GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Phaeobacter inhibens BS107

Align prephenate dehydrogenase (EC 1.3.1.12) (characterized)
to candidate GFF2491 PGA1_c25230 protein TyrC

Query= BRENDA::J9XQS6
         (287 letters)



>lcl|FitnessBrowser__Phaeo:GFF2491 PGA1_c25230 protein TyrC
          Length = 306

 Score =  285 bits (728), Expect = 1e-81
 Identities = 142/245 (57%), Positives = 180/245 (73%), Gaps = 2/245 (0%)

Query: 40  DRAADIVADAGMVIVSVPIHVTEQVIGKLPPLPKDCILV-DLASVKEFVARVLAEALP-G 97
           D AA+   DA ++++ VP+   + V+  + P+ K    V D+ SVK  V   +   +P G
Sbjct: 58  DTAAEAAQDADLIVLCVPVGAMDAVMADIAPVLKPGATVSDVGSVKRHVIDAVQPHIPEG 117

Query: 98  VAVIPAHPVAGTERSGPDSGFASLFRNRWCIITPPADADPAKLEALSALWQTLGAKVEIM 157
           V  +PAHP+AGTE SGP++GFA L+ NRWC++ P   +D A ++ L  LW+ +GA V+ M
Sbjct: 118 VHFVPAHPLAGTEHSGPEAGFAELYDNRWCLLVPVEGSDRAPVDRLRQLWEGMGANVDEM 177

Query: 158 DARHHDMVLAVTSHLPHLIAYTIVGTASDLEGVTESEVIKYSAGGFRDFTRIAASDPTMW 217
           DA HHD+VLAVTSH PHLIAYT+VG A DL  VT+SEVIKYSA GFRDFTRIAASDPTMW
Sbjct: 178 DADHHDLVLAVTSHAPHLIAYTMVGVADDLRRVTDSEVIKYSAAGFRDFTRIAASDPTMW 237

Query: 218 RDVFLSNRDAVLDMLQRFTEDLTALQKAIRVGDGQQLFDHFTRTRAIRRSIIELGQDDDR 277
           RDVFL+N+DA L++L RFTE+L ALQ+AIR GDG+ L  +FTRTRAIRR IIE GQD   
Sbjct: 238 RDVFLTNKDATLEILGRFTEELFALQRAIRTGDGEHLHQYFTRTRAIRRGIIEAGQDTAA 297

Query: 278 PDFGR 282
           P+FGR
Sbjct: 298 PNFGR 302


Lambda     K      H
   0.322    0.138    0.414 

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: 265
Number of extensions: 8
Number of successful extensions: 1
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: 287
Length of database: 306
Length adjustment: 26
Effective length of query: 261
Effective length of database: 280
Effective search space:    73080
Effective search space used:    73080
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

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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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code, or see changes to Amino acid biosynthesis since the publication.

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