Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate 8501367 DvMF_2099 glutamine synthetase, type I (RefSeq)
Query= BRENDA::Q8PY99 (447 letters) >FitnessBrowser__Miya:8501367 Length = 447 Score = 471 bits (1212), Expect = e-137 Identities = 238/444 (53%), Positives = 305/444 (68%), Gaps = 7/444 (1%) Query: 7 CTTKEDVLEAVKERDVKFIRTQFTDTLGIIKSWAIPAEQLEEAFENGVMFDGSSIQGFTR 66 C +DV+ AVKE +V FI+ F D LG +KS+ + +LE AFE G+ FDGSSI GFTR Sbjct: 8 CKNGDDVIRAVKEYNVSFIQFWFVDILGNLKSFQVTPSELESAFEEGMGFDGSSILGFTR 67 Query: 67 IEESDMKLALDPSTFRILPWRPATGAVARILGDVYLPDGNPFKGDPRYVLKTAIKEAEKM 126 IEESDM D +TF+I WRP VAR+ DV PDG P++GDPRY+L+ ++A + Sbjct: 68 IEESDMVAFPDATTFQICAWRPMERPVARMFCDVRNPDGTPYEGDPRYILRKLTEKAAQK 127 Query: 127 GFSMNVGPELEFFLFKLDANGNPTTELTDQGGYFDFAPLDRAQDVRRDIDYALEHMGFQI 186 G++ VGPELEFFLF P D GGYFD PLD DVRRDI +AL+ MG + Sbjct: 128 GYTYYVGPELEFFLFASSQCPQPI----DAGGYFDAPPLDLGNDVRRDIIFALQRMGIPV 183 Query: 187 EASHHEVAPSQHEIDFRFGDVLCTADNVVTFKYVVKSIAYHKGYYASFMPKPLFGVNGSG 246 E SHHEVAPSQHEID R+ + + AD V+T+K VVK +A G YA+FMPKP+FG NGSG Sbjct: 184 EYSHHEVAPSQHEIDLRYNEAMKMADVVMTYKVVVKEMARKHGVYATFMPKPIFGQNGSG 243 Query: 247 MHSNQSLFKDGKNVFYDPDTPTKLSQDAMYYIGGLLKHIREFTAVTNPVVNSYKRLVPGY 306 MH +QSLF++G+N F+DP+ P LS + YI GLLKH REF VTN +NSYKRLVPGY Sbjct: 244 MHVHQSLFRNGRNAFFDPNDPHHLSGECRSYIAGLLKHAREFCCVTNQWINSYKRLVPGY 303 Query: 307 EAPVYISWSAQNRSSLIRIPATRGN---GTRIELRCPDPACNPYLAFALMLRAGLEGIKN 363 EAPVY++W+ +NRS+LIR+P + TRIELR PDPACNPYLAF++ML AGLEGI+ Sbjct: 304 EAPVYLAWAQRNRSALIRVPMYKPGKEAATRIELRSPDPACNPYLAFSVMLAAGLEGIEK 363 Query: 364 KIDPGEPTNVNIFHLSDKEREERGIRSLPADLKEAIDEMKGSKFVKEALGEHVFSHYLCA 423 + + NIFH+ +++ + GI SLP L EA E+KGS ++E LGEH ++ + Sbjct: 364 SYELPKAVEANIFHMGEEDLTKHGIGSLPGSLYEAAMELKGSALMQEVLGEHTHANLVGN 423 Query: 424 KEMEWDEYKAVVHPWELSRYLSML 447 K +EWD Y+ V +EL RYL +L Sbjct: 424 KLIEWDAYRTHVSEFELQRYLPVL 447 Lambda K H 0.320 0.137 0.414 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: 597 Number of extensions: 20 Number of successful extensions: 3 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: 447 Length of database: 447 Length adjustment: 33 Effective length of query: 414 Effective length of database: 414 Effective search space: 171396 Effective search space used: 171396 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 (21.8 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