Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate AZOBR_RS08850 AZOBR_RS08850 glutamine synthetase
Query= curated2:Q9HNI2 (454 letters) >FitnessBrowser__azobra:AZOBR_RS08850 Length = 447 Score = 186 bits (471), Expect = 2e-51 Identities = 129/390 (33%), Positives = 188/390 (48%), Gaps = 27/390 (6%) Query: 73 QESDMRLDPDPETFAVLPWRSNGDGGSARLICDVVDREGNAFAGGPRQVLKNVLARADDM 132 + SD+ + PD T +PW +A++I D V +G+ PR VLK VL+ ++ Sbjct: 71 ENSDIYMIPDERTIRFVPWYEEP---TAQVITDCVYADGSPVNFSPRHVLKRVLSLYEER 127 Query: 133 GYSVSIGPEPEFFLFEKDDDGNATTTAH-DQGGYFDLAPKDLASDIRREI--IFTL---- 185 G+ + PE EFFL + + D + + G + + D E IF + Sbjct: 128 GWKPMVAPELEFFLVQVNKDPDYPLVPPVGRNGRVESGRQAFGIDAVNEFDPIFEMVYDF 187 Query: 186 -EAMGFEIEASHHEVARGQHEINFKYDDALTTADNIATFRAVVRAVAEQHDVHATFMPKP 244 EA +I+ HE Q EINF + DAL AD F+ R A +H V+ATFM KP Sbjct: 188 CEAQDIDIDTLTHEAGAAQIEINFNHGDALELADQAFLFKRTAREAALRHQVYATFMAKP 247 Query: 245 IGEINGSGMHSHISLFDED-GENVFADNDDEFNLSETAY--QFMGGVLEHAPAFTAVTNP 301 + GS MH H S+ D D G N+F+D N ++T + G+ ++ P + P Sbjct: 248 MQNEPGSAMHIHQSVVDADSGRNLFSDA----NGADTPLFMSHIAGLQKYLPYAMPLLAP 303 Query: 302 TVNSYKRLVPGYEAPVYIAWSGVNRSALIRVPDAAGVSARFEIRSPDPSCNPYLALAAVI 361 VNSY+RLVP +AP+ + W NR+ +RVP + S R E R NPYLA+AA + Sbjct: 304 NVNSYRRLVPNSDAPINVHWGRDNRTTGLRVPVSPADSRRVENRVAGADANPYLAIAASL 363 Query: 362 AAGLDGIDTDADPGDAVREDIYEFDEDKRDAYGIDTLPGHLGDAVTALESDPVMQDALGE 421 A G G+ +P D V+ Y R A+ TLP H GDA+ + +++ LGE Sbjct: 364 ACGYLGMAQGLEPTDPVKGSAY------RLAF---TLPRHQGDALQKFNACKPLKEVLGE 414 Query: 422 HVCEKFAEAKRHEYAEYKASVSEWETDRYL 451 + K EY Y +S WE + L Sbjct: 415 KFLDAVTCVKEAEYEAYHRVISSWERENLL 444 Lambda K H 0.316 0.135 0.396 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: 540 Number of extensions: 23 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: 454 Length of database: 447 Length adjustment: 33 Effective length of query: 421 Effective length of database: 414 Effective search space: 174294 Effective search space used: 174294 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