Align Glutamate--putrescine ligase (EC 6.3.1.11) (characterized)
to candidate WP_011840249.1 RSPH17029_RS01120 glutamine synthetase family protein
Query= reanno::psRCH2:GFF4215 (457 letters) >NCBI__GCF_000015985.1:WP_011840249.1 Length = 464 Score = 355 bits (912), Expect = e-102 Identities = 192/458 (41%), Positives = 264/458 (57%), Gaps = 4/458 (0%) Query: 4 PRAVQLNEANAFLKEHPEVQYVDLLITDMNGVVRGKRIERASLHKVYEKGINLPASLFAL 63 P L+EA FL HPE++ D+++ D NG+ RGK I R L Y+ G +LP S+ L Sbjct: 7 PSGSTLSEAETFLAAHPEIEAFDIVLHDANGIGRGKIIRRHELLSFYKGGRHLPISILGL 66 Query: 64 DINGITVESSGLGMDIGDSDRTCFPIPNTLCKEPWQKRPTAQLLMTMHERDGDPFFADPR 123 DI G V +GL D GD D +PIP TL P ++ M M++ DG P +DPR Sbjct: 67 DICGEDVHETGLIWDQGDGDLRAWPIPGTLVPLHGTTPPRGEVFMCMYDLDGRPMSSDPR 126 Query: 124 EVLRQVVSKFDELGLTICAAFELEFYLIDQEN-INGRPQPPRSPISGKRPHSTQVYLIDD 182 L + V ELGL AAFELEF+L+ E +GR QP + G+R T+VY +D Sbjct: 127 HALARQVEALAELGLHPSAAFELEFFLLANERGPDGRVQPAADVLDGRRSAKTEVYSVDH 186 Query: 183 LDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKN 242 L + DI GA+ GI A+ ++ E AP Q+E+ LH+ D ++A D + LKR+++ Sbjct: 187 LHGMMPLFSDIYAGAEAAGIKAETMISEYAPGQYELTLHYRTDVLQAADDLMRLKRIVRA 246 Query: 243 IAYDHEMDTTFMAKPYPGQAGNGLHVHISLLDKNGNNIFATENPLE-SAPLRHAIGGLQE 301 A H + FMAKP AG+G+H+H+SL D G NIF E + S P+ HA+GGL+E Sbjct: 247 QARRHGVTACFMAKPVESYAGSGMHLHVSLCDAEGRNIFVEETEGQWSRPILHALGGLRE 306 Query: 302 TMAASMAFLCPNVNSYRRFGAQFYVPNAPCWGMDNRTVALRVPTDSPDAVRVEHRVAGAD 361 TM SM P+ NS+RRF +Q Y P +P WG++NR+VALR+P A R+EHR AG D Sbjct: 307 TMGESMLVFAPHANSWRRFASQSYAPVSPSWGVNNRSVALRIPAGDIRARRIEHRPAGVD 366 Query: 362 ANPYLMLASILAGVHHGLTNKIEPDAPIEGNSYEQV--EQSLPTNLRDALRELDDSEIMA 419 ANPYL+ A++LAG+ GL +I+P GN YE Q +PT R A+ S + Sbjct: 367 ANPYLVAATVLAGIRRGLEQQIDPGPETTGNGYEDPGDTQPIPTCWRSAIAAAQHSAFLR 426 Query: 420 RYISPDYIDIFVACKESELAEFEHSISDLEYNWYLHTV 457 + PD F A K +E A +I D++Y+ YLHTV Sbjct: 427 EALGPDMHRTFTAIKAAEYARVARTIPDVDYDLYLHTV 464 Lambda K H 0.319 0.136 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: 599 Number of extensions: 32 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: 457 Length of database: 464 Length adjustment: 33 Effective length of query: 424 Effective length of database: 431 Effective search space: 182744 Effective search space used: 182744 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 10 2024. 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