GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Gallaecimonas xiamenensis 3-C-1

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_008482275.1 B3C1_RS00900 threonine ammonia-lyase, biosynthetic

Query= SwissProt::Q7XSN8
         (339 letters)



>NCBI__GCF_000299915.1:WP_008482275.1
          Length = 500

 Score =  182 bits (462), Expect = 2e-50
 Identities = 111/304 (36%), Positives = 172/304 (56%), Gaps = 22/304 (7%)

Query: 38  TPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGVVTHSSGNHA 97
           TPV     +   +G+ ++ K E  Q   +FK+RGA + I +L  D    GVV  S+GNHA
Sbjct: 23  TPVNRLARLSERLGQDVWLKREDLQPVHSFKLRGAYHKIASLPRD--CPGVVAASAGNHA 80

Query: 98  AAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVAKRVQEETGA 157
             VAL+A+  G  A IV+P  APA KVD VK  G  ++    + ++ +  A+ +  + G 
Sbjct: 81  QGVALSARALGFKAIIVMPTQAPAIKVDAVKALGAEVVLFGDNFDAAKDHAQTLSSQQGF 140

Query: 158 ILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAAKAINPSIRILA 217
             V PF+++  I+GQGT+ LEL++E+P++D + +P+ GGGL +GVA   K + P IR++A
Sbjct: 141 AFVAPFDDEKVIAGQGTLGLELIKELPKLDVLFLPVGGGGLAAGVAAVIKQLKPEIRVVA 200

Query: 218 AEPKGADDSAQSKA---AGKIITLPSTNTIADGLRA-FLGDLTWPVVRDLVDDIIVVDDN 273
            EP   DD+A  KA   AG  +TL    T ADG+    +G  T+ V+   VD+ I V ++
Sbjct: 201 VEP---DDAACFKAAFEAGAPVTLDEVGTFADGVAVKRIGTETFRVMSQFVDEAITVSND 257

Query: 274 AIVDAMKMCYEMLKVAVEPSGAIGLAAALSDEFKQSSAWHE-----SSKIGIIVSGGNVD 328
           AI  A+K  +E ++   EP+GA+ LA           AW E       ++G ++SG N++
Sbjct: 258 AICAAIKDIFEDVRAVAEPAGALSLAGL--------KAWCEQHPEFKGQVGAVLSGANLN 309

Query: 329 LGVL 332
             +L
Sbjct: 310 FHLL 313


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: 326
Number of extensions: 17
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: 500
Length adjustment: 31
Effective length of query: 308
Effective length of database: 469
Effective search space:   144452
Effective search space used:   144452
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 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