GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Shewanella sp. ANA-3

Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate 7023122 Shewana3_0360 alanine-glyoxylate aminotransferase (RefSeq)

Query= metacyc::MONOMER-15919
         (385 letters)



>FitnessBrowser__ANA3:7023122
          Length = 377

 Score =  217 bits (553), Expect = 4e-61
 Identities = 129/353 (36%), Positives = 197/353 (55%), Gaps = 5/353 (1%)

Query: 7   KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGS 65
           +++LM PGP+ V PEVL A A P +GH    +  ++++    ++  F T+N+ T  ++  
Sbjct: 14  RRILMGPGPSDVYPEVLAAQARPTVGHLDPLFVGMMDELKSLIQYAFQTKNEMTMAVSAP 73

Query: 66  GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125
           G+A M+    N+++ G+KV+    G FGER    V+     A+ +D EWG   +  AV+ 
Sbjct: 74  GSAGMETCFVNLVEPGEKVIVCRNGVFGERMRQNVERVGAIAVLVDNEWGTPVDAAAVEA 133

Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185
            L    D K +  VH ETSTGA +  K +  + K Y  L IVD V+SLGG  + VD++ I
Sbjct: 134 ALKANPDAKFLAFVHAETSTGALSDAKTLCALAKQYGCLSIVDAVTSLGGVELRVDEWGI 193

Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKV-GFYLD---LLAYKKYYEEKKQT 241
           D   +GSQKCL+  PGL+ ++ S  A E +K     V  ++LD   ++AY      K+  
Sbjct: 194 DAIYSGSQKCLSCVPGLSPVSFSPNAVEKLKNRKTPVQSWFLDQSLVMAYWTSAGGKRSY 253

Query: 242 PYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTV 301
            +T  VN  YAL+ +L L+ EEG+EN  KRH+ +    RAGLE +G++    E +R   +
Sbjct: 254 HHTAPVNALYALHESLRLLAEEGLENAWKRHQDMHLVLRAGLEKLGLKFVVAEASRLPQL 313

Query: 302 TSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLA 354
            +   PEG++D+  R  L   YN+ +  G   LAGK +RIG MG    +E +A
Sbjct: 314 NAIYIPEGVDDAAVRARLLKDYNLEIGAGLGALAGKAWRIGLMGFGARRENVA 366


Lambda     K      H
   0.316    0.135    0.379 

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: 331
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: 385
Length of database: 377
Length adjustment: 30
Effective length of query: 355
Effective length of database: 347
Effective search space:   123185
Effective search space used:   123185
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 Apr 09 2024. The underlying query database was built on Apr 09 2024.

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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