Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate 6937000 Sama_1174 glutamate--ammonia ligase (RefSeq)
Query= reanno::pseudo5_N2C3_1:AO356_13135 (458 letters) >FitnessBrowser__SB2B:6937000 Length = 455 Score = 369 bits (947), Expect = e-106 Identities = 191/446 (42%), Positives = 265/446 (59%), Gaps = 3/446 (0%) Query: 12 EANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTV 71 EA FL +HP+V +V++ I D NG+ RGK + R + +Y G LP+++ L + G V Sbjct: 8 EAIDFLDKHPQVQHVEVFIIDPNGIPRGKLLHRQEVLSMYRHGRPLPSTILGLTVQGDDV 67 Query: 72 ESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPF-FADPREVLRQV 130 E TGL ++GDAD + +PI L +PW+ +PTAQ+ +TMH G P ADPR VL +V Sbjct: 68 EDTGLVWEVGDADCLAFPIEGGLLMQPWRAQPTAQVHLTMHPEAGMPAAVADPRLVLSKV 127 Query: 131 VTKFDELGLTICAAFELEFYLIDQE-NVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYVD 189 + G A ELEF+L+DQ + NGRPQP G RPH TQVY I +L+ Sbjct: 128 IDSLQADGFYPVMAAELEFFLLDQRFDANGRPQPAMQS-DGHRPHQTQVYGILELERLQP 186 Query: 190 CLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHE 249 L D+ + QGIPA + E AP Q E+ L H D ++A D AV KRL+K +A H Sbjct: 187 FLDDLYHACEVQGIPARTAISEYAPGQVEITLEHRFDALQAMDEAVRYKRLVKGVAAKHG 246 Query: 250 MDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMA 309 M FMAKP+ AG+G+H+H+S+ D DG N FAS++PE L +I G++ TL Sbjct: 247 MQACFMAKPFGELAGSGMHMHVSLADADGNNRFASDNPEGTPELTQSIAGMMATLEDAQL 306 Query: 310 FLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYLLM 369 CPN NS+RRF + Y P + TWG++NRTV+ RVP G A + +EHR+ GADANPYL Sbjct: 307 LFCPNANSFRRFQSASYAPIAKTWGVNNRTVSFRVPGGPAPSRHVEHRICGADANPYLAA 366 Query: 370 AAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYID 429 AA+LA HHG+ N++ PG + GN YE Q+LP + AL + SE M + + Sbjct: 367 AAILAACHHGIRNQLSPGQAIVGNGYEGKHQTLPTDWLSALTNFERSEWMKSVLGEDFHR 426 Query: 430 IFVACKESELEEFEHSISDLEYNWYL 455 I+ K +E +EF + +++WYL Sbjct: 427 IYGRIKRAEYQEFMAEVGQQDWHWYL 452 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: 634 Number of extensions: 33 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: 458 Length of database: 455 Length adjustment: 33 Effective length of query: 425 Effective length of database: 422 Effective search space: 179350 Effective search space used: 179350 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