Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_083769460.1 AFER_RS10185 glutamine synthetase
Query= BRENDA::O07752 (450 letters) >NCBI__GCF_000023265.1:WP_083769460.1 Length = 394 Score = 249 bits (636), Expect = 1e-70 Identities = 151/400 (37%), Positives = 207/400 (51%), Gaps = 11/400 (2%) Query: 54 SPVWHTFCIDQCSIAFTADISVVGDQRLRIDLSALRIIG--DGLAWAPAGFFEQDGTPVP 111 SPV+ F D + + + D RLR D LR + DG A+AP F +DGTP Sbjct: 2 SPVFDAFLTDDSITSSSVSGGPMDDLRLRPDPRFLRPLAPLDGWAFAPVDRFRRDGTPYE 61 Query: 112 ACSRGTLSRIEAALADAGIDAVIGHEVEFLL-VDADGQRLPSTLWAQYGVAGVLEHEAFV 170 C+R L R A LADAG A +G E+E+++ + +P+T YG++ V+E ++ Sbjct: 62 LCTRSALQREVALLADAGASATMGIELEWVVGLAGQDDFVPATSGPAYGLSRVIELADYL 121 Query: 171 RDVNAAATAAGIAIEQFHPEYGANQFEISLAPQPPVAAADQLVLTRLIIGRTARRHGLRV 230 R + A AG+A+ Q HPEY QFE+SLAP PV AAD VL R +I R+GLR Sbjct: 122 RSLYDALETAGLAVAQLHPEYAPAQFELSLAPSDPVGAADASVLARSVIRAVGERYGLRT 181 Query: 231 SLSPAPFAGSIGSGAHQHFSLTMSEGMLFSGGTGAAGMTSAGEAAVAGVLRGLPDAQGIL 290 S +P G +G+G H H L +F+GG G G+ GE+ +A +L LP I Sbjct: 182 SFAPVVDVGGVGNGGHIHLGLYRDGEPIFAGGDGPGGVRPEGESVIAWLLEELPAILAIA 241 Query: 291 CGSIVSGLRMRPGNWAGIYACWGTENREAAVRFVKGGA-GSAYGGNVEVKVVDPSANPYL 349 VS LR+ P +WAG Y WG ENREAA+R V NVE+K D ANPYL Sbjct: 242 APHPVSYLRLVPSHWAGAYRVWGIENREAALRLVPAATLVDGRAANVELKGADLGANPYL 301 Query: 350 ASAAILGLALDGMKTKAVLPSETTVDPTQLSDVDRDRAGILRLAADQADAIAVLDSSKLL 409 + ++LG+A + P DP G+ RL D A + L SS+LL Sbjct: 302 LATSLLGIARHALADPRTPPPPVEGDPAH-------HGGLERLPGDLAATLGALRSSELL 354 Query: 410 RCILGDPVVDAVVAVRQLEHERYGDLDPAQLADKFRMAWS 449 + +LG + A+ AVR+ E R+ D P +L R +WS Sbjct: 355 QDVLGRSFLTAIGAVREAELARFADATPEELVAAMRWSWS 394 Lambda K H 0.319 0.135 0.399 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: 498 Number of extensions: 27 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: 450 Length of database: 394 Length adjustment: 32 Effective length of query: 418 Effective length of database: 362 Effective search space: 151316 Effective search space used: 151316 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: 50 (23.9 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