GapMind for Amino acid biosynthesis

 

Aligments for a candidate for hisN in Desulfovibrio vulgaris Miyazaki F

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate 8500294 DvMF_1050 Inositol-phosphate phosphatase (RefSeq)

Query= curated2:P56160
         (259 letters)



>lcl|FitnessBrowser__Miya:8500294 DvMF_1050 Inositol-phosphate
           phosphatase (RefSeq)
          Length = 279

 Score =  112 bits (280), Expect = 8e-30
 Identities = 84/248 (33%), Positives = 115/248 (46%), Gaps = 9/248 (3%)

Query: 5   LQLALELAEKAGKLTLDYFGRRSLQV--FSKRDDTPVTEADRNAEELIRQGISAKFPDDG 62
           L +AL+ A KAG   L     R  +V   +K      TE D  +E  I   I   +PD  
Sbjct: 22  LAVALDAA-KAGCAVLARGRSRLARVRTTTKSPGDITTELDARSEAAIFARIRQAYPDHA 80

Query: 63  LFGEEFDEHPSGNGR---RWIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINFPAL 119
             GEE  +    +G    RWI+DP+DGT +++HG+P Y V +ALEV G   LGV+  P  
Sbjct: 81  RLGEESGDSTGDSGASPFRWIVDPLDGTVNYVHGIPYYAVSVALEVNGVAVLGVVADPGR 140

Query: 120 GELYQAERGSGAFMNGSPVQV---SAIAENSASTVVFTEKEYLLDPPSNHPVDQLRIDAG 176
            E + A RG GAF NG PV V   + + E    TVV   K   ++          R  AG
Sbjct: 141 REFFTAVRGQGAFCNGRPVHVARRTRMDEAVVGTVVPPPKWPGMEGYLEQFCAVARCAAG 200

Query: 177 LVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQSIIDGEG 236
           + RG         VA+GR +      +  WD +A   +V EAGG   D  G    +    
Sbjct: 201 MRRGGAAALDLAYVAAGRLDGFFVVSLKRWDLSAGALLVREAGGAVADIDGHPDPLHANR 260

Query: 237 LVSANNAM 244
           L +AN+ +
Sbjct: 261 LAAANSTL 268


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: 197
Number of extensions: 14
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: 259
Length of database: 279
Length adjustment: 25
Effective length of query: 234
Effective length of database: 254
Effective search space:    59436
Effective search space used:    59436
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 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, 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