GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Marivita geojedonensis DPG-138

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_085634976.1 MGEO_RS01815 hydroxyectoine utilization dehydratase EutB

Query= SwissProt::Q7XSN8
         (339 letters)



>NCBI__GCF_002115805.1:WP_085634976.1
          Length = 333

 Score =  157 bits (398), Expect = 3e-43
 Identities = 99/306 (32%), Positives = 160/306 (52%), Gaps = 12/306 (3%)

Query: 27  AQARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASK 86
           A+  IA     TP++ S   +   G++   K E  Q  GAFK+RGA NS+  L D   +K
Sbjct: 11  ARNTIAGVADGTPLVPSALTETF-GQEFLLKLEIAQPIGAFKLRGALNSVLNLPD--GAK 67

Query: 87  GVVTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRES 146
           GV   S+GNH   VA AA+ RG+ A + +   AP  K+  V+  G        S +  + 
Sbjct: 68  GVTCCSTGNHGRGVAFAARQRGLRAVVCMSNLAPQSKIAGVRVLGAEARIIGQSQDEAQD 127

Query: 147 VAKRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAA 206
            A+R+  E G + + PF++   ++GQ T+ LELLE  P++DTI+VP+SGGGL  G+A  A
Sbjct: 128 EAERLAAEEGLVDISPFDDPYVVAGQATIGLELLEARPDLDTILVPLSGGGLAGGIAYTA 187

Query: 207 KAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRAFLG---DLTWPVVRDL 263
           K I P IR++           +S  AG  + +    ++AD L   +G    L++ + R+ 
Sbjct: 188 KQIRPDIRVIGITMDRGAAMYESVKAGHPVEVEEVPSLADSLGGGIGLQNRLSFALCREF 247

Query: 264 VDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHESSKIGIIVS 323
           +DDI++V +  I  +++  Y   ++  E +  +G+AA       QS     +     I++
Sbjct: 248 LDDIVLVTEEDIYRSLQTVYYEDRIVCEGACVVGIAAV------QSGRVVLTGPTATIIT 301

Query: 324 GGNVDL 329
           G N+D+
Sbjct: 302 GRNLDM 307


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: 250
Number of extensions: 10
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: 339
Length of database: 333
Length adjustment: 28
Effective length of query: 311
Effective length of database: 305
Effective search space:    94855
Effective search space used:    94855
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: 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