Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate CCNA_03230 CCNA_03230 glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__Caulo:CCNA_03230 Length = 465 Score = 181 bits (460), Expect = 3e-50 Identities = 129/381 (33%), Positives = 190/381 (49%), Gaps = 30/381 (7%) Query: 54 PGFQGI-----EDSDLIFKADPDTYVEVPW--DNVARV-YGYIYKDGKPYGADPRGVLKR 105 P F+G D+D+ D T VPW D A+V + + DG+P PR VL+R Sbjct: 79 PEFEGAVNAVQSDTDIFLTPDFATLAAVPWAQDPTAQVIHDAFHPDGRPVEEAPRQVLRR 138 Query: 106 VIEKLAEMGIKAYIGPEPEFYLFKKNGSWELEI---------PDVGGY-FDILTLDKAKD 155 V+ A+ G + PE EFYL +N + + P+ G + I +++ Sbjct: 139 VLALYADKGWHPIVAPEIEFYLVDRNTDPDYPLKPPIGRSGRPETGRQGYSISAVNEFDA 198 Query: 156 IKREIAEYMPSFGLVPEVLHHEVGKAQHEIDFRYDEALKTADNIISFKYIVKAVAEVHGL 215 + ++ EY GL + L HE G AQ EI+ ++ L+ AD + K ++ A H + Sbjct: 199 LFEDMYEYSERQGLEIDTLIHESGVAQMEINLQHGHPLELADQVFMMKRTIREAALEHEI 258 Query: 216 YATFMPKPIYGMPGNGMHLHISLW-KEGENIFKGEEGLSETALH-FIGGLLKHAKALTAI 273 YATFM KP+ PG+ MH+H S+ K+G N+F E+G H FI G + A+ AI Sbjct: 259 YATFMAKPMANEPGSAMHIHQSIVDKKGRNLFSDEDGAESAMFHGFIAGQQTYLPAIMAI 318 Query: 274 TNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFA 333 P VNSY+R+ APV WGY NR+ +RVP N R+E R P ANPY A A Sbjct: 319 LAPYVNSYRRISRDSGAPVNTQWGYDNRTCGLRVPPSGPNNRRVENRIPSSDANPYLAIA 378 Query: 334 AILMAGLDGIKHKVEPFAYVEENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREA 393 A L AG G+ ++P V +D G R GI+ LP SL ++L + + E Sbjct: 379 ASLAAGYLGMVQGLKPSEPV-----SIDAGAR---GIE-LPRSLSDSLRLFVACQPLVEI 429 Query: 394 LGEAY-KNFIEYKRKEWESYL 413 LG + + K+ E+E+++ Sbjct: 430 LGPTFCAAYDRVKQAEYETFM 450 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: 524 Number of extensions: 30 Number of successful extensions: 4 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: 465 Length adjustment: 33 Effective length of query: 406 Effective length of database: 432 Effective search space: 175392 Effective search space used: 175392 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