GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Acidovorax sp. GW101-3H11

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate Ac3H11_4170 4-hydroxyproline epimerase (EC 5.1.1.8)

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_4170
          Length = 314

 Score =  172 bits (435), Expect = 1e-47
 Identities = 112/331 (33%), Positives = 174/331 (52%), Gaps = 19/331 (5%)

Query: 5   RSIQAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFG 64
           + IQ +DSHT GE TR+V+GG P++   SM E++E L    D  R A +LEPRG + + G
Sbjct: 2   KRIQILDSHTGGEPTRLVIGGFPDLGAGSMAERRERLAREHDAWRAATVLEPRGSDVVVG 61

Query: 65  SVMTQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAG 124
           +++  P  P    G+IF +  GYL MCGHGTIG + +    G    ++P  H + E P G
Sbjct: 62  ALLCTPQDPANAAGVIFFNNSGYLGMCGHGTIGLVASLAYMG---RIQPGEHRI-ETPVG 117

Query: 125 IIRGDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLG 184
            +   +   DG    VS  NVPA+     + VD+PG G V  D+++GG++F +I  S  G
Sbjct: 118 TVTTTLH-TDG---SVSVRNVPAYRLHHQLAVDVPGYGRVVGDVAWGGNWFFLI--SDHG 171

Query: 185 LKIEPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIY-DEPTHPEATYKNVV 243
            ++   N     E  M     + + ++ Q     +   +D +E++ D+     A  +N V
Sbjct: 172 QRVTSDN----LEALMHYSCAVQQALKDQGIRGDNGGEIDHIELFADDEAEEPADSRNYV 227

Query: 244 IFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNA 303
           +      DRSPCGTGTSAK+A L A G+L  G  +   SI+G+ F+        + D   
Sbjct: 228 LCPGKAYDRSPCGTGTSAKIACLAADGKLAPGAVWRQASIIGSQFEASYT----LQDDGK 283

Query: 304 VVPKITGSAYITGFNHFVIDEEDPLKHGFIL 334
           ++P + G A+++     +I++ DP   G  L
Sbjct: 284 LIPTLRGRAHMSAEATLLIEDSDPFGWGIRL 314


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: 281
Number of extensions: 13
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: 335
Length of database: 314
Length adjustment: 28
Effective length of query: 307
Effective length of database: 286
Effective search space:    87802
Effective search space used:    87802
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: 48 (23.1 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