Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_052667893.1 NITAL_RS19675 glutamine synthetase
Query= BRENDA::P64246 (446 letters) >NCBI__GCF_000969705.1:WP_052667893.1 Length = 448 Score = 561 bits (1446), Expect = e-164 Identities = 279/453 (61%), Positives = 337/453 (74%), Gaps = 13/453 (2%) Query: 1 MDRQKEFVLRTLEERDIRFVRLWFTDVLGFLKSVAIAPAELEGAFEEGIGFDGSSIEGFA 60 MD+Q+E+VLRT+EERD+RF+RLWFTDVLGFLKSVAI AELE AF EGIGFDGS+I+GFA Sbjct: 1 MDKQQEYVLRTVEERDVRFIRLWFTDVLGFLKSVAITAAELENAFSEGIGFDGSAIDGFA 60 Query: 61 RVSESDTVAHPDPSTFQVLPWATSSGHHHSARMFCDITMPDGSPSWADPRHVLRRQLTKA 120 RV E+D + PD STFQVLPW S ARMFCDI PDG P ADPR VL+R L +A Sbjct: 61 RVQEADMLVVPDASTFQVLPWRPES--QGVARMFCDIVTPDGQPFAADPRLVLKRTLERA 118 Query: 121 GELGFSCYVHPEIEFFLLKPGPEDGSVPVPVDNAGYFDQAVHDSALNFRRHAIDALEFMG 180 ++GF+ YVHPE+EF+L + G + P P+DN YFD D +FRR AI+ LE MG Sbjct: 119 ADMGFTFYVHPEMEFYLFQGGED----PTPLDNGSYFDMTPLDIQQDFRRQAINMLERMG 174 Query: 181 ISVEFSHHEGAPGQQEIDLRFADALSMADNVMTFRYVIKEVALEEGARASFMPKPFGQHP 240 ISVE+SHHE P Q EIDLR+ADAL+MADN+MTFR V+KE AL+ G ASFMPKP Sbjct: 175 ISVEYSHHEVGPSQHEIDLRYADALTMADNIMTFRLVVKETALQRGVYASFMPKPLEGEY 234 Query: 241 GSAMHTHMSLFEGDVNAFHSADDPLQLSEVGKSFIAGILEHACEISAVTNQWVNSYKRL- 299 G++MH H+SLFEGD NAFH + DP +LS+ KSF+AG++ HA EI+AVTNQWVNSYKRL Sbjct: 235 GNSMHLHLSLFEGDTNAFHDSSDPYRLSKTAKSFLAGLMRHAREITAVTNQWVNSYKRLT 294 Query: 300 ------VQGGEAPTAASWGAANRSALVRVPMYTPHKTSSRRVEVRSPDSACNPYLTFAVL 353 + GEAP SWG +NRSAL+RVPMY P K +S R+E RSPD ACNPYL F+++ Sbjct: 295 ARLHGPLPSGEAPIFVSWGHSNRSALIRVPMYKPRKGASTRIEFRSPDPACNPYLAFSLI 354 Query: 354 LAAGLRGVEKGYVLGPQAEDNVWDLTPEERRAMGYRELPSSLDSALRAMEASELVAEALG 413 LAAGL+G+E+GY L + EDN ++LTP ER A G LPSSL AL+ ME SELVA+ LG Sbjct: 355 LAAGLKGIEEGYELADEYEDNSFELTPAERAAHGIERLPSSLGEALQVMEGSELVADTLG 414 Query: 414 EHVFDFFLRNKRTEWANYRSHVTPYELRTYLSL 446 EH+F +FL NKR EW Y +HVT +EL YL L Sbjct: 415 EHLFAYFLANKRREWDEYTAHVTQFELERYLPL 447 Lambda K H 0.320 0.134 0.408 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: 622 Number of extensions: 28 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: 446 Length of database: 448 Length adjustment: 33 Effective length of query: 413 Effective length of database: 415 Effective search space: 171395 Effective search space used: 171395 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: 51 (24.3 bits)
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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