Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate Pf6N2E2_4509 glutamine synthetase family protein
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4509 Length = 423 Score = 179 bits (453), Expect = 2e-49 Identities = 130/404 (32%), Positives = 202/404 (50%), Gaps = 34/404 (8%) Query: 29 KGMEIPASRLQEAIEDGISFDGSSVPGFQ---GIEDSDLIFKADPDTYVEVPWDN--VAR 83 KG+ +PAS + +GS+V I D+D I PDT PW A+ Sbjct: 18 KGINLPASLF------ALDINGSTVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQ 71 Query: 84 VYGYIYK-DGKPYGADPRGVLKRVIEKLAEMGIKAYIGPEPEFYLFKK---NGSWELEIP 139 + +++ +G+P+ ADPR VL++V+ K E+G+ E EFYL + NG + Sbjct: 72 LLMTMHELEGEPFFADPREVLRQVVTKFDELGLTICAAFELEFYLIDQENVNGRPQPPRS 131 Query: 140 DVGG-------YFDILTLDKAKDIKREIAEYMPSFGLVPEVLHHEVGKAQHEIDFRY-DE 191 + G + I LD+ D ++I E G+ + + E AQ E++ + + Sbjct: 132 PISGKRPHSTQVYLIDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVAD 191 Query: 192 ALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHLHISLW-KEGENIFKGEE 250 +K D + K ++K +A H + TFM KP G GNG+H+HIS+ K+G+NIF E+ Sbjct: 192 PIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASED 251 Query: 251 GLSETAL-HFIGGLLKHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRVPA 309 AL H IGG+L+ A A P VNSY+R + P +WG NR+ +RVP Sbjct: 252 PEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPT 311 Query: 310 FWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVEPFAYVEENVYEMDEGKRKELG 369 + R+E+R ANPY A++L G+ +K+EP A VE N YE +E Sbjct: 312 GSADAVRLEHRVAGADANPYLLMASVLAGVHHGLVNKIEPGAPVEGNSYEQNE------- 364 Query: 370 IDTLPGSLGEALDELEKDKVVREALGEAYKN-FIEYKRKEWESY 412 +LP +L +AL EL+ +V+ + + Y + F+ K E E + Sbjct: 365 -QSLPNNLRDALRELDDSEVMAKYIDPKYIDIFVACKESELEEF 407 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: 561 Number of extensions: 37 Number of successful extensions: 5 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: 423 Length adjustment: 32 Effective length of query: 407 Effective length of database: 391 Effective search space: 159137 Effective search space used: 159137 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 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