Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate WP_002719482.1 RSPH17029_RS05065 glutamine synthetase
Query= BRENDA::O33342 (457 letters) >NCBI__GCF_000015985.1:WP_002719482.1 Length = 459 Score = 409 bits (1052), Expect = e-119 Identities = 222/460 (48%), Positives = 290/460 (63%), Gaps = 10/460 (2%) Query: 4 PGSPPLAWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLL 63 PG+ + + EL+ V +G +DTV+VA DMQGRL GKR ++F+D CC YLL Sbjct: 2 PGN--MTFDELKEAVESGGIDTVLVACVDMQGRLMGKRFHAQYFIDG-GHHETHCCDYLL 58 Query: 64 AVDVDLNTVPGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLVWADGSEVAVS 123 A+D+++ TVPGY + W+ GYGD VM PD++TLR +PW+PGTALV+ DL+ ++V S Sbjct: 59 AIDMEMTTVPGYKNSGWEKGYGDYVMKPDMATLRALPWMPGTALVLCDLLDHHHNDVPQS 118 Query: 124 PRSILRRQLDRLKARGLVADVATELEFIVFDQPY----RQAWASG-YRGLTPASDYNIDY 178 PR+IL+RQ+ R +A G A +ATELEF +F+ + ASG R L P S YN DY Sbjct: 119 PRAILKRQIARAEAMGFKAMMATELEFFLFETSFDAVRNSMQASGQIRDLKPISAYNEDY 178 Query: 179 AILASSRMEPLLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNG 238 I +S+ E ++R +R G+ GAG+ E KGE + GQ+EI +Y +AL T DNHAI K Sbjct: 179 HIFQTSKEEEVMRALRNGLYGAGIPVECSKGEADAGQEEINVKYSDALDTADNHAITKTA 238 Query: 239 AKEIADQHGKSLTFMAKYDERE-GNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVA 297 K+IA GKS+TFMAKYD R G+S H+H SL DG F D PHGMS + R F+A Sbjct: 239 VKDIAHAAGKSVTFMAKYDHRRAGSSSHVHQSLWTLDGKPAFFDPEAPHGMSELMRQFLA 298 Query: 298 GQLATLREFTLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHG-QNIRVECRV 356 GQLA E T AP +NSYKRF FAPT W DNRT RV G G + IRVECR+ Sbjct: 299 GQLAHAEEITAFLAPYVNSYKRFCVGMFAPTKAVWSRDNRTAGFRVCGEGTKAIRVECRI 358 Query: 357 PGGDVNQYLAVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSA 416 G D+N YLA AAL+A GL GIE+ + L G+ Y A V +P TL AA + S Sbjct: 359 GGADLNPYLACAALLAAGLDGIEKKMDLEAEMRGDMYSTAGVREIPKTLRAAAERLKGST 418 Query: 417 LVREAFGEDVVAHYLNNARVELAAFNAAVTDWERIRGFER 456 ++REA G++VV HY + A E++ + VTD+E R FER Sbjct: 419 MLREAMGDEVVEHYHHAAEWEISEQDRVVTDFELARLFER 458 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: 549 Number of extensions: 18 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: 457 Length of database: 459 Length adjustment: 33 Effective length of query: 424 Effective length of database: 426 Effective search space: 180624 Effective search space used: 180624 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