Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate BPHYT_RS23160 BPHYT_RS23160 glutamine synthetase
Query= curated2:Q9UY99 (439 letters) >FitnessBrowser__BFirm:BPHYT_RS23160 Length = 444 Score = 202 bits (514), Expect = 2e-56 Identities = 144/434 (33%), Positives = 212/434 (48%), Gaps = 38/434 (8%) Query: 17 VQLIFVDINGMPKGMEIPASRL---------QEAIEDGISFDGSSVPGFQGIEDSDLIFK 67 ++ I D+ G+ +G IP S+ Q + ++ D G+ D D++ Sbjct: 16 IEAIIPDMAGIARGKIIPRSKFESGESMRLPQAVMIQTVTGDYPEDGTLTGVTDPDMVCV 75 Query: 68 ADPDTYVEVPW--DNVARV-YGYIYKDGKPYGADPRGVLKRVIEKLAEMGIKAYIGPEPE 124 D T +PW D A+V + ++ DG P PR VL+RV+E G K I PE E Sbjct: 76 PDASTIRMIPWAVDPTAQVIHDCVHFDGTPVAISPRRVLRRVLELYKAKGWKPVIAPELE 135 Query: 125 FYLFKKNGSWELEI---------PDVGGY-FDILTLDKAKDIKREIAEYMPSFGLVPEVL 174 FYL N +L + P+ G + I +++ + +I EY L + L Sbjct: 136 FYLVDMNKDPDLPLQPPIGRTGRPETGRQAYSIEAVNEFDPLFEDIYEYCEVQELEVDTL 195 Query: 175 HHEVGKAQHEIDFRYDEALKTADNIISFKYIVKAVAEVHGLYATFMPKPIYGMPGNGMHL 234 HEVG AQ EI+F + + LK AD++ FK V+ A H +YATFM KP+ G PG+ MH+ Sbjct: 196 IHEVGAAQMEINFMHGDPLKLADSVFLFKRTVREAALRHKMYATFMAKPMEGEPGSAMHM 255 Query: 235 HISLWKE--GENIFKGEEGLSETAL-HFIGGLLKHAKALTAITNPTVNSYKRLVPGYEAP 291 H SL E G N+F G +G + +I GL K+ AL I P +NSY+RL AP Sbjct: 256 HQSLVDEETGHNLFTGPDGKPTSLFTSYIAGLQKYTPALMPIFAPYINSYRRLSRFMAAP 315 Query: 292 VYISWGYKNRSALIRVPAFWGNGARIEYRCPDPSANPYFAFAAILMAGLDGIKHKVEPFA 351 + ++WGY NR+ R+P RIE R P NPY A AA L AG G+ K+E Sbjct: 316 INVAWGYDNRTVGFRIPHSGPAARRIENRIPGVDCNPYLAIAATLAAGYLGMTQKLEATE 375 Query: 352 YVEENVYEMDEGKRKELGIDTLPGSLGEALDELEKDKVVREALGEAY-KNFIEYKRKEWE 410 + + YE+ LP +L E L + + + E LGE + K ++ K E+E Sbjct: 376 PLLSDGYELPY---------QLPRNLEEGLTLMGACEPIAEVLGEKFVKAYLALKETEYE 426 Query: 411 SYLEYL---EAKHL 421 ++ + E +HL Sbjct: 427 AFFRVISSWERRHL 440 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: 582 Number of extensions: 44 Number of successful extensions: 4 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: 444 Length adjustment: 32 Effective length of query: 407 Effective length of database: 412 Effective search space: 167684 Effective search space used: 167684 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 09 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