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.
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:
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