Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_090448301.1 BLS63_RS23890 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_900100495.1:WP_090448301.1 Length = 457 Score = 225 bits (574), Expect = 2e-63 Identities = 159/448 (35%), Positives = 217/448 (48%), Gaps = 9/448 (2%) Query: 13 ELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTV 72 + +R+V + V V D G + GK +S F + + G C +L DV Sbjct: 12 DAKRIVEERGLSHVKVGVFDNDGVMRGKYLSRSKFFSALDS-GFAFCDVVLGWDVKDQLY 70 Query: 73 PGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSEVAVSPRSILRRQL 132 + W TGY D + T R IP+ G L I + +A+G+E V PR+ LRR L Sbjct: 71 DNASYTGWHTGYPDAPVRVLPHTCRDIPFEGGMLLFICE--FAEGAE-KVCPRATLRRVL 127 Query: 133 DRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLRD 192 +R +A G A A E EF +FD+ A G+R L P + Y+ + +S L + Sbjct: 128 ERCQALGFDAYAALEYEFFMFDETPESAREKGFRNLKPFTPDWFGYSTIRNSVHAELYHE 187 Query: 193 IRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLTF 252 I E + E G E YD A D A++K K +A ++G TF Sbjct: 188 ILQLAEQMDFPIEGLHTETGPGVIEAAIAYDHAEAAADKGALFKTFMKVLAQRNGLMATF 247 Query: 253 MAKYDER-EGNSCHIHVSLRG-TDGSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLCY 310 MAK+ + G S HIHVSLR G + F D + H MS + R F+AGQ + EF Sbjct: 248 MAKWSGKYPGQSGHIHVSLRDRASGKSAFYDPSQAHNMSQVQRQFIAGQQRLMPEFLCMV 307 Query: 311 APTINSYKRFADSSFAPTALAWGLDNRTCALRVV-GHGQNIRVECRVPGGDVNQYLAVAA 369 APT+NSY+R +APT WG++NRT ALRV+ G ++ R E R+ D N YL +A Sbjct: 308 APTLNSYRRLIPGFWAPTDATWGVENRTAALRVIPGSDKSQRQEYRLGAADGNPYLTLAV 367 Query: 370 LIAGGLYGIERGLQLPEPCVGNAYQGADVER--LPVTLADAAVLFEDSALVREAFGEDVV 427 I GLYG+ + Q EP GNAY E LP TL DAA + S RE FG+ V Sbjct: 368 AIGSGLYGVMQQWQPTEPVSGNAYAMKHPEELALPRTLWDAAQRLKASQAARELFGDPFV 427 Query: 428 AHYLNNARVELAAFNAAVTDWERIRGFE 455 H+ + E + V+DWE R FE Sbjct: 428 EHFAASREWEEREYRRHVSDWELDRYFE 455 Lambda K H 0.321 0.137 0.417 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: 518 Number of extensions: 27 Number of successful extensions: 7 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: 457 Length of database: 457 Length adjustment: 33 Effective length of query: 424 Effective length of database: 424 Effective search space: 179776 Effective search space used: 179776 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 (21.9 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