Align glutamine synthetase (EC 6.3.1.2) (characterized)
to candidate GFF963 HP15_942 glutamate-putrescine ligase
Query= BRENDA::P36205 (439 letters) >FitnessBrowser__Marino:GFF963 Length = 454 Score = 196 bits (497), Expect = 2e-54 Identities = 140/448 (31%), Positives = 221/448 (49%), Gaps = 37/448 (8%) Query: 15 VRFIRLQFTDINGTLKNLEITPDVFLESWEDGIMFDGS----SIEGF--------VRIEE 62 ++F+ L D+NG ++ + P + +E G+ S +I+G + I E Sbjct: 18 LQFVDLLIPDMNGIVRGKRVDPSALAKVFERGVAMPASIFALNIQGTTVEETGLGLDIGE 77 Query: 63 SDMYLKPVLDTFAVLPWTVDGAKSARVICDVYTPDGK-PFEGDPRYRLRRMMEKAEQLGY 121 +D P+ +T + PW +A+++ +Y D + PF DPR L+ ++++ E LG Sbjct: 78 ADRVCLPIENTLTMEPW--QKRPTAQLLLTMYELDRETPFFADPRVVLQNIIKRFEDLGL 135 Query: 122 TPYAGPEMEFFILPI-NEKGEPVPEFLDHGGY-------FDLLPLSKVEEIRRDIAIALE 173 TP A E+EF+++ N G P P G + + L + E D+ A Sbjct: 136 TPVAAFELEFYLIDQENLAGRPQPPKSPLSGKRPAGTQAYSIDDLDEYAEFLADVLDAAH 195 Query: 174 KMGITVEATHHEVAPSQHEVDFRY-DTFLRTADNAQTVKLVIKTMAIFHGYHATFMPKPF 232 + + +A E AP Q EV+ Y D ++ D+A +K +IK MA H TFM KP+ Sbjct: 196 EQELPADALVAESAPGQFEVNLHYVDDAVQACDHATLLKRLIKNMAYDHEMDTTFMAKPY 255 Query: 233 YGVNGSGMHVHMSLFRGD-KNAFY-DPDDPLGLSKELRYFVGGILKHAKALAAVTNPTIN 290 + GSGMH+H+SL G+ +N F D + P + LR+ VGG++ A+ P IN Sbjct: 256 HNQAGSGMHLHVSLVDGEGRNVFAGDAEQPNDM---LRWAVGGLVATMNDAMALFCPNIN 312 Query: 291 SYKRLVPGYEAPVYISWSVGNRSALIRIPKARGKATRLEYRSPDPSCNIYLAFAAILAAG 350 SY+R P Y P +W V NR+A +R+P +A R+E+R N YL AA+LA Sbjct: 313 SYRRFSPEYYVPSAATWGVDNRTASLRLPGGDPEALRIEHRVAGADANPYLLMAAVLAGI 372 Query: 351 LDGIINKIEPPAPVEENIYHMTSERREELNIESLPGSLKEAVEELKKDDVIIDALGEHIF 410 GI N+IEPP +T E + SL +L++A+ EL + V+ D LG Sbjct: 373 HYGISNRIEPPP--------VTVGNAHEQHEASLVNNLRDALRELGQSKVMADYLGSQFL 424 Query: 411 EKFVEAAEKDWKEFSTYVTNWELQRYLY 438 + FV E + EF +++ E YL+ Sbjct: 425 DVFVACKEHELNEFEMTISDLEYLWYLH 452 Lambda K H 0.320 0.139 0.414 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: 486 Number of extensions: 22 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: 439 Length of database: 454 Length adjustment: 33 Effective length of query: 406 Effective length of database: 421 Effective search space: 170926 Effective search space used: 170926 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