Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_013645428.1 METBO_RS09175 glutamate--ammonia ligase
Query= BRENDA::F2RM17 (446 letters) >NCBI__GCF_000191585.1:WP_013645428.1 Length = 440 Score = 229 bits (585), Expect = 1e-64 Identities = 138/424 (32%), Positives = 226/424 (53%), Gaps = 13/424 (3%) Query: 9 QCEDAGVE--LVRLLYVGNDGHTHGHSVKRAHLEDALESGIQLPKLIQSFNAL--GMRVK 64 Q ED G +R+L++ N +++ +D E+ + + + Q + G+ V Sbjct: 4 QLEDLGERSRFLRILWIDNANMIRSKALRLKVDDDVSEAVVGISRAQQGVPVVYDGV-VP 62 Query: 65 DADFDAVGEVRLVPDRSTFRVLDHEDSVAAVCCSLYEIDDQTPWAADPRSALSGFISTLA 124 A D VGEV L D ST R + + + +Y D +PW PR+ L ++ Sbjct: 63 GAPLDPVGEVYLKADNSTIRKVPYAPGNSLAIGDMYV--DGSPWDFCPRNYLRKILNLAR 120 Query: 125 DDDVVPSTALESEFHFYTSEDGDDEPHGTRGLYATASMREFNDIVLETIDALEAQQINVK 184 D+ + + E+EF+ +D + H +T SM ND+++E D LE+Q ++V+ Sbjct: 121 DEGLEIKASFENEFYLLNKDDPLN-CHENTAFGSTNSMNLNNDVIMEIADYLESQGLSVE 179 Query: 185 KHCPEYAAGQHELVTKHREGLTPVDDYVFLRETVAAIAESHGFETTFLPFPF-ETATNGC 243 ++ E QHE+ + + + D+ + RETV +A HG +FLP F + A +GC Sbjct: 180 QYYSESGPCQHEITVHYDDAMKATDNQIIFRETVRGVALKHGMVASFLPKLFADHAGSGC 239 Query: 244 HINLSLWND-TNLFAPTDSDRALSSTGRHFVGGVLAHLPALLALTSPTVNSYARLQPQSG 302 HI+LSLW D N+ D + L +T HF+ G+L HL AL+A+T+PT NSY R+ P S Sbjct: 240 HIHLSLWRDGVNILHDPDENFELGNTAHHFIAGILEHLSALMAITTPTPNSYRRILPSSW 299 Query: 303 AAAFGCWGIGNREAAIRVPEVPTNKRETATRIEFRPADNTANPYLSLLGLLAAGWDGVQN 362 A +GCWG NREA+IRV + P T E + +D T+NPYLS+ ++ +G +G++ Sbjct: 300 AGKYGCWGFDNREASIRVVKEPDG---TIKHFEIKTSDATSNPYLSIGSIIFSGLNGIKE 356 Query: 363 EIDPGRPLDEDPGNCSDELLDERGIERLPQTLGEALDALEKNEVLREALGEQLFDSYLTV 422 ++ P+ DP ++ + I+ LP + +A+ +L K+EVL A+G+ L +Y+ V Sbjct: 357 KLSLPEPVQLDPAKLEEDERLKLNIKDLPSCVDDAIKSLSKDEVLMNAMGDGLSKAYIAV 416 Query: 423 KRHE 426 K E Sbjct: 417 KTEE 420 Lambda K H 0.317 0.134 0.402 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: 495 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: 446 Length of database: 440 Length adjustment: 32 Effective length of query: 414 Effective length of database: 408 Effective search space: 168912 Effective search space used: 168912 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 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