GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Echinicola vietnamensis KMM 6221, DSM 17526

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate Echvi_0848 Echvi_0848 Archaeal fructose-1,6-bisphosphatase and related enzymes of inositol monophosphatase family

Query= curated2:P56160
         (259 letters)



>FitnessBrowser__Cola:Echvi_0848
          Length = 262

 Score =  107 bits (268), Expect = 2e-28
 Identities = 82/266 (30%), Positives = 125/266 (46%), Gaps = 28/266 (10%)

Query: 5   LQLALELAEKAGKLTLDYFGRRSLQVFS------KRDDTPVTEADRNAEELIRQGISAKF 58
           L   + +A +AG      F RR  Q F       K  +  V+  D+ AE+++  G+    
Sbjct: 7   LDKTIAIAREAGA-----FIRRERQSFDLNKVEHKGFNDLVSYVDKEAEKIVVSGLQEIL 61

Query: 59  PDDGLFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPA 118
           P+ G   EE   +  G    WI+DP+DGT +F+HGVP++ V IAL  +G + LGV+    
Sbjct: 62  PEAGFITEEGTINKEGEVYNWIVDPLDGTTNFVHGVPVFSVSIALMKDGEIILGVVYEVN 121

Query: 119 LGELYQAERGSGAFMNGSPVQVSAIAENSASTV-------VFTEKEY---LLDPPSNHPV 168
             E + A +G GAF N +P+ VS     SA  V        F E +    LL     H  
Sbjct: 122 NNECFYATKGGGAFCNDTPIGVSPTPSLSAGLVATGFPYSAFEEVDKYLGLLKDIIQHSH 181

Query: 169 DQLRIDAGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGR 228
              RI +  V     CY    VA+GR +   +  ++ +D A  + I++EAGG   D+ G 
Sbjct: 182 GVRRIGSAAV---DLCY----VAAGRMDGYFEYNLNSYDVAGGVIILQEAGGKVTDFSGG 234

Query: 229 QSIIDGEGLVSANNAMGRNLIAAIGN 254
              + G  LV +N  + + L+  + N
Sbjct: 235 DDYVFGRELVGSNEKIHKELLGKVKN 260


Lambda     K      H
   0.319    0.138    0.415 

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: 188
Number of extensions: 12
Number of successful extensions: 2
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: 259
Length of database: 262
Length adjustment: 25
Effective length of query: 234
Effective length of database: 237
Effective search space:    55458
Effective search space used:    55458
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 (21.7 bits)
S2: 47 (22.7 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