GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Lutibaculum baratangense AMV1

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_051402369.1 N177_RS12980 threonine/serine dehydratase

Query= BRENDA::Q2PGG3
         (331 letters)



>NCBI__GCF_000496075.1:WP_051402369.1
          Length = 340

 Score =  218 bits (554), Expect = 2e-61
 Identities = 128/309 (41%), Positives = 189/309 (61%), Gaps = 11/309 (3%)

Query: 15  IKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKFRGACNAVLSLDAEQ 74
           ++ A +R+     RTP++ S  L+  +GR +  K E LQ+ G+FKFRGA NA+ SLDA+ 
Sbjct: 25  VRRASERLSGEAVRTPLVRSAILDERAGRPVLLKAEVLQRTGSFKFRGAYNAIASLDADA 84

Query: 75  AAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIRYGGKVIWSEATMSS 134
            AKGVV  SSGNHA  ++ AA++ G+ A IV+P  AP  KV    R G  V+  +    S
Sbjct: 85  RAKGVVACSSGNHAQGVAEAARLFGVRATIVMPADAPALKVARTKRSGAHVVTYDRVNES 144

Query: 135 REEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEID----AIVVPISGGGLI 190
           REEIA +++ ETG+  + PY+D R+ISGQGT+ +E+ EQ + +      I+VP SGGGL 
Sbjct: 145 REEIALRIVAETGADFVPPYDDRRVISGQGTVGIEIAEQAEALGLDPARILVPCSGGGLS 204

Query: 191 SGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAG-KIITLPVTNTIADGLRASL-GDLTW 248
           +G+ALAA+++ P  R+   EP+  DD A+S  +G +      + +I D L A   G++T+
Sbjct: 205 AGIALAAEALMPWARVTTVEPEAFDDHARSFRSGEREGNTARSGSICDALLADRPGEITF 264

Query: 249 PVVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFRNNPSCRDCKN 308
            V R  V   + + + E+  AM+  +E LK+ VEP GA+GLAAVL+      P     + 
Sbjct: 265 AVNRPRVPSGLAVSDDEVRTAMRFAFEELKLVVEPGGAVGLAAVLAGRLDEGP-----QP 319

Query: 309 IGIVLSGGN 317
           + +VLSGGN
Sbjct: 320 VVVVLSGGN 328


Lambda     K      H
   0.316    0.133    0.380 

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: 285
Number of extensions: 12
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: 331
Length of database: 340
Length adjustment: 28
Effective length of query: 303
Effective length of database: 312
Effective search space:    94536
Effective search space used:    94536
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