GapMind for Amino acid biosynthesis

 

Alignments for a candidate for glnA in Phyllobacterium brassicacearum STM 196

Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_106709310.1 CU102_RS02280 glutamine synthetase

Query= curated2:Q9UY99
         (439 letters)



>NCBI__GCF_003010955.1:WP_106709310.1
          Length = 475

 Score =  217 bits (553), Expect = 6e-61
 Identities = 141/375 (37%), Positives = 193/375 (51%), Gaps = 28/375 (7%)

Query: 60  EDSDLIFKADPDTYVEVPW--DNVARVY-GYIYKDGKPYGADPRGVLKRVIEKLAEMGIK 116
           +D DL    D  T  EVPW  D  A+V    + KDG+     PR VLKRV+    + G+K
Sbjct: 99  DDGDLKLMPDLSTLSEVPWEADPTAQVICDLVNKDGQAVEFTPRNVLKRVVAAYNKKGLK 158

Query: 117 AYIGPEPEFYLFKKNGSWELEI-PDVG----------GYFDILTLDKAKDIKREIAEYMP 165
             + PE EFYL KKN   +  + P VG          GY  I  +++  ++  +I  +  
Sbjct: 159 PVVAPEIEFYLVKKNPDPDYPLTPPVGRSGRAIGGGQGY-SIAGVNEFDELIDDIYHFSE 217

Query: 166 SFGLVPEVLHHEVGKAQHEIDFRYDEALKTADNIISFKYIVKAVAEVHGLYATFMPKPIY 225
           S GL  + L HE G AQ EI+ R+ + ++ AD +  FK  ++  A  H +YATFM KPI 
Sbjct: 218 SQGLEIDTLIHEEGAAQLEINLRHGDPIELADQVFLFKRTIREAALKHDMYATFMAKPIQ 277

Query: 226 GMPGNGMHLHISLW--KEGENIFKGEEGLSETAL-HFIGGLLKHAKALTAITNPTVNSYK 282
           G PG+ MH+H S+   K G N+F   +G    A  HFIGG+ KH  A   +  P VNSY+
Sbjct: 278 GQPGSAMHIHQSIVDKKTGRNVFSNPDGTESDAFRHFIGGMQKHVPASLVMFAPYVNSYR 337

Query: 283 RLVPGYEAPVYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDG 342
           RL P   APV + WGY NR+   RVP       R+E R P   ANPY A AA L  GL G
Sbjct: 338 RLTPAASAPVNVKWGYDNRTTAFRVPRSDPAARRVENRIPSSDANPYLALAASLACGLIG 397

Query: 343 IKHKVEPFAYVEENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGEAYK-NF 401
           + +++EP A     V +          +  LP  L EA    E DK +   LGE +   +
Sbjct: 398 MNNRIEPDAPASTTVND---------SLIELPRGLIEATILFEHDKDLIAMLGEPFAITY 448

Query: 402 IEYKRKEWESYLEYL 416
              KR E+E+++E +
Sbjct: 449 AAIKRAEFETFMEVI 463


Lambda     K      H
   0.318    0.139    0.420 

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: 606
Number of extensions: 27
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: 439
Length of database: 475
Length adjustment: 33
Effective length of query: 406
Effective length of database: 442
Effective search space:   179452
Effective search space used:   179452
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: 51 (24.3 bits)

This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.

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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