GapMind for Amino acid biosynthesis

 

Alignments for a candidate for pre-dehydr in Synechococcus elongatus PCC 7942

Align Prephenate dehydrogenase; PDH; EC 1.3.1.12 (characterized)
to candidate Synpcc7942_0660 Synpcc7942_0660 arogenate dehydrogenase

Query= SwissProt::O69721
         (323 letters)



>FitnessBrowser__SynE:Synpcc7942_0660
          Length = 323

 Score =  117 bits (292), Expect = 5e-31
 Identities = 92/279 (32%), Positives = 134/279 (48%), Gaps = 16/279 (5%)

Query: 12  VLGLGLIGGSIMRAAAAAGREVFGYNRSVEGAHGARSDGFDAITDLNQTLTRAAATEA-L 70
           ++GLGLIGGS+       G  + GY+R       A + G   + D + +   A  TEA +
Sbjct: 50  IVGLGLIGGSLGFDWRDRGHRLLGYSRRPATCERAIARG---VVD-HASPDPAVLTEAEV 105

Query: 71  IVLAVPMPALPGMLAHIRKS-APGCPLTDVTSVKCAVLDEVTAAGLQARYVGGHPMTGTA 129
           IVLA P+  L   +  +R    P   +TDV SVK  ++  +    L  R+VGGHPM GTA
Sbjct: 106 IVLATPLGVLETTVRELRDYWHPEAIVTDVGSVKQPIVAALDP--LWPRFVGGHPMAGTA 163

Query: 130 HSGWTAGHGGLFNRAPWVVSVDDHVDPTVWSMVMTLALDCGAMVVPAKSDEHDAAAAAVS 189
            +G  A   GLF   P+V++  D  DP   ++V  LA + G++V+      HD A A +S
Sbjct: 164 ENGIEAALRGLFQNRPYVLTPTDQTDPAAIAVVAQLAQELGSVVLHCDPASHDRAVATIS 223

Query: 190 HLPHLLAEALAVTAAEVP------LAFALAAGSFRDATRVAATAPDLVRAMCEANTGQLA 243
           HLP  ++ +L  T  + P      LA  LA+  F D +RV    P+L   M   N   L 
Sbjct: 224 HLPVFISASLIQTCLQEPDPAVQTLAATLASSGFCDTSRVGGGNPELGVMMARYNQAALL 283

Query: 244 PAADRIIDLLSRARDSLQS--HGSIADLADAGHAARTRY 280
              DR    L R + ++ +    +IA +       R RY
Sbjct: 284 EQIDRYQIQLERLKTAIAAADEPAIAAILQQNQEMRPRY 322


Lambda     K      H
   0.319    0.131    0.390 

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: 242
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: 323
Length of database: 323
Length adjustment: 28
Effective length of query: 295
Effective length of database: 295
Effective search space:    87025
Effective search space used:    87025
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