Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate CCNA_03240 CCNA_03240 glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__Caulo:CCNA_03240 Length = 460 Score = 154 bits (388), Expect = 7e-42 Identities = 128/430 (29%), Positives = 197/430 (45%), Gaps = 35/430 (8%) Query: 15 KFVQLIFVDINGMPKGMEIPASRLQEAIEDGISFDGSSV---PGFQGIEDSDLIFK---A 68 KFV++ F + G+P+G + L+ E G GS + ED+ L+++ A Sbjct: 22 KFVEVFFTSMTGVPRGKRLRVHELEAIYEYGRFLPGSVLVVDTNGADCEDTGLVWEDGDA 81 Query: 69 D------PDTYVEVPW--DNVARVYGYIYK-DGKPYGADPRGVLKRVIEKLAEMGIKAYI 119 D P T PW +VA+V +Y+ DG P DPR VL+RV+++ A G+ Sbjct: 82 DRRARPVPGTLTLAPWLGPDVAQVMLSLYELDGTPNDLDPRHVLQRVLDRYAADGLTPVA 141 Query: 120 GPEPEFYLFK----KNG------SWELEIPDVG-GYFDILTLDKAKDIKREIAEYMPSFG 168 E E+YL NG S + + G + + L+ RE+ + + G Sbjct: 142 ACELEYYLVDLQRGPNGELLPAKSLQTGLRPTGIQVYGLPELEAHAPFLRELWDVADTLG 201 Query: 169 LVPEVLHHEVGKAQHEIDFRYD-EALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGM 227 + E E AQ E+ ++ +AL+ AD+ + +K K VA HG+ ATFM KP Sbjct: 202 VPLEGAISEFAPAQVELTLKHKPDALRAADDAVLYKRAAKGVALRHGMEATFMAKPWSDR 261 Query: 228 PGNGMHLHISLWKEGENIFKGEEGL--SETALHFIGGLLKHAKALTAITNPTVNSYKRLV 285 GNG H+H+S+ N E + S+ H IGG+ AI P NSY+R Sbjct: 262 AGNGFHVHLSVNDAAGNNLCASEDIEGSDLLKHAIGGMKVLLGEGMAILAPNANSYRRFK 321 Query: 286 PGYEAPVYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKH 345 APV +WG NR+ +RVPA +E+R NPY A +L + GI + Sbjct: 322 ANSYAPVAPTWGVNNRTVSLRVPAGPPKTRHVEHRVAGADGNPYLVLAVLLASAHHGITN 381 Query: 346 KVEPFAYVEENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGEAYKN-FIEY 404 K++P V + Y + LP + A+D E+ V+R+ LG+ + + F+ Sbjct: 382 KIDPGPAVIGDGYAAAAKENIR-----LPNNWFAAVDLFEQSSVLRDYLGDRFVDMFVSV 436 Query: 405 KRKEWESYLE 414 KR E + E Sbjct: 437 KRTEQARFFE 446 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: 587 Number of extensions: 40 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: 460 Length adjustment: 33 Effective length of query: 406 Effective length of database: 427 Effective search space: 173362 Effective search space used: 173362 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