GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisN in Pseudomonas simiae WCS417

Align Histidinol-phosphatase; HolPase; EC 3.1.3.15; Histidinol-phosphate phosphatase (uncharacterized)
to candidate GFF4537 PS417_23220 inositol monophosphatase

Query= curated2:P56160
         (259 letters)



>FitnessBrowser__WCS417:GFF4537
          Length = 271

 Score =  107 bits (266), Expect = 3e-28
 Identities = 80/262 (30%), Positives = 126/262 (48%), Gaps = 11/262 (4%)

Query: 1   MTPDLQLALELAEKAGKLTLDYFGRR-SLQVFSKRDDTPVTEADRNAEELIRQGISAKFP 59
           M P L +AL  A  A +L      R  +++V  K     V+E DR AE+ I   +   +P
Sbjct: 1   MQPMLNIALRAARSASELIFRSIERLDTIKVDEKDAKDYVSEVDRAAEQKIIDALRKAYP 60

Query: 60  DDGLFGEEFDEHP-SGNGRR--WIIDPIDGTRSFIHGVPLYGVMIALEVEGAMQLGVINF 116
             G+ GEE   H  SG G    WIIDP+DGT +F+ G+P + V IA +  G ++  V+  
Sbjct: 61  THGILGEETGLHKGSGEGEDYLWIIDPLDGTTNFLRGIPHFAVSIACKYRGRLEHAVVLD 120

Query: 117 PALGELYQAERGSGAFMNGSPVQVS--AIAENSASTVVFTEKEYLLDPPSNHPVDQLRI- 173
           P   E + A RG GA +NG  ++VS     + +     F  ++  +D   N+ +   R  
Sbjct: 121 PVRQEEFTASRGRGAQLNGRRLRVSGRTSLDGALLGTGFPFRDDQMDNLENY-LGMFRAL 179

Query: 174 ---DAGLVRGWGDCYGHMLVASGRAEVAVDKIMSPWDCAAVIPIVEEAGGCCFDYRGRQS 230
               AG+ R          VA+GR +   +  +S WD AA   +++EAGG   D+ G   
Sbjct: 180 VGQTAGIRRAGAASLDLAYVAAGRFDAFWESGLSEWDMAAGALLIQEAGGLVSDFTGGHD 239

Query: 231 IIDGEGLVSANNAMGRNLIAAI 252
            ++   +V+ N    + ++ AI
Sbjct: 240 FLEKGHVVAGNTKCFKAVLTAI 261


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: 184
Number of extensions: 9
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: 271
Length adjustment: 25
Effective length of query: 234
Effective length of database: 246
Effective search space:    57564
Effective search space used:    57564
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