Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate 6938541 Sama_2644 glutamate--ammonia ligase (RefSeq)
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__SB2B:6938541 Length = 451 Score = 187 bits (475), Expect = 6e-52 Identities = 131/409 (32%), Positives = 207/409 (50%), Gaps = 27/409 (6%) Query: 29 KGMEIPASRLQEAIEDGISFDGSSVPGFQGIEDSDLIFKADPD--TYVEVPW--DNVARV 84 +GM +P S L + + D + ++ + ++D+ F PD E+PW + A+V Sbjct: 41 QGMRLPESVLLQTVTGDYVNDDTY---YELLNEADVDFLCVPDENAVFELPWCVEATAQV 97 Query: 85 YGYIY-KDGKPYGADPRGVLKRVIEKLAEMGIKAYIGPEPEFYLFKKNGSWELEI----- 138 +Y + G P PR VLK+V++ E G + + PE EFYL +NG +L + Sbjct: 98 IHDVYDRMGNPIELSPRNVLKKVLKLYEEKGWEPVVAPEMEFYLVARNGDPDLPLNPPLG 157 Query: 139 ----PDVGGY-FDILTLDKAKDIKREIAEYMPSFGLVPEVLHHEVGKAQHEIDFRYDEAL 193 P+ G F I ++ + ++ E+ + GL + L HE G AQ EI+F + AL Sbjct: 158 RSGLPEAGRQSFSIDAANEYDPLFEDMYEWCEAQGLFIDTLIHEDGPAQMEINFSHGNAL 217 Query: 194 KTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHLHISLW--KEGENIFKGEEG 251 AD + FK ++ A H + ATFM KP+ PG+ MH+H S+ K G+NIF E+G Sbjct: 218 SLADQVFVFKRTLREAALKHNVCATFMAKPVTNEPGSAMHIHQSVVDKKTGKNIFTKEDG 277 Query: 252 L-SETALHFIGGLLKHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRVPAF 310 S L +I GL + + P+VNS++R +PG APV + WG +NR+ +R+P Sbjct: 278 TKSANFLGYIAGLQQFIPEFLPLMAPSVNSFRRFLPGTSAPVNLEWGEENRTCGLRIPES 337 Query: 311 WGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVEPFAYVEENVYEMDEGKRKELGI 370 RIE R P AN Y A AA L+AG G+ ++P N + + Sbjct: 338 SPQNRRIENRIPGADANCYLAIAASLLAGYIGMVEGLKP-----TNPALGRANESRTADT 392 Query: 371 DTLPGSLGEALDELEKDKVVREALGEAY-KNFIEYKRKEWESYLEYLEA 418 + LP +L EAL +++ R+ LG+A+ F+ K+ E E++ + A Sbjct: 393 NCLPLTLEEALTAMDESDAARKYLGDAFTTGFVAVKQAELENFRRVVSA 441 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: 500 Number of extensions: 20 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: 451 Length adjustment: 32 Effective length of query: 407 Effective length of database: 419 Effective search space: 170533 Effective search space used: 170533 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