GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Clostridium tyrobutyricum FAM22553

Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_017896025.1 PN53_RS14945 alanine--glyoxylate aminotransferase family protein

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



>NCBI__GCF_000816635.1:WP_017896025.1
          Length = 392

 Score =  232 bits (592), Expect = 1e-65
 Identities = 131/366 (35%), Positives = 222/366 (60%), Gaps = 13/366 (3%)

Query: 10  LMIPGPTMVPPEVLNAMAL----PVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGS 65
           +M PGPT V   V  A ++    P + ++  D+    ++T  +L KV  T+N+  ++ G 
Sbjct: 6   IMTPGPTEVSENVRIARSIRCTNPDLDNKFYDF---YKETCNRLGKVLNTKNEVRVLCGE 62

Query: 66  GTAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKE 125
           G   ++ A +++ ++GD+VL I  G FGE FA+ ++ Y G+ +    +       E +KE
Sbjct: 63  GILGLEAACASLTEKGDRVLVIDNGIFGEGFADFIRLYCGKVVFFKADRKHAINIEDLKE 122

Query: 126 ILDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHI 185
            LDK +D K  TVVH +T +G  N I +I  ++K Y  L +VD+V+++GG+ + VDK++I
Sbjct: 123 FLDKDNDFKYATVVHCDTPSGVLNDISKICPLLKKYGILTVVDSVAAMGGENLEVDKWNI 182

Query: 186 DICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVG-FYLDLLAYKKYYEEKKQTPYT 244
           DI + GSQKC++APPGL  +++S+ A+  ++     +G FY +LLA+K YYE+ K  PYT
Sbjct: 183 DIVIGGSQKCISAPPGLTIVSISKDAFSSMENRKSPIGSFYCNLLAWKNYYED-KWFPYT 241

Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304
           P V+  Y L  A+D +L++  +  + RH+ +A +TR  +   G++L+  E   S TVT  
Sbjct: 242 PPVSDIYGLREAVDNILKD--KEILNRHKNIASSTRYAVRKAGLDLYT-EDGYSSTVTVI 298

Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGE-KEVLATLACVELAL 363
           + P+GI+D+K R  +   Y++++AG   +L G++ RIGHMG      +V  TL  ++ +L
Sbjct: 299 QVPDGIQDNKLREYMEENYDVMIAGSFGYLKGEVIRIGHMGENARYDKVSYTLYALQQSL 358

Query: 364 KELGFE 369
           ++ GF+
Sbjct: 359 EKFGFK 364


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: 391
Number of extensions: 22
Number of successful extensions: 4
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: 392
Length adjustment: 30
Effective length of query: 355
Effective length of database: 362
Effective search space:   128510
Effective search space used:   128510
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 Jul 25 2024. The underlying query database was built on Jul 25 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