GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serC in Lentibacillus jeotgali Grbi

Align phosphoserine aminotransferase monomer (EC 2.6.1.1; EC 2.6.1.52) (characterized)
to candidate WP_010530299.1 ON01_RS06955 alanine--glyoxylate aminotransferase family protein

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



>NCBI__GCF_000224785.1:WP_010530299.1
          Length = 405

 Score =  232 bits (591), Expect = 2e-65
 Identities = 131/379 (34%), Positives = 210/379 (55%), Gaps = 17/379 (4%)

Query: 8   KLLMIPGPTMVPPEVLNAMALPVIGHRTKDYSNLLEDTIEKLKKVFITEND-TFLITGSG 66
           + +M PGP    P VL A++ P+IG    ++  ++ +T+  L+  F T N   F + G+ 
Sbjct: 11  RTIMTPGPVEADPRVLRALSTPIIGQFDTEFLRIMNETMALLRYSFQTNNRWAFPVDGTS 70

Query: 67  TAAMDMAISNIIKRGDKVLNIVTGNFGERFANIVKAYKGEAIRLDVEWGDMAEPEAVKEI 126
            A ++  + +II+ GDK+L  + G FG     I      +   +  EWG++ +PE VK  
Sbjct: 71  RAGIEAVLCSIIEPGDKILIPIFGRFGYLLTEIASRCGADIYTMGKEWGEVFDPEEVKAE 130

Query: 127 LDKYDDIKAVTVVHNETSTGARNPIKEIGEVVKDYDALYIVDTVSSLGGDYVNVDKFHID 186
           + K +  K V +VH ETSTG   P+KEIG+  ++ DAL++VD V++LGG     D++ ID
Sbjct: 131 MKKVNP-KVVAMVHGETSTGKMQPLKEIGQFCREQDALFVVDAVATLGGVEFKTDEWCID 189

Query: 187 ICVTGSQKCLAAPPGLAAITVSEKAWEVI-KKNDDKVGF-------------YLDLLAYK 232
             + G+QKCLA P G+A +T +++  ++I ++ D + G              Y DL   +
Sbjct: 190 AAIAGTQKCLAVPSGMAPLTYNDRVEKLIMERKDIERGLADDSDNERRIQSNYFDLSQIQ 249

Query: 233 KYYEEKKQTPYTPSVNLTYALNVALDLVLEEGIENRVKRHERLAKATRAGLEAMGIELFA 292
            Y+   +   +T + ++ YAL   L L+ EEGIE R++RH+   +A  AGLEAMG+ELF 
Sbjct: 250 DYWSPDRLNHHTEATSMLYALREGLRLIQEEGIEQRLERHQLHGEALVAGLEAMGLELFG 309

Query: 293 KERARSVTVTSAKYPEGIEDSKFRGILSNKYNIVVAGGQKHLAGKIFRIGHMGI-CGEKE 351
               +   VT  K PEGI++++ R  L N++ I +AG    L G ++RIG MG  C +  
Sbjct: 310 DGENKMPVVTVIKVPEGIDEAQVRQTLINEFGIEIAGAFGPLKGNVWRIGSMGYSCRKNN 369

Query: 352 VLATLACVELALKELGFEV 370
           +L  L  +E  L   G ++
Sbjct: 370 ILQVLGALEATLLYHGADI 388


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: 352
Number of extensions: 13
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: 405
Length adjustment: 31
Effective length of query: 354
Effective length of database: 374
Effective search space:   132396
Effective search space used:   132396
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