GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Pseudovibrio axinellae Ad2

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_068002199.1 PsAD2_RS03350 threonine/serine dehydratase

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_001623255.1:WP_068002199.1
          Length = 339

 Score =  225 bits (574), Expect = 1e-63
 Identities = 126/320 (39%), Positives = 181/320 (56%), Gaps = 5/320 (1%)

Query: 9   TYDDVASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQL 68
           T  ++  A  R++ +++ TP+L    +++     VF K EN Q+ G+FKFRGA N LS +
Sbjct: 12  TVSEIEKARARLQGYSSMTPLLNYPVLDERVNGRVFIKAENLQRTGSFKFRGAFNRLSLI 71

Query: 69  NEAQRKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDR 128
            + QR  GV+  SSGNHAQ +A SAKILG PA I+MP DAPE K+  TK  G +VI+Y R
Sbjct: 72  PQGQRAGGVVACSSGNHAQGVAASAKILGFPAVIVMPKDAPELKIQRTKALGAEVILYCR 131

Query: 129 YKDDREKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKELFEEVGPL----DALFVCLGG 184
           + +DRE +A  I E  G T I P++   V+ GQGT+  E+ E+   L    D L  C GG
Sbjct: 132 HSEDREAIAHAICEERGATFIHPFNDSGVIVGQGTSGLEIVEQCEALGVSPDVLISCTGG 191

Query: 185 GGLLSGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKGSIV-HIDTPKTIADGAQTQHLG 243
           GGL SG ALA     P+C++Y  EP   +D  +S   G  V +     ++ D   T   G
Sbjct: 192 GGLTSGIALALEKSLPDCQIYTAEPAGFDDYARSLESGERVRNAALSGSVCDAIMTDTPG 251

Query: 244 NYTFSIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRI 303
             +F+I+K +    L+VSDE+ +  + +    +K+VVEP   ++ A+  + +  L  K  
Sbjct: 252 EKSFAILKRRQAKGLSVSDEQAMHAVAYAYFELKLVVEPGAAVALASLLSGQIDLDGKTA 311

Query: 304 GIIISGGNVDIERYAHFLSQ 323
            I ISGGNVD   +   L Q
Sbjct: 312 VITISGGNVDPSVFEAALKQ 331


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: 238
Number of extensions: 12
Number of successful extensions: 4
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: 339
Length adjustment: 28
Effective length of query: 295
Effective length of database: 311
Effective search space:    91745
Effective search space used:    91745
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.

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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