Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_011885444.1 glutamine synthetase
Query= BRENDA::P36687 (439 letters) >NCBI__GCF_000016205.1:WP_011885444.1 Length = 445 Score = 204 bits (520), Expect = 3e-57 Identities = 141/442 (31%), Positives = 218/442 (49%), Gaps = 46/442 (10%) Query: 13 KIKFVQLVFVDINGMPKGMEIPASRLE-------------EAVTDGISFDGSSVPGFQGI 59 +I V+ + D+ G+ +G IP ++ E + VT DGS G+ Sbjct: 13 RITEVEAIIPDMAGIARGKIIPRNKFESGESMRLPQAVMVQTVTGDYPEDGS----LTGV 68 Query: 60 EDSDLVFKADPDTYVEVPW--DNVARV-YGFIYKDNKPYGADPRGILKRALEELEKEGYK 116 D D+V DP T +PW D A+V + ++ D P PR +L+R L+ E +G+K Sbjct: 69 TDPDMVCVPDPSTICLIPWAVDPTAQVIHDCVHFDGSPVEISPRYVLRRVLDLYEAKGWK 128 Query: 117 AYIGPEPEFYLFKKNGTWELEI-PDVGGY---------FDILTLDKARDIRREIAEYMPS 166 + PE EFYL N +L + P VG + I +++ + +I EY Sbjct: 129 PVVAPELEFYLVDMNADPDLPLRPPVGRTGRAETGRQSYSIEAVNEFDPLFEDIYEYCEM 188 Query: 167 FGLIPEVLHHEVGKAQHEIDFRYDEALKTADNIVSFKYITKAVAEMHGLYATFMPKPLFG 226 GL E L HEVG AQ EI+F + +AL AD + FK + A H +YATFM KP+ Sbjct: 189 QGLDIETLIHEVGAAQMEINFMHGDALSLADQVFLFKRTVREAALRHNMYATFMAKPMED 248 Query: 227 FPGNGMHLHISLS--KDGENVFMGEEG-LSEIALHFIGGILKHAKALIAVTNPTVNSYKR 283 PG+ MH+H SL+ + G N+F E G +S + ++ G+ K+ AL+ + P +NSY+R Sbjct: 249 EPGSAMHIHQSLADARTGRNLFADEGGDVSPMFQSYLAGLQKYTPALMPIFAPYINSYRR 308 Query: 284 LVPGYEAPVYISWGYRNRSALIRVPAFWGKGARIEYRCPDPSANPYFAFAAVLKAGLDGI 343 L AP+ + WGY NR+ R+P RIE R P NPY AFAA L AG G+ Sbjct: 309 LSRFMAAPINVQWGYDNRTVGFRIPQSAPAARRIENRIPGVDCNPYLAFAATLAAGYLGL 368 Query: 344 KHKIDPFAYVEENVYEMSEEKRKELGIETLPGSLGEALEELEKDKVVKEALGDAY-KNFI 402 ++ P + + Y++ + LP +L E + + + LGD + K ++ Sbjct: 369 TQQLAPTEPIASDGYDLPYQ---------LPRNLEEGISLMAACTPLAGILGDKFVKAYL 419 Query: 403 NYKWKEWESYLEYL---EEKHM 421 K E+E++ + E +H+ Sbjct: 420 ALKETEYEAFFRVISSWERRHL 441 Lambda K H 0.318 0.139 0.419 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: 539 Number of extensions: 30 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: 445 Length adjustment: 32 Effective length of query: 407 Effective length of database: 413 Effective search space: 168091 Effective search space used: 168091 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 (21.7 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