Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_090446267.1 BLS63_RS15570 glutamine synthetase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_925 (458 letters) >NCBI__GCF_900100495.1:WP_090446267.1 Length = 459 Score = 381 bits (979), Expect = e-110 Identities = 192/452 (42%), Positives = 282/452 (62%), Gaps = 7/452 (1%) Query: 10 LNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGS 69 + EA FL HPEV ++L + D GV RGK + R L VY+ G LP+++ L ING Sbjct: 6 IQEARDFLARHPEVRSLELFLIDAGGVPRGKLLHRDELLAVYQHGRPLPSTILGLTINGE 65 Query: 70 TVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPF-FADPREVLA 128 VE +GL ++GDAD YP+P +LC +PW+ +PT QL ++MH +G P ADPR VLA Sbjct: 66 DVEDSGLVWEVGDADCWTYPLPGSLCLQPWRAQPTGQLQVSMHPSQGLPAAVADPRHVLA 125 Query: 129 NVVRKFDEMGLTICAAFELEFYLIDQE-NVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEY 187 V+ + GL A ELEFYL+D+E + GRP P R ++G+RP +TQVY + +L++ Sbjct: 126 RVIDSLEVDGLHPVMAVELEFYLLDRERDATGRPLPARQ-MNGQRPQATQVYGVYELEQL 184 Query: 188 VDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYD 247 L ++ + QG+P + E AP Q E+ L H D ++A D + KRL+K +A Sbjct: 185 QPFLDELYAACEVQGLPVRTAISEYAPGQLEITLEHRFDALQAIDEGIRYKRLVKGVANK 244 Query: 248 HEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPE----QNAALRHAIGGVLET 303 + FMAKP+ AG+GLH+H+S+ D G N++ASE + LRH+IGG+L T Sbjct: 245 LGLQACFMAKPFAELAGSGLHLHVSLADAQGNNLYASELSDLAGGPGTLLRHSIGGMLAT 304 Query: 304 LPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADA 363 L +A CPN NS+RRF A Y P + WG++NRTV++RVP G A + IEHR+ GADA Sbjct: 305 LLDSLALFCPNANSFRRFQANSYAPLAKSWGVNNRTVSLRVPGGPAASRHIEHRICGADA 364 Query: 364 NPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYI 423 NPYL A++LAG+HHG+ +I+PG +EGN Y Q ++ LP++ ALR L+ S+ + + Sbjct: 365 NPYLAAAAILAGIHHGIRQRIDPGPAIEGNGYAQAKEFLPSDWLTALRALEQSDWARQAL 424 Query: 424 DPKYIDIFVACKESELEEFEHSISDLEYNWYL 455 +++ +F+A K +E +F + + ++ WYL Sbjct: 425 GAEFLKVFLAIKHTEYRQFMAEVGEQDWRWYL 456 Lambda K H 0.318 0.137 0.409 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: 643 Number of extensions: 41 Number of successful extensions: 3 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: 458 Length of database: 459 Length adjustment: 33 Effective length of query: 425 Effective length of database: 426 Effective search space: 181050 Effective search space used: 181050 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 (21.7 bits) S2: 51 (24.3 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
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