GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Planktomarina temperata RCA23

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_044050245.1 RCA23_RS10315 threonine/serine dehydratase

Query= BRENDA::O59791
         (323 letters)



>NCBI__GCF_000738435.1:WP_044050245.1
          Length = 325

 Score =  212 bits (540), Expect = 9e-60
 Identities = 123/314 (39%), Positives = 184/314 (58%), Gaps = 5/314 (1%)

Query: 13  VASASERIKKFANKTPVLTSSTVNKEFVAEVFFKCENFQKMGAFKFRGALNALSQLNEAQ 72
           + +A++R++  A +TP+L S+ V++     V+ K E  Q  G+FKFRG  +A+S L    
Sbjct: 6   IRAAAQRLEGQARRTPLLNSAFVDEIAGRRVWVKAEALQHTGSFKFRGGWSAVSALAAEV 65

Query: 73  RKAGVLTFSSGNHAQAIALSAKILGIPAKIIMPLDAPEAKVAATKGYGGQVIMYDRYKDD 132
           R AGV+ +SSGNHAQ +AL+A++ G+PA I+MP DAP  KV  T+  G +VI+YDR  +D
Sbjct: 66  RSAGVIAYSSGNHAQGVALAARLHGVPAVIVMPKDAPRLKVENTRALGAEVILYDRDHED 125

Query: 133 REKMAKEISEREGLTIIPPYDHPHVLAGQGTAAKEL---FEEVGPLDA-LFVCLGGGGLL 188
           RE +   ++E  GL++I PYD P V+AGQGT   E+     EVG   A + VC GGGGL 
Sbjct: 126 REAIGAALAEARGLSLIKPYDAPEVIAGQGTCGLEIAAQAAEVGIAKADVLVCCGGGGLT 185

Query: 189 SGSALAARHFAPNCEVYGVEPEAGNDGQQSFRKG-SIVHIDTPKTIADGAQTQHLGNYTF 247
           SG ALA    AP+  V  VEP   +D  +S + G    +  +  +I D   T+  G  TF
Sbjct: 186 SGVALALEQEAPDMRVRPVEPVDFDDVTRSLQSGRRESNTRSGGSICDAIVTRSPGEMTF 245

Query: 248 SIIKEKVDDILTVSDEELIDCLKFYAARMKIVVEPTGCLSFAAARAMKEKLKNKRIGIII 307
            ++ E     + V +E+ +  +    +R K+V+EP G ++ AAA    E+L  + +  I 
Sbjct: 246 PLMHELCGPGIVVPEEDCLRAISVAFSRFKLVLEPGGAIALAAALYHGEQLSGEHVICIA 305

Query: 308 SGGNVDIERYAHFL 321
           SGGN+D + +   L
Sbjct: 306 SGGNIDAQMFTRAL 319


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: 237
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: 325
Length adjustment: 28
Effective length of query: 295
Effective length of database: 297
Effective search space:    87615
Effective search space used:    87615
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