GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Thiohalospira halophila DSM 15071 HL 3

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate WP_093427870.1 BM272_RS06005 inositol monophosphatase family protein

Query= curated2:P56160
         (259 letters)



>NCBI__GCF_900112605.1:WP_093427870.1
          Length = 266

 Score =  107 bits (267), Expect = 3e-28
 Identities = 78/250 (31%), Positives = 120/250 (48%), Gaps = 14/250 (5%)

Query: 1   MTPDLQLALELAEKAGKLTLDYFGRRS-LQVFSKRDDTPVTEADRNAEELIRQGISAKFP 59
           M P L +A+  A +AGK      G    L + +K  +  V+E D  AE+ I   I   +P
Sbjct: 1   MDPMLNIAVRAARRAGKTITRAMGNVDRLNIETKAHNDFVSEVDYAAEQAIIDTIRDAYP 60

Query: 60  DDGLFGEEFDEHPSGNGRRWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPAL 119
             G   EE   H       WIIDP+DGT +F+HG P + V IAL  +G +   V+  P  
Sbjct: 61  SHGFIAEESGLHDQERDSVWIIDPLDGTTNFLHGFPQFAVSIALRHKGKLTQAVVYDPTR 120

Query: 120 GELYQAERGSGAFMNGSPVQVSAI--AENSASTVVFTEKE------YLLDPPSNHPVDQL 171
            E++ A RG GA ++G  ++VS     E +     F  KE      YL    + HPV   
Sbjct: 121 EEMFTASRGGGAQLDGRRIRVSGRRGLEGALLGTGFPFKEPEHLDSYLAMFRAFHPV--- 177

Query: 172 RIDAGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSI 231
              AG+ R          +A+GR +   +  ++ WD AA + ++ EAGG   D+ G ++ 
Sbjct: 178 --VAGIRRPGSAALDLAWLAAGRIDGFWEIGLNAWDIAAGVLLIREAGGLVGDFEGGEAY 235

Query: 232 IDGEGLVSAN 241
           ++   LV+++
Sbjct: 236 METGNLVASS 245


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: 185
Number of extensions: 10
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: 266
Length adjustment: 25
Effective length of query: 234
Effective length of database: 241
Effective search space:    56394
Effective search space used:    56394
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 Jul 25 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