GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Microvirga lotononidis WSM3557

Align serine racemase (EC 5.1.1.18) (characterized)
to candidate WP_009491092.1 MICLODRAFT_RS10110 threonine ammonia-lyase

Query= BRENDA::Q2PGG3
         (331 letters)



>NCBI__GCF_000262405.1:WP_009491092.1
          Length = 423

 Score =  207 bits (526), Expect = 5e-58
 Identities = 122/321 (38%), Positives = 189/321 (58%), Gaps = 10/321 (3%)

Query: 1   MEANREKYAADILSIKEAHDRIKPYIHRTPVLTSESLNSISGRSLFFKCECLQKGGAFKF 60
           +E +   YA  I  +K A + I+  + RTP++ +  L+ ++G ++F K E +Q  G+FK 
Sbjct: 7   LEDDVADYAITIEDVKRAAETIQGQVLRTPLVPAPRLSQLTGSTVFVKHENMQPTGSFKE 66

Query: 61  RGACNAVLSLDAEQAAKGVVTHSSGNHAAALSLAAKIQGIPAYIVVPKGAPKCKVDNVIR 120
           RGA   + SL   +   GV+  S+GNHA A++  A+  GIPA IV+P G P  K +N   
Sbjct: 67  RGATTKLESLTEAERKHGVIAMSAGNHAQAVAYHARRLGIPATIVMPVGTPLVKAENTRS 126

Query: 121 YGGKVIWSEATMSSREEIASKVLQETGSVLIHPYNDGRIISGQGTIALELLEQIQEIDAI 180
           YG +VI    T+      A ++    G V +HPY+D ++++GQGTIALE+L    ++D I
Sbjct: 127 YGARVILEGETLYESAARAREIADAEGLVFVHPYDDPKVMAGQGTIALEMLADAPDLDQI 186

Query: 181 VVPISGGGLISGVALAAKSIKPSIRIIAAEPKGADDAAQSKVAGKIITLPVTN-TIADGL 239
           VVPI GGGLISG+A+AAK++KPS  II  E      + ++ + G+    P+   T+A+G+
Sbjct: 187 VVPIGGGGLISGIAIAAKALKPSTEIIGVE-AALYPSFRNAILGE--NRPIGGATLAEGI 243

Query: 240 RA-SLGDLTWPVVRDLVDDVVTLEECEIIEAMKMCYEILKVSVEPSGAIGLAAVLSNSFR 298
              ++G L  P+VRDLV +++ +EE  I  A+     + +   E +GA GLAA+L+    
Sbjct: 244 AVKTVGQLPLPIVRDLVPNIIAVEEPLIERAVNAYATLQRTMAEGAGAAGLAAMLA---- 299

Query: 299 NNPSCRDCKNIGIVLSGGNVD 319
             P     K +G+VL GGN+D
Sbjct: 300 -QPERFQGKRVGLVLCGGNID 319


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: 307
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: 423
Length adjustment: 30
Effective length of query: 301
Effective length of database: 393
Effective search space:   118293
Effective search space used:   118293
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.

Links

Downloads

Related tools

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