Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate 5208460 Shew_0972 glutamate--ammonia ligase (RefSeq)
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__PV4:5208460 Length = 449 Score = 188 bits (477), Expect = 3e-52 Identities = 132/401 (32%), Positives = 197/401 (49%), Gaps = 25/401 (6%) Query: 29 KGMEIPASRLQEAIEDGISFDGSSVPGFQGIEDSDLIFKADPDTYVEVPWDNVAR---VY 85 KGM +P S L + + G D D D + D + +PW A ++ Sbjct: 41 KGMRLPESVLLQTVT-GDYVDDDLYDSLLDKADIDFVCVPDENAVFMLPWTVEATAQVIH 99 Query: 86 GYIYKDGKPYGADPRGVLKRVIEKLAEMGIKAYIGPEPEFYLFKKNGSWELE-IPDVGGY 144 K G P PR +LK+V++ + G K I PE EFYL +N ++ IP VG Sbjct: 100 DTFDKMGNPIELSPRNLLKKVLKLYEDKGWKPVIAPEMEFYLTHRNSDPDMPLIPPVGRS 159 Query: 145 ---------FDILTLDKAKDIKREIAEYMPSFGLVPEVLHHEVGKAQHEIDFRYDEALKT 195 F I ++ + ++ ++ + GL + L HE G AQ EI+F + +AL Sbjct: 160 GRKESGRQSFSIDAANEYDPLFEDMYDWCEAQGLDIDTLIHEEGTAQMEINFSHGDALSL 219 Query: 196 ADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHLHISLW--KEGENIFKGEEGL- 252 AD + FK ++ A H + ATFM KP+ PG+ MH+H S+ K G+NIF E+G Sbjct: 220 ADQVFVFKRTLREAALKHDVCATFMAKPVTDEPGSAMHIHQSVVDIKTGKNIFTNEDGTK 279 Query: 253 SETALHFIGGLLKHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRVPAFWG 312 S L +IGGL K+ L + P VNS++R +PG APV + WG +NR+ +R+P Sbjct: 280 SAKFLCYIGGLQKYIPELLPLMAPNVNSFRRFLPGTSAPVNLEWGDENRTCGLRIPESSP 339 Query: 313 NGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVEPFAYVEENVYEMDEGKRKELGIDT 372 RIE R AN Y A AA L+ G G+ V+P V+ E +G + Sbjct: 340 QNRRIENRIAGADANSYLAIAATLLCGYMGMVEDVKPSTPVQGRANENRQG-------IS 392 Query: 373 LPGSLGEALDELEKDKVVREALGEAY-KNFIEYKRKEWESY 412 LP +L EAL + + VRE LG+ + +I K+ + E++ Sbjct: 393 LPLTLEEALAVMSESSAVREYLGDTFTSGYIAVKQADLENF 433 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: 478 Number of extensions: 22 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: 449 Length adjustment: 32 Effective length of query: 407 Effective length of database: 417 Effective search space: 169719 Effective search space used: 169719 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