Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 3608443 Dshi_1839 glutamine synthetase, type I (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_2254 (426 letters) >FitnessBrowser__Dino:3608443 Length = 468 Score = 121 bits (304), Expect = 4e-32 Identities = 118/414 (28%), Positives = 180/414 (43%), Gaps = 48/414 (11%) Query: 48 IGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELE-GDPFFADPREVLRQVVAKFDEMG 106 I +D P ++ +P+ T L ++ E + G+ + DPR + A G Sbjct: 61 IDQSDMKLMPDTNSAYVDPFYAEKTLCLHCSIVEPDTGEAYDRDPRGTAEKAEAYLKSSG 120 Query: 107 LTICAAF--ELEFYLIDQENVNGRPQPPRSPIS-----------------GKRPHSTQVY 147 + A F E EF+L D + + G RP Y Sbjct: 121 IGDVAYFGPEAEFFLFDDVRFSVEMNKVSFEVDAQDAAWNSDAEYEMGNMGHRPGIKGGY 180 Query: 148 L-IDDLDEYVDCLQDILEGAKEQGIPADAIVKESAPAQFEV-----NLHHVADPIKACDY 201 ++ +D D ++L K G+ D E A Q E+ +L H AD ++ Y Sbjct: 181 FPVNPIDAAQDLRSEMLSTMKRMGMKVDKHHHEVASCQHELGLIFGSLTHQADELQKYKY 240 Query: 202 AVLLKRLIKNIAYDHEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASE---DPEQN 258 +I N+A+ + TFM KP G G G+HV++SI KDGK +FA + D Q Sbjct: 241 ------VIHNVAHAYGKSATFMPKPIAGDNGTGMHVNMSIW-KDGKPLFAGDKYADLSQE 293 Query: 259 AALRHAIGGVLETLPAQMAFLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSSD 318 A + IGG+L+ A AF P+ NSY+R F P + NR+ +R+P S Sbjct: 294 AL--YFIGGILKHAKALNAFTNPSTNSYKRLIPGFEAPVLRAYSARNRSGCVRIPWAESP 351 Query: 319 -AVRIEHRVAGADANPYLLMASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPN----- 372 A R+E R ANPYL A++L G+ NKI+PG + + Y+ + L Sbjct: 352 KAKRVEARFPDPAANPYLCFAALLMAGLDGIKNKIDPGEASDKDLYDLPPEELAEIPTVC 411 Query: 373 -NLRDAL--RELDDSEVMAKYIDPK-YIDIFVACKESELEEFEHSISDLEYNWY 422 +LR+AL E D ++A + K ID + K E+ +EH+ +EY Y Sbjct: 412 ASLREALDALEADHEFLLAGDVFTKDQIDGYCELKWEEVYAYEHTPHPVEYKLY 465 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: 546 Number of extensions: 28 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: 426 Length of database: 468 Length adjustment: 33 Effective length of query: 393 Effective length of database: 435 Effective search space: 170955 Effective search space used: 170955 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