFGQGQ 249
            +AG +   +  +R++ + ++   HP    +  V  V    +     +   N V +G   
Sbjct: 188 WSAGDILRWSPIVREVAHRELNCVHPDDPTVNGVSHVLWTGDTISEGSNGANAVFYGDKA 247

Query: 250 VDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAVVPKIT 309
           +DRSPCGTGTSA+LA L+++GELKVG+++ +ESI+G+ F G I   TKV  F+A++P I 
Sbjct: 248 IDRSPCGTGTSARLAQLYSRGELKVGDEYTHESIIGSQFVGRIEAATKVGAFDAIMPSIK 307

Query: 310 GSAYITGFNHFVIDEEDPLKHGF 332
           G A ITG N   +D+ DP   GF
Sbjct: 308 GWARITGHNAITVDDNDPYAFGF 330


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: 317
Number of extensions: 11
Number of successful extensions: 3
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