Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_011802240.1 PNAP_RS14305 glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >NCBI__GCF_000015505.1:WP_011802240.1 Length = 459 Score = 191 bits (485), Expect = 4e-53 Identities = 141/437 (32%), Positives = 210/437 (48%), Gaps = 41/437 (9%) Query: 17 VQLIFVDINGMPKGMEIPASRLQE---------AIEDGISFD-GSSVPGFQGIE--DSDL 64 V+ + D+ G+ +G +P + E + G++ + S P + I D D+ Sbjct: 28 VECLVPDLTGVARGKILPRGKFTEDRGMRLPEAVVAMGVTGEFPESGPYYDVISPTDKDM 87 Query: 65 IFKADPDTYVEVPWDN---VARVYGYIYKDGKPYGADPRGVLKRVIEKLAEMGIKAYIGP 121 + DP T VPW + ++ GK PR VL+RV E G+ + P Sbjct: 88 HLRPDPSTVRIVPWASNPTAQVIHDCFDPAGKLIPFAPRSVLRRVCELYEAEGLVPVVAP 147 Query: 122 EPEFYLFKKNGSWELEI-PDVGGY---------FDILTLDKAKDIKREIAEYMPSFGLVP 171 E EFYL +N + P +G + I +++ + +I +Y L Sbjct: 148 ELEFYLVARNTDPNTLLRPPIGRSGRAETSRQAYSIDAVNEFDPLFEDIYDYCEKMELNV 207 Query: 172 EVLHHEVGKAQHEIDFRYDEALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNG 231 + L HEVG Q EI+F + L AD + FK V+ A H +YATFM KPI G PG+ Sbjct: 208 DTLIHEVGAGQMEINFFHAHPLGLADEVFFFKRTVREAALRHNMYATFMAKPIAGEPGSA 267 Query: 232 MHLHISLWKE--GENIFKGEEGL-SETALHFIGGLLKHAKALTAITNPTVNSYKRLVPGY 288 MH+H S+ + G NIF +G SE H+IGGL ++ A A+ P VNSY+RL Sbjct: 268 MHVHQSILSKETGLNIFSNPDGSESEAFFHYIGGLQRYIPAAMALVAPYVNSYRRLSRDT 327 Query: 289 EAPVYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVE 348 AP+ I+WG+ NR+ IR P R+E R ANPY A A L G GIK+K++ Sbjct: 328 AAPINIAWGHDNRTVGIRSPIATPQARRVENRVIGADANPYVALAMTLACGYLGIKNKIK 387 Query: 349 PFAYVEENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGEAYKN-FIEYKRK 407 P ++ + Y L +LP SLGEALD L ++ + E LG + + E K Sbjct: 388 PKPEMKGDAY---------LSPYSLPRSLGEALDWLRRESDLHEVLGREFVTVYSEIKEM 438 Query: 408 EWESYLEYL---EAKHL 421 E+ +++ + E +HL Sbjct: 439 EFAEFMKVISPWEREHL 455 Lambda K H 0.318 0.139 0.420 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: 537 Number of extensions: 31 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: 439 Length of database: 459 Length adjustment: 33 Effective length of query: 406 Effective length of database: 426 Effective search space: 172956 Effective search space used: 172956 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