Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate YP_426340.1 Rru_A1252 L-glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >NCBI__GCF_000013085.1:YP_426340.1 Length = 450 Score = 208 bits (529), Expect = 3e-58 Identities = 146/439 (33%), Positives = 216/439 (49%), Gaps = 43/439 (9%) Query: 17 VQLIFVDINGMPKGMEIPASRLQEAIEDGISFDGSSV-----PGFQGIEDSDLIFKADPD 71 V+ + D+NG+ +G +PA + ++ED SSV G D + DPD Sbjct: 17 VECLLSDMNGIVRGKVLPARKFLRSLEDNSLRIPSSVFLVTVTGEYPFADDNNTVVIDPD 76 Query: 72 TYVEVPWDNVARVYGY----------IYK-DGKPYGADPRGVLKRVIEKLAEMGIKAYIG 120 + + + GY YK +G P PR VLKRV+ +E G K + Sbjct: 77 ADLRPDFRTLCVAPGYRTPTAFVVVDAYKSNGIPLDLSPRQVLKRVLALYSEQGWKPVVA 136 Query: 121 PEPEFYLFKKNGSWELEIPDVGGY----------FDILTLDKAKDIKREIAEYMPSFGLV 170 PE EFYL + N +L + G + + + + +D+ I E+ GL Sbjct: 137 PEIEFYLTQVNADPDLPLSPPAGRSGRPETSPQPYGLEAITEFEDLIENIYEHAEIAGLQ 196 Query: 171 PEVLHHEVGKAQHEIDFRYDEALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGN 230 + L HE G AQ EI+F + + + +D ++ FK +V+ VA HG+YATFM KP+ PG+ Sbjct: 197 IDTLIHEAGAAQLEINFLHGDPITLSDQVVVFKRLVRQVALKHGVYATFMAKPMADQPGS 256 Query: 231 GMHLHISLWK--EGENIFKGEEGLSETAL-HFIGGLLKHAKALTAITNPTVNSYKRLVPG 287 MH+H SL + G+N+F ++G H+IGGL +T + P +NS++R+ P Sbjct: 257 AMHIHQSLVEIGTGKNLFVRDDGSDSPMFRHYIGGLQALLAQVTPLFAPNINSFRRMRPH 316 Query: 288 YEAPVYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKV 347 + AP+ + GY NRS +RVP R+E R P ANPY A AA L G GI ++ Sbjct: 317 HSAPINLECGYDNRSCGLRVPLSDPANRRLENRLPGADANPYLAMAASLACGYIGIMERI 376 Query: 348 EPFAYVE-ENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGE-AYKNFIEYK 405 EP VE N Y TLP +L EALD LEK V++ LGE ++ F K Sbjct: 377 EPSIMVEGGNAYRRSR---------TLPRTLDEALDRLEKCTVIKNVLGEHFFEAFTMIK 427 Query: 406 RKEWESYLEYL---EAKHL 421 R E +++ + + E HL Sbjct: 428 RVELDAFQDVISSWERNHL 446 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: 558 Number of extensions: 30 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: 450 Length adjustment: 32 Effective length of query: 407 Effective length of database: 418 Effective search space: 170126 Effective search space used: 170126 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