Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate WP_086509872.1 BZY95_RS10470 glutamine synthetase
Query= reanno::pseudo5_N2C3_1:AO356_13135 (458 letters) >NCBI__GCF_002151265.1:WP_086509872.1 Length = 458 Score = 481 bits (1238), Expect = e-140 Identities = 242/452 (53%), Positives = 320/452 (70%), Gaps = 4/452 (0%) Query: 11 NEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGST 70 ++A FL HP++ +DLLI+D+NGV+RGKRI R +L KVY +GINLPAS+FALDING T Sbjct: 7 DQAREFLDRHPDIDSIDLLISDLNGVMRGKRIPRENLDKVYHQGINLPASVFALDINGHT 66 Query: 71 VESTGLGLDIGDADRICYPIPDTLCNEPWQKRPT-AQLLMTMHELEGEPFFADPREVLRQ 129 +E+TGLGL IGD+DR+C P+ TL PW + AQLLMTM E + PFFADPR+VL + Sbjct: 67 IEATGLGLAIGDSDRVCRPVTGTLMPTPWLRGGRQAQLLMTMVERDESPFFADPRQVLSR 126 Query: 130 VVTKFDELGLTICAAFELEFYLIDQENV-NGRPQPPRSPISGKRPHSTQVYLIDDLDEYV 188 + + E GL AA E+EFYL+D+E GR QPPRSP SG+R +Q+Y I +LDEY Sbjct: 127 QLERLSERGLVPVAAVEMEFYLLDRERTAEGRIQPPRSPRSGERATQSQLYSIGELDEYA 186 Query: 189 DCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDH 248 D L D+ A+ QG+P D +KE AP QFE+ L H D +KACD AVLLKRLIK +A +H Sbjct: 187 DFLDDVRRAAECQGLPLDTTLKECAPGQFEITLGHCDDALKACDSAVLLKRLIKGVALNH 246 Query: 249 EMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASE--DPEQNAALRHAIGGVLETLPA 306 + TFMAKPY +AGNG HVH+S+LD G+N+FA+E DP + L A+ G+LE +PA Sbjct: 247 GFEATFMAKPYGLEAGNGTHVHLSLLDDTGRNVFAAENGDPLGSETLHRAVAGLLELMPA 306 Query: 307 QMAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPY 366 MA PN+NS+RRF YVP +PTWG DNR+VALR+P+G DA R+EHRVAGAD NPY Sbjct: 307 CMAICAPNLNSFRRFQPGLYVPMTPTWGFDNRSVALRIPSGCNDARRIEHRVAGADVNPY 366 Query: 367 LLMAAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPK 426 LL+A +LAG+ +G+ ++ P APVEGN+YEQ E +L N+ + AL L+ SE + + Sbjct: 367 LLLAVLLAGIDYGIDRQLTPPAPVEGNAYEQFEPTLTNSWQQALDLLEASEPLKAALGAD 426 Query: 427 YIDIFVACKESELEEFEHSISDLEYNWYLHTV 458 ++ +F+A + +E E+ ++S LEY WYL V Sbjct: 427 FVHVFLANRRAEREQAMQAVSQLEYAWYLRHV 458 Lambda K H 0.318 0.137 0.408 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: 660 Number of extensions: 24 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: 458 Length of database: 458 Length adjustment: 33 Effective length of query: 425 Effective length of database: 425 Effective search space: 180625 Effective search space used: 180625 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