Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_057507762.1 ABB28_RS05950 glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >NCBI__GCF_001431535.1:WP_057507762.1 Length = 465 Score = 221 bits (562), Expect = 5e-62 Identities = 150/434 (34%), Positives = 227/434 (52%), Gaps = 43/434 (9%) Query: 17 VQLIFVDINGMPKGMEIPASRLQE----AIEDGISFDGSSVPG--------FQGIEDSDL 64 V+ + DI G+ +G IPA + + +GI ++V G DSD+ Sbjct: 33 VECLVPDITGIARGKIIPADKFSHDYGTRLPEGIF--ATTVTGDYPDDYYELTSPSDSDM 90 Query: 65 IFKADPDTYVEVPW--DNVARVYGYIY-KDGKPYGADPRGVLKRVIEKLAEMGIKAYIGP 121 + + DP+T VPW D A++ Y K G+P+ PR VL+RV++ E+G++ + P Sbjct: 91 VLRPDPETVRMVPWATDPTAQIIHDCYTKSGQPHELAPRNVLRRVLDAYTELGLRPVVAP 150 Query: 122 EPEFYLFKKNGSWELEIPDVGGY----------FDILTLDKAKDIKREIAEYMPSFGLVP 171 E EF+L +KN + + G + I +++ I + +Y + L Sbjct: 151 ELEFFLVQKNTDPDFPLLPPAGRSGRPETARQSYSIDAVNEFDPILDLMYDYADAMKLDV 210 Query: 172 EVLHHEVGKAQHEIDFRYDEALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNG 231 + L HE G AQ E++F + A+ AD + FK ++ A HG+YATF+ KP+ PG+ Sbjct: 211 DTLIHESGAAQLEVNFTHAGAMNLADQVFLFKRTMREAAMRHGVYATFLAKPMENEPGSA 270 Query: 232 MHLHISLWK--EGENIFKGE---EG-LSETALHFIGGLLKHAKALTAITNPTVNSYKRLV 285 MH+H SL + +G N+F G+ EG S H++GGL K A A P VNSY+RLV Sbjct: 271 MHIHQSLLRISDGANVFAGDGDGEGEFSPVFGHYLGGLQKFAPQAMAFFAPNVNSYRRLV 330 Query: 286 PGYEAPVYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKH 345 G +P + WG+ NR+ +RVP + R+E R ANPY A AA L GL G++ Sbjct: 331 FGEVSPSNVHWGFDNRTCGLRVPMDTPDNMRVESRFAGSDANPYLAMAATLACGLLGLRG 390 Query: 346 KVEPFAYVEENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGEAY-KNFIEY 404 ++ P A V G KELG D LP SLGEALD LE+ ++ LGE + + +I Sbjct: 391 QLAPDAPV--------SGSAKELGYD-LPRSLGEALDGLEQCAELQALLGERFCRAYISV 441 Query: 405 KRKEWESYLEYLEA 418 KRKE+E++ + + Sbjct: 442 KRKEYETFFRVISS 455 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: 554 Number of extensions: 32 Number of successful extensions: 5 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 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