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_066603399.1 V473_RS10210 threonine ammonia-lyase

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_001046645.1:WP_066603399.1
          Length = 415

 Score =  219 bits (557), Expect = 1e-61
 Identities = 121/318 (38%), Positives = 174/318 (54%), Gaps = 3/318 (0%)

Query: 5   LVLP-TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALN 63
           L LP T DD+ +A  RI     KTP L S T++      V+ K EN Q   A+K RGALN
Sbjct: 11  LPLPITVDDILAARTRIAGSIVKTPTLISQTLSNMLGCNVYLKFENLQFTAAYKERGALN 70

Query: 64  ALSQLNEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQV 123
            L QL++A +  GV+  S+GNHAQ +A   K LG+P  I+MP   P  K+  T+G+G  V
Sbjct: 71  RLIQLDDAAKAKGVIAASAGNHAQGLAYHGKRLGVPVTIVMPTTTPTVKITQTQGHGATV 130

Query: 124 IMYDRYKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPLDALFVCLG 183
           + Y    DD    A+ + E +GLT + P+D P ++AGQGT A E+ E+   +D L + +G
Sbjct: 131 VQYGEKFDDAYAHARLMEEEQGLTFVHPFDEPDIMAGQGTVALEMLEDAPEIDTLIIPIG 190

Query: 184 GGGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIVHIDTPKTIADGAQTQHLG 243
           GGGL SG   AAR   P+ ++YGV+ E        F KG+ +  D   T+A+G   +  G
Sbjct: 191 GGGLFSGMGTAARAMKPDIQLYGVQAEL-YPSMYDFIKGADLACD-GDTLAEGIAVKQPG 248

Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRI 303
             T   ++   DD+L VS+  L + L       K VVE  G    AA    +EK   + +
Sbjct: 249 ELTRRFVERLADDVLLVSERRLEEALSLLLQIEKTVVEGAGAAGLAALLTYREKFAGRNV 308

Query: 304 GIIISGGNVDIERYAHFL 321
           G++++GGN+D    A+ L
Sbjct: 309 GLVLTGGNIDTRLLANVL 326


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: 305
Number of extensions: 9
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: 415
Length adjustment: 30
Effective length of query: 293
Effective length of database: 385
Effective search space:   112805
Effective search space used:   112805
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