Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate GFF4215 Psest_4288 Glutamine synthetase
Query= BRENDA::P12425 (444 letters) >FitnessBrowser__psRCH2:GFF4215 Length = 457 Score = 176 bits (445), Expect = 2e-48 Identities = 133/452 (29%), Positives = 207/452 (45%), Gaps = 35/452 (7%) Query: 12 LVKEENVKYIRLQFTDILGTIKNVEIPVSQLGKALDNKVMFDGS----SIEGF------- 60 L + V+Y+ L TD+ G ++ I + L K + + S I G Sbjct: 16 LKEHPEVQYVDLLITDMNGVVRGKRIERASLHKVYEKGINLPASLFALDINGITVESSGL 75 Query: 61 -VRIEESDMYLYPDLNTFVIFPWTAEKGKVARFICDIYNPDGTPFEGDPRNNLKRILKEM 119 + I +SD +P NT PW +K A+ + ++ DG PF DPR L++++ + Sbjct: 76 GMDIGDSDRTCFPIPNTLCKEPW--QKRPTAQLLMTMHERDGDPFFADPREVLRQVVSKF 133 Query: 120 EDLGFSDFNLGPEPEFFLFKLDE-KGEPTLELNDKGG-------YFDLAPTDLGENCRRD 171 ++LG + E EF+L + G P + G + + D +C +D Sbjct: 134 DELGLT-ICAAFELEFYLIDQENINGRPQPPRSPISGKRPHSTQVYLIDDLDEYVDCLQD 192 Query: 172 IVLELEEMGFEIEASHHEVAPGQHEIDFKY-AGAVRSCDDIQTFKLVVKTIARKHGLHAT 230 I+ +E G +A E AP Q E++ + A +++CD K ++K IA H + T Sbjct: 193 ILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTT 252 Query: 231 FMPKPLFGVNGSGMHCNLSLF-KNGVNAFFDENADLQLSETAKHFIAGIVKHATSFTAVT 289 FM KP G G+G+H ++SL KNG N F EN S +H I G+ + + A Sbjct: 253 FMAKPYPGQAGNGLHVHISLLDKNGNNIFATENP--LESAPLRHAIGGLQETMAASMAFL 310 Query: 290 NPTVNSYKRLVPGYEAPCYVAWSAQNRSPLIRIPASRGISTRVEVRSVDPAANPYLALSV 349 P VNSY+R + P W NR+ +R+P + RVE R ANPYL L+ Sbjct: 311 CPNVNSYRRFGAQFYVPNAPCWGMDNRTVALRVPTDSPDAVRVEHRVAGADANPYLMLAS 370 Query: 350 LLAAGLDGIKNKLEAPAPIDRNIYVMSKEERMENGIVDLPATLAEALEEFKSNEVMVKAL 409 +LA G+ NK+E API+ N Y E++E LP L +AL E +E+M + + Sbjct: 371 ILAGVHHGLTNKIEPDAPIEGNSY-----EQVEQ---SLPTNLRDALRELDDSEIMARYI 422 Query: 410 GEHLFEHFIEAKEIEWDMFRTQVHPWEREQYM 441 + F+ KE E F + E Y+ Sbjct: 423 SPDYIDIFVACKESELAEFEHSISDLEYNWYL 454 Lambda K H 0.319 0.137 0.406 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: 513 Number of extensions: 33 Number of successful extensions: 6 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: 444 Length of database: 457 Length adjustment: 33 Effective length of query: 411 Effective length of database: 424 Effective search space: 174264 Effective search space used: 174264 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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