GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Sphingopyxis indica DS15

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_089216356.1 CHB69_RS12555 threonine ammonia-lyase

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_900188185.1:WP_089216356.1
          Length = 416

 Score =  219 bits (557), Expect = 1e-61
 Identities = 124/319 (38%), Positives = 179/319 (56%), Gaps = 14/319 (4%)

Query: 9   TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68
           T DDV +A+ERI     +TP L S T+++   AEV+ K EN Q   A+K RGALNAL  L
Sbjct: 17  TLDDVRAAAERINGAVVRTPTLKSQTLSEMVGAEVWLKFENLQFTAAYKERGALNALLLL 76

Query: 69  NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDR 128
           ++A R  GV+  S+GNHAQ +A   K LGIP  I+MP   P+ KV+ T  +G +++++  
Sbjct: 77  DDAARARGVIAASAGNHAQGLAYHGKRLGIPVTIVMPKTTPQVKVSQTASHGAEIVLFGE 136

Query: 129 YKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLGGGGLL 188
             DD    A+E+ +  GLT + P+DHPHV AGQGT A E+ E+V  LD L V +GGGGLL
Sbjct: 137 KFDDAYAHARELEKERGLTFVHPFDHPHVAAGQGTVALEMLEDVPELDTLIVPIGGGGLL 196

Query: 189 SGSALAARHFAPNCEVYGVEPE------AGNDGQQSFRKGSIVHIDTPKTIADGAQTQHL 242
           +G   AAR    +  + GV+ E      A  +G     +G         T+A+G   +  
Sbjct: 197 TGMGTAARGIKNDMRLVGVQAELYPSMYAELNGVDMACEGD--------TLAEGIAVKEP 248

Query: 243 GNYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKR 302
           G YT  ++ E  DDI+ V++  L   +       K VVE  G    AA  A  E+   ++
Sbjct: 249 GAYTRKVVAELNDDIVLVAERHLERAVSLLLQIEKTVVEGAGAAGLAAMLAHPEEFAGRK 308

Query: 303 IGIIISGGNVDIERYAHFL 321
           +G++++GGN+D    A+ L
Sbjct: 309 VGLVLTGGNIDTRLLANVL 327


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: 319
Number of extensions: 12
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: 323
Length of database: 416
Length adjustment: 30
Effective length of query: 293
Effective length of database: 386
Effective search space:   113098
Effective search space used:   113098
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: 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