Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_086508337.1 BZY95_RS02000 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_002151265.1:WP_086508337.1 Length = 459 Score = 228 bits (581), Expect = 3e-64 Identities = 160/449 (35%), Positives = 217/449 (48%), Gaps = 11/449 (2%) Query: 13 ELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTV 72 + R+V + V V D+ G + GK + F ++ G C +L D Sbjct: 14 DARRIVEQRGLSHVKVGMFDIDGVMVGKYMRRDKFFHALS-EGFAFCDVVLGWDSKDELY 72 Query: 73 PGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSEVAVSPRSILRRQL 132 W TGY D + + R +P L +A+ G + PR +LRR L Sbjct: 73 DNVTYTGWHTGYPDAALRLIPESCRELPCEGDMLLFLAEFTGPAGE---ICPRGLLRRVL 129 Query: 133 DRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRMEPLLRD 192 + +A G A A E EF +F + G+R L P + + Y++L SS L + Sbjct: 130 AKAEAMGFTACGALEYEFFLFQETPESVREKGFRNLKPFTPDMMGYSMLRSSVHGELYHE 189 Query: 193 IRLGMAGA-GLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHGKSLT 251 + LGMA A E + E G E R DEAL D A++K K A + G T Sbjct: 190 L-LGMAEAMDFPIEGLHTETGPGVLEAAIRVDEALAAGDKGALFKTFTKVWAQRRGLMAT 248 Query: 252 FMAKYD-EREGNSCHIHVSLRGTD-GSAVFADSNGPHGMSSMFRSFVAGQLATLREFTLC 309 FMAK+ + G S HIH+SL D G + F D++ PHGMS + R FVAGQ + EF Sbjct: 249 FMAKWSPDYPGQSGHIHLSLNHADSGESAFFDADQPHGMSDIQRHFVAGQQKLMPEFLAM 308 Query: 310 YAPTINSYKRFADSSFAPTALAWGLDNRTCALRVV-GHGQNIRVECRVPGGDVNQYLAVA 368 +APT+NSY R +APT WG++NRT ALRV+ G ++ RVE R+ D N YLA+A Sbjct: 309 FAPTVNSYTRLIPGFWAPTDATWGVENRTTALRVIPGSAKSQRVEYRLGSADANPYLALA 368 Query: 369 ALIAGGLYGIERGLQLPEPCVGNAYQGADVER--LPVTLADAAVLFEDSALVREAFGEDV 426 A I GLYGIE L+ E GN+Y+ A E L TL +AA + S R FG+ Sbjct: 369 AAIGSGLYGIEHQLEPDEMVTGNSYELAHPEHQALSRTLWEAAQRLKASDAARSLFGDAF 428 Query: 427 VAHYLNNARVELAAFNAAVTDWERIRGFE 455 V H+ E F +TDWE R FE Sbjct: 429 VEHFAATREWEERQFRRHITDWELDRYFE 457 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: 556 Number of extensions: 31 Number of successful extensions: 6 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: 459 Length adjustment: 33 Effective length of query: 424 Effective length of database: 426 Effective search space: 180624 Effective search space used: 180624 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 09 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