Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate GFF1137 PGA1_c11520 gamma-glutamylputrescine synthetase PuuA
Query= curated2:Q9HNI2 (454 letters) >FitnessBrowser__Phaeo:GFF1137 Length = 452 Score = 201 bits (512), Expect = 3e-56 Identities = 140/452 (30%), Positives = 212/452 (46%), Gaps = 40/452 (8%) Query: 22 IEAQGIDFLRLQFTDILGTVKNVSIPA---------HQAEKAFTE---GIYFDGSSIEGF 69 +E + +D + +D+ G + ++PA H + F + G + + + +G+ Sbjct: 16 LEGRRLDEVECIISDLPGIARGKAVPASKFAKQDYFHLPDSIFYQTITGDWAEAADDDGW 75 Query: 70 VRIQESDMRLDPDPETFAVLPWRSNGDGGSARLICDVVDREGNAFAGGPRQVLKNVLARA 129 + E DM L PD T PW GD + ++I D DR+ PR VLK V+ Sbjct: 76 I---EKDMILKPDMSTATAAPW--TGDW-TLQVIHDAYDRDHKPIPFSPRNVLKRVVQLY 129 Query: 130 DDMGYSVSIGPEPEFFLFEKDDD---------GNATTTAHDQGGYFDLAPKDLASDIRRE 180 D G+ + PE EFFL ++ D G + A + Y + D + + Sbjct: 130 HDKGWQPVVAPEMEFFLVARNIDPAREIEPMMGRSGRPAAARQAY-SMTAVDEFGPVIDD 188 Query: 181 IIFTLEAMGFEIEASHHEVARGQHEINFKYDDALTTADNIATFRAVVRAVAEQHDVHATF 240 I EA GFEI+ E GQ EIN ++ D + AD + F+ ++R A +HD ATF Sbjct: 189 IYDFAEAQGFEIDGITQEGGAGQLEINLRHGDPVKLADEVFYFKRLIREAALRHDCFATF 248 Query: 241 MPKPIGEINGSGMHSHISLFD-EDGENVFADNDDEFNLSETAYQFMGGVLEHAPAFTAVT 299 M KPI + GS MH H S+ D E G+N+F+ + ++ Y F+GG+ H PA AV Sbjct: 249 MAKPIADEPGSAMHIHHSIIDMESGDNIFSG--PQGGETDAFYHFIGGLQNHLPAGLAVM 306 Query: 300 NPTVNSYKRLVPGYEAPVYIAWSGVNRSALIRVPDAAGVSARFEIRSPDPSCNPYLALAA 359 P VNSY+R V AP+ + W+ NR+ IRVP + + R E R CNPYL +A Sbjct: 307 APYVNSYRRYVKEQAAPINLEWARDNRTTGIRVPLSGPEARRVENRIAGMDCNPYLGIAL 366 Query: 360 VIAAGLDGIDTDADPGDAVREDIYEFDEDKRDAYGIDTLPGHLGDAVTALESDPVMQDAL 419 +A G G+ + P + D Y D D +P +G A+ E + + L Sbjct: 367 SLACGYLGLVNEERPRKQFKGDAYAGDGD---------IPQVMGQALDLFEEASALHEVL 417 Query: 420 GEHVCEKFAEAKRHEYAEYKASVSEWETDRYL 451 G ++ KR EY E+ +S WE + L Sbjct: 418 GPEFARVYSIVKRAEYDEFLQVISPWEREHLL 449 Lambda K H 0.316 0.135 0.396 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: 561 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: 454 Length of database: 452 Length adjustment: 33 Effective length of query: 421 Effective length of database: 419 Effective search space: 176399 Effective search space used: 176399 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