GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Planktomarina temperata RCA23

Align Serine racemase; D-serine ammonia-lyase; D-serine dehydratase; L-serine ammonia-lyase; L-serine dehydratase; EC 4.3.1.17; EC 4.3.1.18; EC 5.1.1.18 (characterized)
to candidate WP_044048880.1 RCA23_RS02360 threonine/serine dehydratase

Query= SwissProt::Q7XSN8
         (339 letters)



>NCBI__GCF_000738435.1:WP_044048880.1
          Length = 309

 Score =  142 bits (357), Expect = 1e-38
 Identities = 96/304 (31%), Positives = 155/304 (50%), Gaps = 14/304 (4%)

Query: 24  IREAQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDE 83
           +  A  RI P+V +TPVL +     + G  L  K E  Q  G+FK RGA NS+ ++D  +
Sbjct: 7   VSHAWTRIKPHVLRTPVLETD----VFGMPLTLKLEQLQHTGSFKARGAMNSLLSMDVPK 62

Query: 84  ASKGVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIES 143
           A  G+V  S GNH AAVA AA   G  A I +P  A   K++ ++  G  ++    +  +
Sbjct: 63  A--GLVAASGGNHGAAVAWAAARLGHRARIYVPELAGDAKINLIQSLGADLVVVPGAYAN 120

Query: 144 RESVAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVA 203
               A   ++++GA  +H F+   T++GQGTV  E  E+    DT+++ + GGGLI G  
Sbjct: 121 ALEQALSYEKDSGAAQIHAFDAPGTVAGQGTVMAEWEEQGLMADTVLIAVGGGGLIGG-- 178

Query: 204 LAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRD 262
            A   +    +++  EP  A    Q+   G   T+  +   A+ L A   G + + + R 
Sbjct: 179 -AMAWLEGRRKLVGVEPFNAPTLTQALEHGPQTTVEVSGLAANALGAKQAGRICYDLARA 237

Query: 263 LVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIGIIV 322
              + + V+D AI DA K  +  L++ VEP+GA  LAA LS  ++      +  ++ +++
Sbjct: 238 TGTNCVNVEDEAIADAQKRLWTALRLVVEPAGAAALAALLSGAYRP----QKDERLAVLL 293

Query: 323 SGGN 326
            G N
Sbjct: 294 CGAN 297


Lambda     K      H
   0.316    0.133    0.381 

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: 214
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: 339
Length of database: 309
Length adjustment: 28
Effective length of query: 311
Effective length of database: 281
Effective search space:    87391
Effective search space used:    87391
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 (21.6 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