GapMind for Amino acid biosynthesis

 

Alignments for a candidate for PPYAT in Salinicoccus carnicancri Crm

Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_026090172.1 C792_RS0101225 alanine--glyoxylate aminotransferase family protein

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



>NCBI__GCF_000330705.1:WP_026090172.1
          Length = 382

 Score =  262 bits (670), Expect = 1e-74
 Identities = 147/361 (40%), Positives = 218/361 (60%), Gaps = 5/361 (1%)

Query: 7   KKLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITENDTFLITGSG 66
           +KLL+ PGPT +PPEV + MA  +IGHR+ D++ L+E+    LK +  T+N   +++ SG
Sbjct: 3   QKLLLTPGPTPIPPEVSSRMAEGMIGHRSNDFNKLMENIQPGLKAILGTKNPVAILSSSG 62

Query: 67  TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126
           T+A++ A+ N+++  + ++ IV+G+FG+RF NI K Y  E    DVEWG  A+P   KE 
Sbjct: 63  TSALETAMVNLVRPDESIVIIVSGSFGDRFRNIAKTYPFEVHVYDVEWGQAADPGRFKEF 122

Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDY--DALYIVDTVSSLGGDYVNVDKFH 184
           LD  +++KAV     ETST   +P+ E+GE VK Y  + L+IVD VS +GG   ++++ +
Sbjct: 123 LDTKENVKAVFSQSCETSTAVIHPLNELGEAVKSYSSETLFIVDGVSIVGGMTFDMEQDN 182

Query: 185 IDICVTGSQKCLAAPPGLAAITVSEKAWEVIKKNDDKVGFYLDLLAYKKYYEEKKQTPYT 244
           ID  VTGSQK L  PPGLA + +++ A +    N D   FYLD+  Y K  EE   TP+T
Sbjct: 183 IDCLVTGSQKALMLPPGLAFVAMNDTARQKASDN-DLPRFYLDINRYFKALEE-HSTPFT 240

Query: 245 PSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFAKERARSVTVTSA 304
           P+V+L   L   L+   EEGIEN  +RH  +    RAGL A+ + +   +   S TVT+ 
Sbjct: 241 PAVSLIQGLEKVLETYREEGIENVFERHRNMRDMLRAGLRALDLTMLVADEHASPTVTAF 300

Query: 305 KYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGICGEKEVLATLACVELALK 364
           +  E  E    +  L +++ I +AGGQK L GKI RIGHMG     +++  L  +E  L 
Sbjct: 301 QSSED-ELKVIKNKLKSEHQITIAGGQKDLKGKILRIGHMGYMFPHDMIRVLTAIEAILT 359

Query: 365 E 365
           +
Sbjct: 360 D 360


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: 318
Number of extensions: 12
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: 382
Length adjustment: 30
Effective length of query: 355
Effective length of database: 352
Effective search space:   124960
Effective search space used:   124960
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 26 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