GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argA in Synechococcus elongatus PCC 7942

Align acetylglutamate kinase (EC 2.7.2.8) (characterized)
to candidate Synpcc7942_1496 Synpcc7942_1496 acetylglutamate kinase

Query= BRENDA::A0A0H2X8L7
         (447 letters)



>FitnessBrowser__SynE:Synpcc7942_1496
          Length = 301

 Score =  133 bits (335), Expect = 7e-36
 Identities = 100/286 (34%), Positives = 146/286 (51%), Gaps = 21/286 (7%)

Query: 16  VRLLSSMASAKEISQYLKRFSQLDAKRFAVVKVGGAVLRDD--LEALTSSLSFLQEVGLT 73
           VR+LS      E   YL++F    A R  VVK GGA ++ +   EA+   + FL  VG+ 
Sbjct: 14  VRILS------EALPYLQQF----AGRTVVVKYGGAAMKQEELKEAVMRDIVFLACVGMR 63

Query: 74  PIVLHGAGPQLDAELSAAGIEKQTVNGLRVTSPHALAIVRKVFQAS-NLKLVEALQQNGA 132
           P+V+HG GP+++A L   GIE Q  NGLRVT    + +V  V     N  +V  +   G 
Sbjct: 64  PVVVHGGGPEINAWLGRVGIEPQFHNGLRVTDADTMEVVEMVLVGRVNKDIVSRINTTGG 123

Query: 133 RATSITGG---VFEAEYLNRDTYGLVGEVKAVNLAPIEASLQAGSIPVITSLGETPSGQI 189
           RA    G    +  A   +++  G VGEV +VN   IE  L+ G IPVI+S+    +GQ 
Sbjct: 124 RAVGFCGTDGRLVLARPHDQEGIGFVGEVNSVNSEVIEPLLERGYIPVISSVAADENGQS 183

Query: 190 LNVNADFAANELVQELQPYKIIFLTGTGGLLDAEGK---LIDSINLSTEYDHLMQQPWIN 246
            N+NAD  A E+   L   K+I LT T G+L+   +   LI  +N+    + L+ Q  + 
Sbjct: 184 FNINADTVAGEIAAALNAEKLILLTDTRGILEDPKRPESLIPRLNIPQSRE-LIAQGIVG 242

Query: 247 GGMRVKIE-QIKDLLDRLPLESSVSITRPADLAKELFTHKGSGTLV 291
           GGM  K++  I+ L   +     +    P  L  E+FT  G GT++
Sbjct: 243 GGMIPKVDCCIRSLAQGVRAAHIIDGRIPHALLLEIFTDAGIGTMI 288


Lambda     K      H
   0.318    0.134    0.383 

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: 285
Number of extensions: 17
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: 447
Length of database: 301
Length adjustment: 30
Effective length of query: 417
Effective length of database: 271
Effective search space:   113007
Effective search space used:   113007
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 (21.7 bits)
S2: 49 (23.5 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