Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate WP_015934113.1 MNOD_RS37225 glutamine synthetase
Query= curated2:Q9HNI2 (454 letters) >NCBI__GCF_000022085.1:WP_015934113.1 Length = 478 Score = 196 bits (498), Expect = 1e-54 Identities = 153/481 (31%), Positives = 214/481 (44%), Gaps = 47/481 (9%) Query: 8 SSALTDNERAVLDDIEAQGIDFLRLQFTDILGTVKNVSIPAHQAEKAFTEGIYFDGSSIE 67 + A D R V + + + ID +RL F D G ++ ++ A +A KA T G + + Sbjct: 11 TDAQADAARDVRERCDPERIDTVRLSFPDQHGILRGKTLVASEAVKALTGGCAITTTMLA 70 Query: 68 ----------------GF-VRIQE--SDMRLDPDPETFAVLPWRSNGDGGSARLICDVVD 108 GF +R E +D+ + PDP TF LPW + L+CD+ Sbjct: 71 KDTSHRTVFPVFTAGGGFGMREMEGAADVVMVPDPTTFRTLPWAPR----TGWLLCDLYF 126 Query: 109 REGNAFAGGPRQVLKNVLARADDMGYSVSIGPEPEFFLFEKDDDGNATTTAHDQG----- 163 ++G R + ++VL R + G E EF +F+ DD A A G Sbjct: 127 QDGRPVPFATRGIYRSVLDRLSERSLEYVAGLEVEFHVFKLDDPRMAPADAGQPGEPPSV 186 Query: 164 -----GYFDLAPK--DLASDIRREIIFTLEAMGFEIEASHHEVARGQHEINFKYDDALTT 216 GY L + D I + + A+G + + E Q E F+ Sbjct: 187 SLISHGYQYLTEQRYDQVEPILEILRKDVLALGLPLRSIEVEYGPSQCEFTFQPTAGAVP 246 Query: 217 ADNIATFRAVVRAVAEQHDVHATFMPKP-IGEINGSGMHSHISLFD-EDGENVFADNDDE 274 AD + FR+ V+ +H HATFM +P I + SG H H SL D G N F D Sbjct: 247 ADLMVLFRSAVKQTCRRHGYHATFMCRPRIPNVVSSGWHLHQSLRDARTGANAFVPGDGS 306 Query: 275 FNLSETAYQFMGGVLEHAPAFTAVTNPTVNSYKRLVPGYEAPVYIAWSGVNRSALIRVPD 334 LS F+GG+L HA A T T PT+N YKR AP W NR +IRV Sbjct: 307 QPLSGFGMGFLGGLLAHARAATVFTTPTINGYKRYRSYSLAPDRAVWGRDNRGVMIRVLG 366 Query: 335 AAGVSA-RFEIRSPDPSCNPYLALAAVIAAGLDGIDTDADPGDAVREDIYEFDEDKRDAY 393 G A R E R +P+ NPYL +AA + AGLDG D + DPG + + YE + Sbjct: 367 GPGDPATRLENRVGEPAANPYLYMAAQVLAGLDGADRNLDPGPSA-DTPYEAE------- 418 Query: 394 GIDTLPGHLGDAVTALESDPVMQDALGEHVCEKFAEAKRHEYAEYKASVSEWETDRYLEK 453 D LP L +AV AL DP + ALGE + + K E +++ ++EWE Y E Sbjct: 419 -ADLLPTSLREAVFALREDPFFRGALGESFVDYYTHIKNAEIERFQSEITEWEQREYFEI 477 Query: 454 F 454 F Sbjct: 478 F 478 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: 592 Number of extensions: 40 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: 478 Length adjustment: 33 Effective length of query: 421 Effective length of database: 445 Effective search space: 187345 Effective search space used: 187345 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