GapMind for Amino acid biosynthesis

 

Alignments for a candidate for preph-dehydratase in Synechococcus elongatus PCC 7942

Align Prephenate dehydratase; PDT; EC 4.2.1.51 (uncharacterized)
to candidate Synpcc7942_0881 Synpcc7942_0881 prephenate dehydratase

Query= curated2:Q44104
         (304 letters)



>FitnessBrowser__SynE:Synpcc7942_0881
          Length = 291

 Score =  167 bits (422), Expect = 4e-46
 Identities = 111/288 (38%), Positives = 155/288 (53%), Gaps = 14/288 (4%)

Query: 4   IAYFGPVGTFTEQAARTFMA-------AGDELVAAETIPKALDAVRRGEADAACVPVENS 56
           IA+ GPVGT+ E AA  F A           L+A  +IP  L  +  G  D A VPVENS
Sbjct: 6   IAHLGPVGTYAEMAALRFQAWLTQQDQQPSRLLACRSIPATLQTLADGAVDYAVVPVENS 65

Query: 57  VEGAVPATLDSLAVGEPLIGVAEAL-LPV-HFSVLTRDDVGEIRTVASHPHALAQVRKWL 114
           VEG+V ATLDSL    P + +  AL LP+ H  +    D   IR V SHP ALAQ ++WL
Sbjct: 66  VEGSVAATLDSLWQ-LPQLSIQRALILPIAHALISFESDRTAIRQVLSHPQALAQCQQWL 124

Query: 115 EDNLPGARVVAAGSTAAAAVAVQAGEFDAAVTAPVAVEHYPLKVLATEVADVRDARTRFL 174
           + +LP A ++ A ST  A   ++     A + +  A E Y + + +  + D  D RTRF 
Sbjct: 125 QRHLPQAELIPANSTTEALQDLERHPQRAVIASTRAAELYQMPIQSFPINDSPDNRTRFW 184

Query: 175 LMRRPPVVLPEPTGADRTSIVAAAANRTGTLAELLTELATRGINLTRLDARPHKQNFGEY 234
           ++ R P     P GA  +   +  AN  G L + L  LA R INL+R+++RP K++ GEY
Sbjct: 185 VISRSPT----PGGACTSLNFSLDANVPGALVKPLQILADRRINLSRIESRPTKRSLGEY 240

Query: 235 RFFIDFEGHVAEPRIADALAALRRRCRDVRFLGSFARADGVAATIEPA 282
            FF+D E  + +P IA A+ A+      +R LGS+   D   + + PA
Sbjct: 241 LFFLDLEADLRDPAIAAAVQAVADCTEQLRVLGSYDSLDFTQSVLVPA 288


Lambda     K      H
   0.320    0.133    0.381 

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: 204
Number of extensions: 11
Number of successful extensions: 4
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: 304
Length of database: 291
Length adjustment: 26
Effective length of query: 278
Effective length of database: 265
Effective search space:    73670
Effective search space used:    73670
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 (21.8 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