Align Glutamine synthetase; GS; EC 6.3.1.2; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha (uncharacterized)
to candidate BPHYT_RS09955 BPHYT_RS09955 glutamine synthetase
Query= curated2:O27612 (442 letters) >FitnessBrowser__BFirm:BPHYT_RS09955 Length = 445 Score = 191 bits (484), Expect = 5e-53 Identities = 133/395 (33%), Positives = 191/395 (48%), Gaps = 29/395 (7%) Query: 57 SSVEGFVDINESDLVLKPDPDTFSTLPWRPEEKGVCRFICDIYWPDGKPFEGDPRYVLKR 116 ++ E FV ++ D+V PDP+T +PW E+ V I D DGKP PR VL+R Sbjct: 60 ANFERFVGPSDPDMVCIPDPNTVRLVPWAIEQVAVV--IHDCVGLDGKPIGISPRAVLRR 117 Query: 117 ALDKYAHLGYEYNVGPEPEFFILDQDED---------GNIIPHDCGAY-FDVEPVDQGTD 166 L Y G+ V PE EF+++ Q+++ G H+ G F ++ V++ Sbjct: 118 VLRLYEARGWRPVVAPEMEFYLIAQNKNPHEPLRPPLGRAGRHEAGRQSFSIDAVNEFDP 177 Query: 167 FRRKLVMDLEALNFDVEVSHHEVAPGQHEIDFKFDKALKTADAVITFKQAIKAIVDKIGY 226 F + L E VE HEV GQ EI+F AL AD V FK+A++ + G Sbjct: 178 FFQDLSRFCEMTQLGVETLVHEVGAGQMEINFSHGDALDLADRVFLFKRAVRETAFRHGI 237 Query: 227 MVTFMPKPFFGENGSGMHCHQSLF--KDGENVFYDPDTETQLSEEALYF--IGGLLKHAP 282 TFM KP E GS MH HQS+ + G+N+F PD S L+F IGGL K+ P Sbjct: 238 FATFMAKPMEHEPGSAMHIHQSIVDRESGQNIFSLPDG----SASPLFFNYIGGLQKYMP 293 Query: 283 ALTAVCAPTVNSYKRLVPGYEAPVYIAYGLKNRSTLIRIPASRGKGTRVELRMPDPSCNP 342 + AP VNSY+RL AP+ + +G NR+ IR+P S G R+E R+P NP Sbjct: 294 QAMPMFAPYVNSYRRLSRFTAAPINVRWGYDNRTCGIRVPNSEPDGRRLENRVPGVDVNP 353 Query: 343 YLAFAAMLEAGMNGIQNKIDPGEPTEIDVYEKSMSELREMGIETLPSSLWEAYHALEEDD 402 YLA AA L G G+ + + P Y+ LP L +A AL + Sbjct: 354 YLAMAATLACGYLGMVEQQEASAPMIESAYDLEYE---------LPRGLEDALKALSKCT 404 Query: 403 VIKGALGGHVYEKFMEIKHREWDDYRVRVFKYELE 437 + LG + + +K +E++ + + +E E Sbjct: 405 ELAEVLGDSFVQAYCAVKEKEFETFSQGITAWERE 439 Lambda K H 0.320 0.141 0.433 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: 21 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: 442 Length of database: 445 Length adjustment: 32 Effective length of query: 410 Effective length of database: 413 Effective search space: 169330 Effective search space used: 169330 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 (21.8 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