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 5209913 Shew_2361 proline racemase (RefSeq)

Query= BRENDA::A8DEZ8
         (335 letters)



>FitnessBrowser__PV4:5209913
          Length = 346

 Score =  232 bits (591), Expect = 1e-65
 Identities = 120/334 (35%), Positives = 195/334 (58%), Gaps = 11/334 (3%)

Query: 8   QAIDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVM 67
           + +D+HT GE  RI++ G P I G+++  K+ YL  +LD  R  +M EPRGH DM+G+++
Sbjct: 18  KTLDAHTEGEPLRILLEGYPEIPGDTILAKRRYLTAHLDQYRKLLMHEPRGHADMYGAII 77

Query: 68  TQPCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGIIR 127
           T P    ADFG++F+   GY +MCGHG +  +T A+ETG +   +    + ++APAG+I 
Sbjct: 78  TAPITTGADFGVLFLHNEGYSSMCGHGILALVTVAVETGTLALGDTPREIKIDAPAGLIH 137

Query: 128 GDVTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKI 187
                 +    +VSF NVP++       V + G+G V +DI FGG+++A + A  LGL  
Sbjct: 138 AKAYRDETGELKVSFRNVPSWAEALDCRVTVEGIGEVAYDIGFGGAYYAYVDADGLGLSC 197

Query: 188 EPQNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIY------DEPTHPEATYKN 241
            P+N  +L +   +    I   +  QHP LAH    DL  +Y       + +  +A  ++
Sbjct: 198 APENVAQLIDWGRR----IKHAVMAQHP-LAHPLEADLGFLYGTIFTSSKTSSNDAHSRH 252

Query: 242 VVIFGQGQVDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADF 301
           V +F  G+VDRSP GTG + ++A LHA+GE+ +GE+   ESI+    +   ++       
Sbjct: 253 VCVFADGEVDRSPTGTGVAGRIALLHARGEVALGERLRIESIVDGAMQVCALDNADFYGK 312

Query: 302 NAVVPKITGSAYITGFNHFVIDEEDPLKHGFILK 335
            AV+P+++G A+ITG + F++D +D  + GF+L+
Sbjct: 313 AAVIPEVSGRAFITGRHEFILDPKDQFQQGFMLR 346


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: 346
Number of extensions: 18
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: 346
Length adjustment: 28
Effective length of query: 307
Effective length of database: 318
Effective search space:    97626
Effective search space used:    97626
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