Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_053936829.1 WG78_RS05700 glutamate--ammonia ligase
Query= reanno::pseudo1_N1B4:Pf1N1B4_2254 (426 letters) >NCBI__GCF_001294205.1:WP_053936829.1 Length = 469 Score = 129 bits (325), Expect = 1e-34 Identities = 111/405 (27%), Positives = 183/405 (45%), Gaps = 35/405 (8%) Query: 51 ADRICYPIPDTLCNEPWQKRPTAQLLMTMHE-LEGDPFFADPREVLRQVVAKFDEMGLTI 109 +D + P T +P+ PT + + E +G + DPR + ++ A GL Sbjct: 64 SDMLLAPDTTTAKLDPFYDEPTVFITCDVIEPSDGKGYDRDPRSIAKRAEAYLKSSGLGD 123 Query: 110 CAAF--ELEFYLID-----------------QENVNGRPQPPRSPISGKRPHSTQVYL-I 149 A F E EF++ D +E + +G RP Y + Sbjct: 124 TAYFGPEPEFFIFDGVTWGADMSGCFVKIKSEEGAWSSAEDYEGGNTGHRPTVKGGYFPV 183 Query: 150 DDLDEYVDCLQDILEGAKEQGIPADAIVKESAPA-QFEVNLHHVADPIKACDYAVLLKRL 208 +D + D ++ +E G+P + E A A Q E+ + ++ D+ +LK + Sbjct: 184 PPVDSHQDIRASMVLVLEELGVPVEVFHHEVATAGQNEIGTKF-SSLVQRADWTQILKYV 242 Query: 209 IKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASED-PEQNAALRHAIGG 267 + N+A+ + TFM KP G G+G+HVH S+ KDGKN+FA + + IGG Sbjct: 243 VHNVAHQYGKTATFMPKPIVGDNGSGMHVHQSVW-KDGKNLFAGNGYAGLSEFALYYIGG 301 Query: 268 VLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSSD-AVRIEHRV 326 +++ A A P NSY+R + P + NR+ +IR+P SD A RIE R Sbjct: 302 IIKHAKALNAITNPGTNSYKRLVPHYEAPVKLAYSARNRSASIRIPHVQSDKARRIEARF 361 Query: 327 AGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYE---QNEQSLPN---NLRDALRE 380 ANPYL +++L G+ NKI PG P + N Y+ + ++ +P +L +AL Sbjct: 362 PDPLANPYLCFSALLMAGLDGVQNKIHPGDPADKNLYDLPPEEDKLIPTVCASLDEALDA 421 Query: 381 LD-DSEVMAK--YIDPKYIDIFVACKESELEEFEHSISDLEYNWY 422 LD D E + + +ID ++ K E+ + +E++ Y Sbjct: 422 LDKDREFLTRGGVFSNDFIDAYIELKMVEVNRTRMTTHPVEFDMY 466 Lambda K H 0.318 0.137 0.411 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: 532 Number of extensions: 30 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: 426 Length of database: 469 Length adjustment: 33 Effective length of query: 393 Effective length of database: 436 Effective search space: 171348 Effective search space used: 171348 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