GapMind for Amino acid biosynthesis

 

Aligments for a candidate for pre-dehydr in Paraburkholderia bryophila 376MFSha3.1

Align Prephenate dehydrogenase protein; EC 1.3.1.12 (characterized, see rationale)
to candidate H281DRAFT_03923 H281DRAFT_03923 prephenate dehydrogenase (EC 1.3.1.12)

Query= uniprot:D8IR44_HERSS
         (295 letters)



>lcl|FitnessBrowser__Burk376:H281DRAFT_03923 H281DRAFT_03923
           prephenate dehydrogenase (EC 1.3.1.12)
          Length = 313

 Score =  320 bits (819), Expect = 3e-92
 Identities = 173/290 (59%), Positives = 209/290 (72%), Gaps = 8/290 (2%)

Query: 2   FKKVVIFGVGLIGGSFALALRRAGQA---AHIVGVGRSLQSLERARELGIID---AVATD 55
           F K+VIFGVGLIGGS A ALR  G+A     ++GVGRS  S  RA ELG+ID   A++ D
Sbjct: 9   FNKLVIFGVGLIGGSLARALRERGEADGARTVIGVGRSAASTGRAVELGVIDSSAALSDD 68

Query: 56  AA--SAVQGADLILVAAPVAQTGPILASIAPHLEPQAIVTDAGSTKSDVVAAARMALGDR 113
           AA   A+  AD++L+AAPVAQT P+L  IAP L    IVTDAGSTKSDVVAAAR ALG R
Sbjct: 69  AALREALADADVVLLAAPVAQTQPLLECIAPFLGADTIVTDAGSTKSDVVAAARAALGAR 128

Query: 114 IVQFIPAHPIAGREKHGPEAALAELYEGKKVVITALPENDAADVEIVAAAWRACGAVIHR 173
           I QF+P HPIAGRE  G EAAL +LY G+ VV+  LPEN    VE +AA WRA GA++  
Sbjct: 129 IGQFVPGHPIAGRESSGVEAALPDLYVGRNVVLCPLPENAPGTVERIAAMWRATGALVRD 188

Query: 174 LSPQEHDAVFASVSHLPHVLAFALVDDIAAKPHAATLFQYAASGFRDFTRIAASSPEMWR 233
           ++P++HD VFASVSHLPHVL+FALV+ I   P AA  F +AA GFRDFTRIAASSPEMWR
Sbjct: 189 MAPEQHDRVFASVSHLPHVLSFALVEQILNSPDAALKFSFAAGGFRDFTRIAASSPEMWR 248

Query: 234 DITLANRDALLTEVDAYLLQLQNIRAMIAAGDGPGIEKIYASAQHARQQW 283
           D+ +ANR ALL E+DAY   L  +R  I A DG  +E ++A ++ AR +W
Sbjct: 249 DVCIANRVALLDELDAYSAVLARLRTAIEAADGAALEAVFARSRLARTEW 298


Lambda     K      H
   0.320    0.132    0.376 

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: 304
Number of extensions: 7
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: 295
Length of database: 313
Length adjustment: 27
Effective length of query: 268
Effective length of database: 286
Effective search space:    76648
Effective search space used:    76648
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