GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aro-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)



>FitnessBrowser__Burk376:H281DRAFT_03923
          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 (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