GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Acidovorax sp. GW101-3H11

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 Ac3H11_2042 Threonine dehydratase biosynthetic (EC 4.3.1.19)

Query= SwissProt::Q7XSN8
         (339 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_2042
          Length = 519

 Score =  168 bits (425), Expect = 3e-46
 Identities = 101/308 (32%), Positives = 167/308 (54%), Gaps = 13/308 (4%)

Query: 29  ARIAPYVHKTPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGV 88
           AR+     ++ +  + S+   +  ++  K E  Q   +FK+RGA N +  L  ++  +GV
Sbjct: 17  ARVYDVAVESALEPAKSLSRRLHNKVLLKREDQQPVFSFKLRGAYNKMAHLTPEQLQRGV 76

Query: 89  VTHSSGNHAAAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVA 148
           +  S+GNHA  VA++A   G  A +V+P   P  KVD VK  GG ++    S       A
Sbjct: 77  ICASAGNHAQGVAMSAHKLGTRAVVVMPTTTPQLKVDAVKTLGGEVVLHGESYSDAYEHA 136

Query: 149 KRVQEETGAILVHPFNNKNTISGQGTVSLELLEEVP-----EIDTIIVPISGGGLISGVA 203
            R+Q+E G   VHPF++   I+GQGT+++E+L ++      ++D + V I GGGL+SGVA
Sbjct: 137 ARLQKEQGLTFVHPFDDPLVIAGQGTIAMEILRQLQSLGSNQLDAVFVAIGGGGLVSGVA 196

Query: 204 LAAKAINPSIRILAAEPKGADDSAQSKAAGKIITLPSTNTIADGLRA-FLGDLTWPVVRD 262
              KA+ P I+++  +   +D   QS  A + +TLP     +DG     +G+ T+ V + 
Sbjct: 197 NYIKAVRPEIKVIGVQMNDSDAMIQSVNAHQRVTLPDVGLFSDGTAVKLVGEETFRVAQG 256

Query: 263 LVDDIIVVDDNAIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHES--SKIGI 320
           LVD+ + VD +A+  A+K  +   +  VEP+GA+ +AA      KQ  A H++       
Sbjct: 257 LVDEFVTVDTDAVCAAIKDIFVDTRSIVEPAGALAVAA-----IKQYVATHKTKGETYAA 311

Query: 321 IVSGGNVD 328
           I+ G N++
Sbjct: 312 ILCGANMN 319


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: 304
Number of extensions: 10
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: 339
Length of database: 519
Length adjustment: 32
Effective length of query: 307
Effective length of database: 487
Effective search space:   149509
Effective search space used:   149509
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: 50 (23.9 bits)

This GapMind analysis is from Sep 17 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