Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate 350313 BT0785 glutamine synthetase I (NCBI ptt file)
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__Btheta:350313 Length = 500 Score = 136 bits (342), Expect = 2e-36 Identities = 121/445 (27%), Positives = 194/445 (43%), Gaps = 50/445 (11%) Query: 35 ASRLQEAIEDGISFDGSSVPGFQGIEDSDLIF-----KADPDTYVEVPWDNVARVYGYIY 89 A+ L + G DGSS+ F SDL A D + E+P ++ + + Sbjct: 61 AAYLDAILTCGERVDGSSLFPFIEAGSSDLYVVPRFRTAFVDPFAEIP--TLSMLCSFFN 118 Query: 90 KDGKPYGADPRGVLKRVIEKLAEM-GIKAYIGPEPEFYLFKKNGSWELEIPDVGGYFDIL 148 KDG+P + P L + + ++ G++ E E+Y+ + + D GY + Sbjct: 119 KDGEPLESSPEHTLHKACKAFTDVTGMEFQAMGELEYYVISPDTGM-FQATDQRGYHESA 177 Query: 149 TLDKAKDIKREIAEYMPSFGLVPEVLHHEVGK--------AQHEIDFRYDEALKTADNII 200 K D + + Y+ G + H EVG Q+EI+F A AD ++ Sbjct: 178 PYAKFNDFRTQCMSYIAQTGGQIKYGHSEVGNFTLDGMIYEQNEIEFLPVHAEDAADQLM 237 Query: 201 SFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHLHISLWKEGENIFKGEEGLSETALHFI 260 K++++ + +G TF PK G G+G+H+H+ + K+G+N + LSETA I Sbjct: 238 IAKWVIRNLGYRYGYNVTFAPKITAGKAGSGLHVHMRIVKDGQNQMLKDGVLSETARKAI 297 Query: 261 GGLLKHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRVPAFW--------- 311 G+++ A ++TA N SY RLVP EAP + WG +NRS L+RVP W Sbjct: 298 AGMMELAPSITAFGNTNPTSYFRLVPHQEAPTNVCWGDRNRSVLVRVPLGWAAKTDMCTL 357 Query: 312 ------------GNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHK----VEPFAYVEE 355 +E R PD SA+ Y A + +A G + + + YV Sbjct: 358 ANPLESESHFDTSQKQTVEMRSPDGSADLYQLLAGLAVACRHGFEIEQALDIAKRTYVNV 417 Query: 356 NVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGEAYKNFIEYKRKEWESYLEY 415 N+++ E + K + LP S + + L+K + V E I+ ++ SY Sbjct: 418 NIHQ-KENEDKLKALAQLPDSCAASAECLQKQRAVFEQYNVFSPAMIDGIIRKLRSY--- 473 Query: 416 LEAKHLPKDTKRVTEWELE---RYF 437 E K L D + E LE +YF Sbjct: 474 -EDKTLRADMEGKPEEMLELVHKYF 497 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: 533 Number of extensions: 31 Number of successful extensions: 1 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: 500 Length adjustment: 33 Effective length of query: 406 Effective length of database: 467 Effective search space: 189602 Effective search space used: 189602 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