GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Microvirga lotononidis WSM3557

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_085985190.1 MICLODRAFT_RS33510 threonine ammonia-lyase, biosynthetic

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_000262405.1:WP_085985190.1
          Length = 519

 Score =  179 bits (453), Expect = 2e-49
 Identities = 99/280 (35%), Positives = 156/280 (55%), Gaps = 3/280 (1%)

Query: 43  VFFKCENFQKMGAFKFRGALNALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKI 102
           V  K E+ Q + +FK RGA   ++ L     + GV+  S+GNHAQ +A++AK LG  A I
Sbjct: 44  VRLKREDLQPVFSFKLRGAYARMAGLPREALERGVICASAGNHAQGVAVAAKKLGAKATI 103

Query: 103 IMPLDAPEAKVAATKGYGGQVIMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQG 162
           +MP   P  K+ A KG GG+VI++    D+    A+++   +GLT I PYD P V+AGQG
Sbjct: 104 VMPRTTPAIKIQAVKGQGGRVILHGESFDEAYSHAQQLEAEKGLTFIHPYDDPDVIAGQG 163

Query: 163 TAAKELF-EEVGPLDALFVCLGGGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRK 221
           T   E+  +   PL+A+FV +GGGGL +G A+  +   P  +V GVEPE       +   
Sbjct: 164 TVGMEILRQHPDPLEAIFVPIGGGGLAAGVAVYTKFLRPEVKVIGVEPEDAASMAAALAA 223

Query: 222 GSIVHIDTPKTIADGAQTQHLGNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVE 281
           G  V ++     ADG   +  G  TF + +E +D+++TVS +E+   +K      + + E
Sbjct: 224 GDRVILNQVGLFADGVAVRQAGEETFRLCRELLDEVITVSTDEICAAVKDIFEDTRAIAE 283

Query: 282 PTGCLSFAAARAMKEKLKNKRIGIII--SGGNVDIERYAH 319
           P+G +S A  +   E+   ++ G++   SG N++ +R  H
Sbjct: 284 PSGAVSLAGLKKYVEREGARQQGLVAVNSGANMNFDRLRH 323


Lambda     K      H
   0.318    0.135    0.384 

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: 345
Number of extensions: 12
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: 323
Length of database: 519
Length adjustment: 31
Effective length of query: 292
Effective length of database: 488
Effective search space:   142496
Effective search space used:   142496
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 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