Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate GFF963 HP15_942 glutamate-putrescine ligase
Query= reanno::pseudo3_N2E3:AO353_08595 (458 letters) >FitnessBrowser__Marino:GFF963 Length = 454 Score = 622 bits (1605), Expect = 0.0 Identities = 290/449 (64%), Positives = 374/449 (83%), Gaps = 1/449 (0%) Query: 11 NEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGST 70 + A++FL+ HPE+ +VDLLI DMNG+VRGKR++ ++L KV+E+G+ +PAS+FAL+I G+T Sbjct: 6 SSADSFLQAHPELQFVDLLIPDMNGIVRGKRVDPSALAKVFERGVAMPASIFALNIQGTT 65 Query: 71 VESTGLGLDIGDADRICYPIPNTLCNEPWQKRPTAQLLMTMHELEGE-PFFADPREVLAN 129 VE TGLGLDIG+ADR+C PI NTL EPWQKRPTAQLL+TM+EL+ E PFFADPR VL N Sbjct: 66 VEETGLGLDIGEADRVCLPIENTLTMEPWQKRPTAQLLLTMYELDRETPFFADPRVVLQN 125 Query: 130 VVRKFDDMGLTICAAFELEFYLIDQENVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVD 189 ++++F+D+GLT AAFELEFYLIDQEN+ GRPQPP+SP+SGKRP TQ Y IDDLDEY + Sbjct: 126 IIKRFEDLGLTPVAAFELEFYLIDQENLAGRPQPPKSPLSGKRPAGTQAYSIDDLDEYAE 185 Query: 190 CLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHE 249 L D+L+ A EQ +PADA+V ESAP QFEVNLH+V D ++ACD+A LLKRLIKN+AYDHE Sbjct: 186 FLADVLDAAHEQELPADALVAESAPGQFEVNLHYVDDAVQACDHATLLKRLIKNMAYDHE 245 Query: 250 MDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMA 309 MDTTFMAKPY QAG+G+H+H+S++D +G+N+FA + + N LR A+GG++ T+ MA Sbjct: 246 MDTTFMAKPYHNQAGSGMHLHVSLVDGEGRNVFAGDAEQPNDMLRWAVGGLVATMNDAMA 305 Query: 310 FLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLM 369 CPN+NSYRRF ++YVP++ WG+DNRT ++R+P G +A+RIEHRVAGADANPYLLM Sbjct: 306 LFCPNINSYRRFSPEYYVPSAATWGVDNRTASLRLPGGDPEALRIEHRVAGADANPYLLM 365 Query: 370 ASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYID 429 A+VLAG+H+G++N+IEP GN++EQ+E SL NNLRDALREL S+VMA Y+ +++D Sbjct: 366 AAVLAGIHYGISNRIEPPPVTVGNAHEQHEASLVNNLRDALRELGQSKVMADYLGSQFLD 425 Query: 430 IFVACKESELEEFEHSISDLEYNWYLHTV 458 +FVACKE EL EFE +ISDLEY WYLHTV Sbjct: 426 VFVACKEHELNEFEMTISDLEYLWYLHTV 454 Lambda K H 0.318 0.137 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: 745 Number of extensions: 30 Number of successful extensions: 2 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: 454 Length adjustment: 33 Effective length of query: 425 Effective length of database: 421 Effective search space: 178925 Effective search space used: 178925 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