GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Shewanella loihica PV-4

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 5207772 Shew_0293 threonine dehydratase (RefSeq)

Query= SwissProt::Q7XSN8
         (339 letters)



>FitnessBrowser__PV4:5207772
          Length = 516

 Score =  182 bits (463), Expect = 1e-50
 Identities = 108/298 (36%), Positives = 169/298 (56%), Gaps = 17/298 (5%)

Query: 38  TPVLSSTSIDAIVGKQLFFKCECFQKAGAFKIRGASNSIFALDDDEASKGVVTHSSGNHA 97
           TP+ S   + A +G Q+F K E  Q   +FK+RGA N I  L  +E  +GVV  S+GNHA
Sbjct: 32  TPLSSLNKLSARLGCQVFLKREDMQPVHSFKLRGAYNRIAELSQEECQRGVVCASAGNHA 91

Query: 98  AAVALAAKLRGIPAYIVIPRNAPACKVDNVKRYGGHIIWSDVSIESRESVAKRVQEETGA 157
             VA++A  RG+ A IV+P+  P  KVD V+R GG ++    S +     A+++  + G 
Sbjct: 92  QGVAMSASARGVSAVIVMPQTTPDIKVDAVRRLGGTVVLYGQSFDMANEHAQQLARDEGR 151

Query: 158 ILVHPFNNKNTISGQGTVSLELLEEVPEIDTIIVPISGGGLISGVALAAKAINPSIRILA 217
           I V PF+++  I+GQGTV+ E+L++  +++ + VP+ GGGLI+G+A   KA+ P ++I+ 
Sbjct: 152 IYVAPFDDEAVIAGQGTVAQEMLQQQRDLEVVFVPVGGGGLIAGIAAYYKAVMPQVKIIG 211

Query: 218 AEPKGADDSAQSKA---AGKIITLPSTNTIADGLRA-FLGDLTWPVVRDLVDDIIVVDDN 273
            EP   +DSA  KA   A + + L      ADG+    +G   + + R+ VD ++ V  +
Sbjct: 212 VEP---EDSACLKAALEADERVVLSQVGLFADGVAVKQIGAEPFRLAREYVDQVVTVTSD 268

Query: 274 AIVDAMKMCYEMLKVAVEPSGAIGLAAA---LSDEFKQSSAWHESSKIGIIVSGGNVD 328
            I  A+K  +E  +   EP+GA+ LA     + DE K         K+  I+SG NV+
Sbjct: 269 EICAAVKDIFEDTRAIAEPAGALSLAGLKKYIGDEGK-------GQKVAAILSGANVN 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: 313
Number of extensions: 16
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: 516
Length adjustment: 32
Effective length of query: 307
Effective length of database: 484
Effective search space:   148588
Effective search space used:   148588
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