GapMind for Amino acid biosynthesis

 

Alignments for a candidate for serB in Marivita geojedonensis DPG-138

Align Phosphoserine aminotransferase; EC 2.6.1.52 (characterized, see rationale)
to candidate WP_085635109.1 MGEO_RS02560 2-aminoethylphosphonate--pyruvate transaminase

Query= uniprot:F9VNX9
         (372 letters)



>NCBI__GCF_002115805.1:WP_085635109.1
          Length = 393

 Score =  100 bits (248), Expect = 9e-26
 Identities = 104/374 (27%), Positives = 156/374 (41%), Gaps = 14/374 (3%)

Query: 2   LLIPGPVEVPRSVREASTLVVNHRSEKFREIVRKLES----LMNKHFSASRTALLTGSGT 57
           LL PGP+    SV++A         + FR + R L S    L+    S      + GSG+
Sbjct: 16  LLTPGPLTTAYSVKQAMLKDWGSWDDDFRAMTRALRSRLLALIGGGASDYDCVPIQGSGS 75

Query: 58  LAVEAMVYSLIKPNEKVISFPYGEFGNRLVDSLRRRGAQVKVYEKKIGEIFSIDEIKKAL 117
             VEAM+ S +  + KV+    G +G R   +L        + +K        DE+   L
Sbjct: 76  YCVEAMLGSFVPRDGKVLVLANGAYGLRAAQTLGYLERDYHLLDKGDYLPPRGDEVAAIL 135

Query: 118 DENKDATAVALVHNETSSGMAFRNLEDVVSEVKRRGLKLLVDSVSGFAAYKLLVNEWKID 177
             +   T V  +H ETSSG+    +E++    K  G KLL+DS+S F A  L   +    
Sbjct: 136 AADPAITHVLAIHCETSSGIQ-NPVEEIAEATKAAGRKLLIDSMSAFGALPLDPVKLNCA 194

Query: 178 AVATGSQKALASVPGMSFVALSDDGIEEIQGESLPSYLDISLHLKFQDK-GETPFTPAVG 236
           A  + + K +  VPG  FV    D IE  +G S    LD+       +K G+  FTP   
Sbjct: 195 AFVSSANKCIEGVPGFGFVIARKDEIEASKGNSHSLSLDVHAQWATMEKTGQWRFTPPTH 254

Query: 237 VFNASLRAAELLEIE-GIENRWKRHEACARFVREVLSSYGFLLFGNENNFSNTVVAGVPP 295
           V  A L+A +L E E G+  R  R+      V + +   GF     +   S  +V    P
Sbjct: 255 VVAAFLKALDLHEAEGGVSARGARYTRNRDVVVQGMRDLGFETLLADRWLSPIIVTFFCP 314

Query: 296 IPDYRKKLLNEFNIEISGGMGELKEKIV-----RIGLLGVVDSRAVNKLLEATA-KLLDK 349
             D        ++   + G      K+      RIG++G +D   + +++EA    L D 
Sbjct: 315 -ADPSFTFQGFYDAMKARGFIIYPGKLTVVNSFRIGVIGQMDEHVMRRVVEAARDALTDM 373

Query: 350 NYDYLPPRECKLPE 363
           N     P    L E
Sbjct: 374 NVSSAAPPAAALEE 387


Lambda     K      H
   0.316    0.135    0.377 

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: 301
Number of extensions: 16
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: 372
Length of database: 393
Length adjustment: 30
Effective length of query: 342
Effective length of database: 363
Effective search space:   124146
Effective search space used:   124146
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