Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate GFF2676 PGA1_c27180 putative glutamine synthetase
Query= BRENDA::O33342 (457 letters) >FitnessBrowser__Phaeo:GFF2676 Length = 450 Score = 394 bits (1013), Expect = e-114 Identities = 216/451 (47%), Positives = 284/451 (62%), Gaps = 6/451 (1%) Query: 9 LAWTELERLVAAGDVDTVIVAFTDMQGRLAGKRISGRHFVDDIATRGVECCSYLLAVDVD 68 L++ L VA G VDTV+V DMQGRL GKR +HFV+ A CC+YLLA D+ Sbjct: 2 LSFDTLVDQVADGTVDTVLVCLVDMQGRLMGKRFHAKHFVNG-AWEETHCCNYLLATDLA 60 Query: 69 LNTVPGYAMASWDTGYGDMVMTPDLSTLRLIPWLPGTALVIADLV-WADGSEVAVSPRSI 127 + T GYA SW+ GYGD VM PDL+TLR +PWL GT +V+ D++ EV SPR+I Sbjct: 61 MATPDGYASTSWENGYGDYVMKPDLATLRPVPWLEGTVMVLCDVLDHHSHEEVPHSPRAI 120 Query: 128 LRRQLDRLKARGLVADVATELEFIVFDQPYRQAWASGYRGLTPASDYNIDYAILASSRME 187 L+RQ++RLK G A ATELEF +F++ + SG+R L P S YN DY+IL +SR E Sbjct: 121 LKRQVNRLKEMGFDAMCATELEFFLFEKSFDAIRKSGFRDLEPISGYNEDYSILQTSREE 180 Query: 188 PLLRDIRLGMAGAGLRFEAVKGECNMGQQEIGFRYDEALVTCDNHAIYKNGAKEIADQHG 247 +LR IR + AGL E KGE GQ+E+ +Y A+ T H I K+ KEIA Q G Sbjct: 181 HVLRPIRNHLWDAGLPIENSKGEAETGQEELNIKYAAAMDTAAYHTIAKHAVKEIAQQQG 240 Query: 248 KSLTFMAKYD-EREGNSCHIHVSLRGTDGSAVFADSNGPHGMSSMFRSFVAGQLATLREF 306 ++TF+ K+ E+ G+S H+H SL DG F D + GMSS+ ++++AG L ++ Sbjct: 241 HAVTFLPKWSHEKVGSSSHVHQSL-WQDGKPAFFDESDALGMSSLMKAYMAGLLKYAPDY 299 Query: 307 TLCYAPTINSYKRFADSSFAPTALAWGLDNRTCALRVVGHGQN-IRVECRVPGGDVNQYL 365 T AP INSYKRF +FAPT + W +DNRT R+ G G IRVECR+PG D+N YL Sbjct: 300 TAFMAPYINSYKRFMKGTFAPTRIIWSVDNRTAGYRLCGVGSKAIRVECRIPGSDMNPYL 359 Query: 366 AVAALIAGGLYGIERGLQLPEPCVGNAYQGADVERLPVTLADAAVLFEDSALVREAFGED 425 A+A ++A G+ GIE GL+L P G+ YQG D +P TL DAA + SA++R A G+ Sbjct: 360 AIAGMLAAGIAGIEEGLELQAPTTGDVYQG-DTGMIPGTLRDAATALKSSAMLRAAMGDA 418 Query: 426 VVAHYLNNARVELAAFNAAVTDWERIRGFER 456 VV HY+ A VE+ F VTD+E RGFER Sbjct: 419 VVDHYVRAAEVEIEDFERIVTDYEIARGFER 449 Lambda K H 0.321 0.137 0.417 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: 595 Number of extensions: 27 Number of successful extensions: 7 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: 457 Length of database: 450 Length adjustment: 33 Effective length of query: 424 Effective length of database: 417 Effective search space: 176808 Effective search space used: 176808 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 (21.9 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