GapMind for catabolism of small carbon sources

 

Alignments for a candidate for prdF in Sphingomonas indica Dd16

Align proline racemase (EC 5.1.1.4) (characterized)
to candidate WP_085216990.1 B9N75_RS00310 4-hydroxyproline epimerase

Query= BRENDA::A8DEZ8
         (335 letters)



>NCBI__GCF_900177405.1:WP_085216990.1
          Length = 332

 Score =  243 bits (619), Expect = 6e-69
 Identities = 129/323 (39%), Positives = 185/323 (57%), Gaps = 1/323 (0%)

Query: 10  IDSHTAGEATRIVVGGIPNIKGNSMPEKKEYLEENLDYLRTAIMLEPRGHNDMFGSVMTQ 69
           ID HTAG   R+V GG P ++G SM E++    E  D++RT +  EPRGH  M G  +  
Sbjct: 8   IDGHTAGNPVRLVAGGAPPLRGASMAERRLDFLERFDWIRTGLCFEPRGHAMMSGGFLYP 67

Query: 70  PCCPDADFGIIFMDGGGYLNMCGHGTIGAMTAAIETGVVPAVEPVTHVVMEAPAGIIRGD 129
           P   D+D GI+F++  G L MCGHGTIG +T  +E G++   E    + +E PAGII   
Sbjct: 68  PTRDDSDCGILFIETSGSLPMCGHGTIGMVTFGLENGLITPRE-AGGLRIEVPAGIIDIA 126

Query: 130 VTVVDGKAKEVSFLNVPAFLYKEGVEVDLPGVGTVKFDISFGGSFFAIIHASQLGLKIEP 189
                 + + V   NVPA+L ++ +E+D+PG G +  D+++GG+++AI+        ++ 
Sbjct: 127 YRTDGDRVRSVRIHNVPAYLARQALEIDVPGFGPLTVDVAYGGNYYAIVEPQGAYTGLDD 186

Query: 190 QNAGKLTELAMKLRDIINEKIEIQHPTLAHIKTVDLVEIYDEPTHPEATYKNVVIFGQGQ 249
             A +L  L+  +R+ +    E  HP  A I+ V  V   D P    A  +N V +G   
Sbjct: 187 LGAERLVALSRIVREQVRAAYEPVHPLDASIRGVSHVLWADAPKGDGADGRNAVFYGDSA 246

Query: 250 VDRSPCGTGTSAKLATLHAKGELKVGEKFVYESILGTLFKGEIVEETKVADFNAVVPKIT 309
           +DRSPCGTGTSA+LA L   G L VG+ FV+ES +G+ F G +  E +V +  A+VP I 
Sbjct: 247 IDRSPCGTGTSARLAQLAGTGRLSVGDAFVHESYIGSRFTGRVEAEARVGELPAIVPSIE 306

Query: 310 GSAYITGFNHFVIDEEDPLKHGF 332
           GSA  TG+N   ID EDP   GF
Sbjct: 307 GSAIATGYNTIWIDREDPFWAGF 329


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: 331
Number of extensions: 17
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 24 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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