Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha; EC 6.3.1.2 (characterized)
to candidate WP_012402884.1 BPHY_RS18060 glutamine synthetase
Query= SwissProt::Q60182 (454 letters) >NCBI__GCF_000020045.1:WP_012402884.1 Length = 444 Score = 192 bits (487), Expect = 2e-53 Identities = 138/462 (29%), Positives = 225/462 (48%), Gaps = 35/462 (7%) Query: 9 VEQAIEYVKKNNVKFIRFQFVDILGFPKNVAYPVKAGEKGIEELREIFE------NGVWF 62 +++ E++KK+++ I D+ G + P E G E +R G + Sbjct: 1 MQEIDEFLKKHHITEIEAIIPDMAGIARGKIIPRSKFESG-ESMRLPQAVMIQTVTGEYP 59 Query: 63 DGSSITGFVGIEESDMLLKPDLSTLSVLPWRPEEKSVARVICDVYKDEKTPFEGDPRSRL 122 D ++TG + + DM+ PD ST+ ++PW + A+VI D + TP PR L Sbjct: 60 DDGTLTG---VTDPDMVCVPDPSTIRIIPWAVDP--TAQVIHDCVHFDGTPVAISPRRVL 114 Query: 123 KAILEELKKEMNGEYFVGPEPEFFL--LKRDPHNP-----HRWVPADDGGY-FDVEPLDD 174 + +L+ L K + + PE EF+L + +DP P R A+ G + +E +++ Sbjct: 115 RRVLD-LYKAKGWKPVIAPELEFYLVDMNKDPDLPLCPPVGRTGRAETGRQAYSIEAVNE 173 Query: 175 APDIRRDIVLALENLGFHVEASHHEVAPGQHEVDFKFDNALKTADSVITFKMTIKNIAKK 234 + DI + V+ HEV Q E++F + LK AD V FK T++ A + Sbjct: 174 FDPLFEDIYEYCDIQELEVDTLIHEVGAAQMEINFLHGDPLKLADQVFLFKRTVREAALR 233 Query: 235 HGLKATFMPKPFFGMNGNGMHCHQSVWFN--GEPSFYDPEGPYNGLSETCLSYIAGILSH 292 H + ATFM KP G G+ MH HQS+ G+ F +G + Y+AG+ + Sbjct: 234 HHMYATFMAKPMEGEPGSAMHVHQSLVDEETGQNLFTGSDGKPTDVFN---QYLAGLQKY 290 Query: 293 AKALVAITNPTVNSYKRLVPGYEAPVNIAWANKNRSAIIRVPAARGKATRIEFRAPDPTC 352 AL+ I P +NSY+RL AP+N+ W NR+ R+P + +A RIE R P C Sbjct: 291 TPALMPIFAPYINSYRRLSRFMAAPINVQWGYDNRTVGFRIPHSGPQARRIENRIPGVDC 350 Query: 353 NPYLAFACMLAAGLDGIKKKMTAPEPVERNIFKMSEEEKKQLGIESVPANLAAALDELEC 412 NPYLA A LAAG GI +++T EP+ + +++ + +P NL L + Sbjct: 351 NPYLAIAGTLAAGYLGITQRLTPTEPLSSDGYELPYQ---------LPRNLEEGLTLMSA 401 Query: 413 DEVLQKALGKHIYENYMEIKRAEWDDFRTAVTDWETGKYLIY 454 E L + +G+ + Y+ +K E++ F ++ WE L++ Sbjct: 402 CEPLAEIMGEQFVKAYLALKETEYEAFFRVISSWERRHLLLH 443 Lambda K H 0.319 0.137 0.421 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: 536 Number of extensions: 24 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: 454 Length of database: 444 Length adjustment: 33 Effective length of query: 421 Effective length of database: 411 Effective search space: 173031 Effective search space used: 173031 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 (21.7 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