GapMind for Amino acid biosynthesis

 

Alignments for a candidate for lysZ in Synechococcus elongatus PCC 7942

Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.- (uncharacterized)
to candidate Synpcc7942_1496 Synpcc7942_1496 acetylglutamate kinase

Query= curated2:A0RWW1
         (266 letters)



>FitnessBrowser__SynE:Synpcc7942_1496
          Length = 301

 Score =  127 bits (318), Expect = 4e-34
 Identities = 87/255 (34%), Positives = 132/255 (51%), Gaps = 29/255 (11%)

Query: 2   ITIKIGGSIV--DSLHPSAIPDIKKAAAGGV--VLVHGGGKEVTKVCEQLGKEPRFVTSP 57
           + +K GG+ +  + L  + + DI   A  G+  V+VHGGG E+     ++G EP+F    
Sbjct: 32  VVVKYGGAAMKQEELKEAVMRDIVFLACVGMRPVVVHGGGPEINAWLGRVGIEPQFHNG- 90

Query: 58  GNIKSRYTDKETAEIFTMVMSGRINKCIVRMLQQHGVNAVGLSGIDGGLIRAERKSRLVI 117
                R TD +T E+  MV+ GR+NK IV  +   G  AVG  G DG L+ A        
Sbjct: 91  ----LRVTDADTMEVVEMVLVGRVNKDIVSRINTTGGRAVGFCGTDGRLVLA-------- 138

Query: 118 VNERGRKQAIEG-GYTGRITSVNSELLETLLGKGIVPVVSPIAMGNEYELLNVDGDRAAA 176
                R    EG G+ G + SVNSE++E LL +G +PV+S +A     +  N++ D  A 
Sbjct: 139 -----RPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQSFNINADTVAG 193

Query: 177 NIAGATKSERILFVTDVDGLMMD----EKLVSRLSAAEAEEIRPK--IGPGMEKKVLAAT 230
            IA A  +E+++ +TD  G++ D    E L+ RL+  ++ E+  +  +G GM  KV    
Sbjct: 194 EIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRELIAQGIVGGGMIPKVDCCI 253

Query: 231 EALKMGVREAIIARG 245
            +L  GVR A I  G
Sbjct: 254 RSLAQGVRAAHIIDG 268


Lambda     K      H
   0.316    0.135    0.370 

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: 199
Number of extensions: 7
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: 266
Length of database: 301
Length adjustment: 26
Effective length of query: 240
Effective length of database: 275
Effective search space:    66000
Effective search space used:    66000
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 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