GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Sphingobium czechense LL01

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_066603969.1 V473_RS11265 threonine/serine dehydratase

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_001046645.1:WP_066603969.1
          Length = 330

 Score =  209 bits (531), Expect = 1e-58
 Identities = 116/315 (36%), Positives = 176/315 (55%), Gaps = 5/315 (1%)

Query: 9   TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68
           T  D+  A+  I   A +TP+L +  +N      V  K E  Q  G+FKFRGA N L++L
Sbjct: 8   TIHDIIDAARIIAPAAVRTPLLENHALNDRLGRRVLIKFEGAQHTGSFKFRGAYNRLARL 67

Query: 69  NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDR 128
           +  QR AGV+ +SSGNHAQ +A +A++L +PA I+MP DAP  K+A  +  G +++ YDR
Sbjct: 68  DAQQRAAGVVAWSSGNHAQGVAAAAQLLALPATIVMPSDAPAIKLANNRALGAEIVTYDR 127

Query: 129 YKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDA----LFVCLGG 184
           + + RE++A  ++   G T++P +D P V+AGQGTA  E+ ++     A    + VC GG
Sbjct: 128 HSESREEIATALAHSRGATLVPSFDDPFVIAGQGTAGLEILDQAAEAGAIIGQILVCCGG 187

Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHI-DTPKTIADGAQTQHLG 243
           GGL +G A A +  AP   +Y VEP   +D  +S   G   +I    ++I D       G
Sbjct: 188 GGLTAGIATAVKARAPEIALYAVEPAGFDDTARSLASGVRENIAPDARSICDALMAPSPG 247

Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRI 303
             TF I +  +   L VSD+++ D ++F  + +K+VVEP G ++ AA             
Sbjct: 248 AMTFPINQALLSGGLVVSDDQVRDAMRFAFSTLKLVVEPGGAVALAAVLNGLAPPCGDAS 307

Query: 304 GIIISGGNVDIERYA 318
            +++SG NVD   YA
Sbjct: 308 VVVLSGSNVDPAAYA 322


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: 219
Number of extensions: 6
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: 330
Length adjustment: 28
Effective length of query: 295
Effective length of database: 302
Effective search space:    89090
Effective search space used:    89090
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: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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