Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate GFF4213 Psest_4286 Glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__psRCH2:GFF4213 Length = 452 Score = 194 bits (494), Expect = 4e-54 Identities = 139/406 (34%), Positives = 206/406 (50%), Gaps = 36/406 (8%) Query: 29 KGMEIPASRLQEAI-----EDGISFDGSSVPGFQGIEDSDLIFKADPDTYVEVPW--DNV 81 KGM +P S L + + ED I ++ D D+ + DP+ VPW + Sbjct: 45 KGMRLPESVLLQTVTGDYVEDDIYYE------LLDPADIDMFCRPDPNAVFLVPWAIEPT 98 Query: 82 ARVYGYIY-KDGKPYGADPRGVLKRVIEKLAEMGIKAYIGPEPEFYLFKKNGSWELEI-P 139 A+V Y K G P PR +LKRV++ A+ G + + PE EFYL K+ +L P Sbjct: 99 AQVIHDTYDKMGNPIELSPRNILKRVLKMYADRGWQPIVAPEMEFYLTKRCEDPDLPFQP 158 Query: 140 DVGGY---------FDILTLDKAKDIKREIAEYMPSFGLVPEVLHHEVGKAQHEIDFRYD 190 +G F I ++ + ++ ++ + GL + L HE G AQ EI+FR+ Sbjct: 159 PIGRSGRQETGRQSFSIDAANEFDPLFEDMYDWCEAQGLDLDTLIHEEGTAQMEINFRHG 218 Query: 191 EALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHLHISLWKE--GENIFKG 248 EAL AD I+ FK ++ A H + ATFM KP+ G PG+ MHLH S+ G NIF Sbjct: 219 EALHLADQILVFKRTMREAALKHNVAATFMAKPMTGEPGSAMHLHQSVIDRNTGRNIFSN 278 Query: 249 EEG-LSETALHFIGGLLKHAKALTAITNPTVNSYKRLVPGYEAPVYISWGYKNRSALIRV 307 E+G +S+ LH +GGL K+ L + P VNS++R +P APV + WG +NR+ +RV Sbjct: 279 EDGSMSQLFLHHVGGLQKYIPELLPMFAPNVNSFRRFLPDTSAPVNVEWGEENRTVGLRV 338 Query: 308 PAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVEPFAYVEENVYEMDEGKRKE 367 P R+E R ANPY A AA L+ G G+ ++ P V+ YE R+ Sbjct: 339 PDSDPQNRRVENRLAGADANPYLAIAASLLCGYIGMVEQLPPSQPVKGRGYE-----RRN 393 Query: 368 LGIDTLPGSLGEALDELEKDKVVREALGEAY-KNFIEYKRKEWESY 412 L LP +L AL+ +E + + + L + ++ KR E E+Y Sbjct: 394 L---RLPLTLEAALERMETCRELEKYLSPKFITGYVAVKRAEQENY 436 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: 529 Number of extensions: 32 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: 452 Length adjustment: 32 Effective length of query: 407 Effective length of database: 420 Effective search space: 170940 Effective search space used: 170940 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