Align Glutamine synthetase; GS; Glutamate--ammonia ligase; Glutamine synthetase I alpha; GSI alpha; EC 6.3.1.2 (characterized)
to candidate 3608834 Dshi_2226 Glutamate--putrescine ligase (RefSeq)
Query= SwissProt::Q60182 (454 letters) >FitnessBrowser__Dino:3608834 Length = 456 Score = 172 bits (436), Expect = 2e-47 Identities = 137/460 (29%), Positives = 199/460 (43%), Gaps = 36/460 (7%) Query: 10 EQAIEYVKKNNVKFIRFQFVDILGFPKNVAYPVKAGEKGIEELREIFENGVWFDGSSITG 69 E A Y++ + + D+ G + A P K ++ N ++F +ITG Sbjct: 15 EPARAYLEGRRLDEVECIVADLAGVARGKAMPAA---KFARQMSFYLPNSIFFQ--TITG 69 Query: 70 ------FVGIEESDMLLKPDLSTLSVLPWRPEEKSVARVICDVYKDEKTPFEGDPRSRLK 123 G E DM+LKPD ST + PW + ++I D+ P PR+ LK Sbjct: 70 GWAEAALDGFTEPDMVLKPDFSTATPAPWTADW--TLQIIHDIEDQSGAPMPVAPRNVLK 127 Query: 124 AILEELKKEMNGEYFVGPEPEFFLLKRD--------PHNPHRWVPADDGGYFDVEPLDDA 175 ++ L K + V PE EF+L R+ P A + + +D+ Sbjct: 128 RVIA-LYKARGWKPVVAPEMEFYLTARNIDPAIAIQPPMGRTGRRAAARQAYSMSAVDEY 186 Query: 176 PDIRRDIVLALENLGFHVEASHHEVAPGQHEVDFKFDNALKTADSVITFKMTIKNIAKKH 235 + DI E G ++ E GQ E++ + + LK AD V FK I+ A +H Sbjct: 187 GPVIDDIYDFAEAQGLEIDGITQEGGAGQIEINLRHGDPLKLADEVFYFKRLIREAALRH 246 Query: 236 GLKATFMPKPFFGMNGNGMHCHQSVW--FNGEPSFYDPEGPYNGLSETCLSYIAGILSHA 293 ATFM KP G+ MH H SV GE F P+G + +IAG+ SH Sbjct: 247 DCFATFMAKPIQDEPGSAMHIHHSVTDIATGENIFTAPDGTETPAFQ---HFIAGLQSHL 303 Query: 294 KALVAITNPTVNSYKRLVPGYEAPVNIAWANKNRSAIIRVPAARGKATRIEFRAPDPTCN 353 +V + P VNSY+R VP AP+N+ WA NR+A +RVP A A R+E R CN Sbjct: 304 GDVVPLYAPYVNSYRRYVPENAAPINLEWARDNRTAGLRVPVANPAARRVENRLAGMDCN 363 Query: 354 PYLAFACMLAAGLDGIKKKMTAPEPVERNIFKMSEEEKKQLGIESVPANLAAALDELECD 413 PYL A LA G G+ + + + SE+ +LG AALD Sbjct: 364 PYLGIAASLACGYLGLLAEKPPKPQYVGDAYSGSEDLAPELG---------AALDLFSEA 414 Query: 414 EVLQKALGKHIYENYMEIKRAEWDDFRTAVTDWETGKYLI 453 + LG Y +KR E+ +F ++ WE L+ Sbjct: 415 TAVHDILGPEFCRVYEIVKRHEYTEFLQVISPWEREHLLL 454 Lambda K H 0.319 0.137 0.421 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: 531 Number of extensions: 31 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: 454 Length of database: 456 Length adjustment: 33 Effective length of query: 421 Effective length of database: 423 Effective search space: 178083 Effective search space used: 178083 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 (21.7 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