Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_086509879.1 BZY95_RS10505 glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >NCBI__GCF_002151265.1:WP_086509879.1 Length = 448 Score = 179 bits (453), Expect = 2e-49 Identities = 129/407 (31%), Positives = 200/407 (49%), Gaps = 26/407 (6%) Query: 29 KGMEIPASRLQEAIEDGISFDGSSVPGFQGIEDSDLIFKADPDTYVEVPW--DNVARVYG 86 KGM +P S L + + G + D D++ + D VPW + A+V Sbjct: 41 KGMRLPESVLLQTVT-GDYVEDELYYSLLDPADIDMLCRPDSSAVYPVPWALEPTAQVIH 99 Query: 87 YIY-KDGKPYGADPRGVLKRVIEKLAEMGIKAYIGPEPEFYLFKKNGSWELEI-PDVGGY 144 Y K G P R LK+V+ AE G K + PE EFYL K+ +L + P +G Sbjct: 100 DCYDKMGNPIELSCRNQLKKVLALYAEQGWKPVVAPEMEFYLTKRCEDPDLPLLPPIGRS 159 Query: 145 ---------FDILTLDKAKDIKREIAEYMPSFGLVPEVLHHEVGKAQHEIDFRYDEALKT 195 F I ++ + ++ ++ GL + L HE G AQ EI+FR+ + L Sbjct: 160 GRQETGRQSFSIDAANEFDPLFEDMYDWCEIQGLDIDTLIHEEGTAQMEINFRHGDPLML 219 Query: 196 ADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHLHISLWKE--GENIFKGEEG-L 252 AD + FK ++ A H + ATFM KPI PG+ MH+H S+ G+++F E+G + Sbjct: 220 ADQVFVFKRTLREAALKHDVVATFMAKPITNEPGSAMHIHQSVLDATTGKSVFANEDGSM 279 Query: 253 SETALHFIGGLLKHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRVPAFWG 312 S+ LH IGG+ + + P VNS++R +P APV + WG +NR+ +RVP Sbjct: 280 SQLFLHHIGGMQRFIPEALPLMAPNVNSFRRFLPDTSAPVNVEWGEENRTCGLRVPDSSP 339 Query: 313 NGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVEPFAYVEENVYEMDEGKRKELGIDT 372 RIE R P AN Y A AA L+ G G+ ++ P A V+ +E R+ L Sbjct: 340 QNRRIENRLPGADANAYLAIAASLLCGYLGMVQQLNPSAPVQGRAFE-----RRNL---R 391 Query: 373 LPGSLGEALDELEKDKVVREALGEAY-KNFIEYKRKEWESYLEYLEA 418 LP +L +AL+ +E + + LG + ++ KR E E++ + + + Sbjct: 392 LPFTLEQALERMENCSELEQYLGHRFVTGYVAVKRVENENFKKVISS 438 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: 464 Number of extensions: 22 Number of successful extensions: 3 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: 448 Length adjustment: 32 Effective length of query: 407 Effective length of database: 416 Effective search space: 169312 Effective search space used: 169312 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 10 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