Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_012041189.1 BBTA_RS04135 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_000015165.1:WP_012041189.1 Length = 479 Score = 182 bits (463), Expect = 2e-50 Identities = 142/462 (30%), Positives = 212/462 (45%), Gaps = 25/462 (5%) Query: 14 LERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVDLNTV- 72 + R+ + T+ +F D G L GK ++ + + G + LLA D TV Sbjct: 21 MRRIAEEQGLKTIRFSFPDQHGILRGKALAVDAALSSLED-GCSITTTLLAKDTSHRTVF 79 Query: 73 ------PGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSEVAVSPRS 126 G+ M+ G D +M D +T R++PW PGT V+ DL +A+G+ V + R+ Sbjct: 80 PVFTAGGGFGMSEMQGG-SDALMVADPTTFRVLPWAPGTGWVLCDLYFANGAPVPFATRN 138 Query: 127 ILRRQLDRLKARGLVADVATELEFIVF--DQPY---RQAWASGYRGLTP-ASDYNIDYAI 180 + R L L RG E+E +F + P A + G G+ P S Y Sbjct: 139 LYRSALAALDQRGYQFKAGLEVECHIFKVEDPRLAPGDAGSPGQPGVPPTVSLLTQGYQY 198 Query: 181 LASSR---MEPLLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKN 237 L R M+P L IR + GL +++ E Q E + + D ++++ Sbjct: 199 LTEQRFDQMQPALETIRANLTALGLPLRSIELEYGPSQCEFVLQPGIGMEPADTMVLFRS 258 Query: 238 GAKEIADQHGKSLTFMA--KYDEREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSF 295 K+IA +HG TFM + + H+H SL DGS F S G+S++ R + Sbjct: 259 AVKQIAQRHGYHATFMCRPRIPNVMSSGWHLHQSLVARDGSNAFMTSE-TDGLSALGRHY 317 Query: 296 VAGQLATLREFTLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVG--HGQNIRVE 353 +AG LA R + PTIN Y+R+ S AP WG DNR +RV+G + R+E Sbjct: 318 MAGLLAHARAAAVFSTPTINGYRRYRAYSLAPDRAIWGRDNRGVMIRVLGGPGDRATRLE 377 Query: 354 CRVPGGDVNQYLAVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFE 413 R+ N YL +A+ IA GL G++R L P P Y+ LP +L +A + Sbjct: 378 NRIGEPAANPYLYMASQIAAGLDGVDRKLD-PGPSADVPYE-TKASLLPKSLHEAVDALK 435 Query: 414 DSALVREAFGEDVVAHYLNNARVELAAFNAAVTDWERIRGFE 455 A R AFG + +Y E+ FNA V+DWE+ FE Sbjct: 436 ADAFFRNAFGATFIDYYTFIKTAEIDRFNAEVSDWEQREYFE 477 Lambda K H 0.321 0.137 0.417 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: 591 Number of extensions: 24 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: 457 Length of database: 479 Length adjustment: 33 Effective length of query: 424 Effective length of database: 446 Effective search space: 189104 Effective search space used: 189104 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 (21.9 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