Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate Dsui_1048 Dsui_1048 glutamine synthetase, type I
Query= reanno::pseudo1_N1B4:Pf1N1B4_2254 (426 letters) >FitnessBrowser__PS:Dsui_1048 Length = 470 Score = 122 bits (306), Expect = 2e-32 Identities = 118/440 (26%), Positives = 193/440 (43%), Gaps = 39/440 (8%) Query: 20 EKGINLPASLFALDI--NGSTVESTGLG--LDIGDADRICYPIPDTLCNEPWQKRPTAQL 75 E+ + +P S F D +G + + + I +D + P P+T +P+ T L Sbjct: 30 EQHVGVPVSAFDEDKFESGHAFDGSSIAGWKGIQASDMLLMPDPNTAYIDPFFDETTLIL 89 Query: 76 LMTMHE-LEGDPFFADPREVLRQVVAKFDEMGLTICAAF--ELEFYLID----------- 121 + E +G + DPR + ++ A G+ A F E EF++ D Sbjct: 90 TCDVVEPADGKGYDRDPRSIAKRAEAYLKSSGIGDTAFFGPEPEFFIFDSVEWKTDMSGT 149 Query: 122 ------QENVNGRPQPPRSPISGKRPHSTQVYL-IDDLDEYVDCLQDILEGAKEQGIPAD 174 +E + +G RP Y + +D + D + + G+P + Sbjct: 150 YVKIFSEEAAWSTAEKFDGGNAGHRPMVKGGYFPVPPVDSFNDMRAQMCLLLEACGVPVE 209 Query: 175 AIVKESAPA-QFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGN 233 E A A Q E+ ++ D +LK ++ N+A+ + TFM KP G G+ Sbjct: 210 VHHHEVATAGQNEIGTVFNT-LVRRADQTQILKYIVHNVAHQYGKTATFMPKPIVGDNGS 268 Query: 234 GLHVHISILDKDGKNIFASED-PEQNAALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQ 292 G+HVH SI KDG+N+FA + + IGG+++ A A P NSY+R Sbjct: 269 GMHVHQSIW-KDGQNLFAGNGYAGLSETALYYIGGIIKHAKALNAITNPGTNSYKRLVPH 327 Query: 293 FYVPNSPCWGLDNRTVAIRVP-TGSSDAVRIEHRVAGADANPYLLMASVLAGVHHGLTNK 351 + P + NR+ +IRVP S+ A RIE R ANPYL A++L G+ NK Sbjct: 328 YEAPVKLAYSAKNRSASIRVPFVQSTKARRIETRFPDPIANPYLCFAALLMAGLDGIQNK 387 Query: 352 IEPGAPVEGNSYE---QNEQSLPN---NLRDALRELD-DSEVMAK--YIDPKYIDIFVAC 402 I PG + N Y+ + + +P +L +AL LD D E + + +ID F+ Sbjct: 388 IHPGDAADKNLYDLPPEEDAKIPTVCASLDEALANLDKDREFLTRGGVFSNDWIDSFIDL 447 Query: 403 KESELEEFEHSISDLEYNWY 422 K E+ + + +E++ Y Sbjct: 448 KMEEVNKLRMTTHPVEFDLY 467 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: 509 Number of extensions: 25 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: 470 Length adjustment: 33 Effective length of query: 393 Effective length of database: 437 Effective search space: 171741 Effective search space used: 171741 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 17 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