Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate AO356_04435 AO356_04435 glutamine synthetase
Query= reanno::pseudo5_N2C3_1:AO356_13135 (458 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_04435 Length = 460 Score = 394 bits (1011), Expect = e-114 Identities = 202/449 (44%), Positives = 278/449 (61%), Gaps = 3/449 (0%) Query: 10 LNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGS 69 + +A AFL ++P++ +L I D NGV RGK + R L VYE G LP+++ L ING Sbjct: 11 VQDALAFLAQNPDIELFELFILDNNGVPRGKLLHRDELLAVYESGRPLPSTILGLTINGD 70 Query: 70 TVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPF-FADPREVLR 128 VE++GL D+GD D YPI +L PW+ PTA + ++MH EG P ADPR +L Sbjct: 71 DVENSGLVWDVGDIDCRAYPISGSLQRMPWRLIPTAAVQVSMHPQEGGPATIADPRYLLS 130 Query: 129 QVVTKFDELGLTICAAFELEFYLIDQENVN-GRPQPPRSPISGKRPHSTQVYLIDDLDEY 187 QV+ G A ELEFYL+D N GRPQP R G RPH+TQVY + +L++ Sbjct: 131 QVIEALQADGYYPVMAAELEFYLLDAHRDNQGRPQPARDT-DGGRPHATQVYGLRELEQI 189 Query: 188 VDCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYD 247 L D+ K QGIPA + E AP Q E+ L H +D ++A D AV KRL+K +A+ Sbjct: 190 EPFLADLYAACKLQGIPARTAISEYAPGQVEITLEHRSDALQAMDEAVRYKRLVKGVAHK 249 Query: 248 HEMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQ 307 H M FMAKP+ AG+G+H+H+S+ D+DG N+FASE + LRHA+GG+L+TL Sbjct: 250 HGMQACFMAKPFDHLAGSGMHMHVSLADRDGHNLFASEAGDGTPLLRHAVGGMLDTLLDS 309 Query: 308 MAFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYL 367 + CPN NSYRRF + Y P + TWG+DNRTV+LRVP G A + +EHR+ GADANPYL Sbjct: 310 LLMFCPNANSYRRFQSNSYAPLAATWGVDNRTVSLRVPGGPAFSRHIEHRICGADANPYL 369 Query: 368 LMAAVLAGVHHGLVNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKY 427 AA+L G+HHG+ + +PG PVEGN Y Q + LP + LR L+ S + + Sbjct: 370 AAAAILGGIHHGIREQCDPGKPVEGNGYAQVIEPLPTDWLTTLRALEASAWARQAFGEAF 429 Query: 428 IDIFVACKESELEEFEHSISDLEYNWYLH 456 +D+++A K +E +F + + ++ WYLH Sbjct: 430 LDVYLAVKRAEYRQFMGEVGEQDWRWYLH 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: 624 Number of extensions: 25 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: 460 Length adjustment: 33 Effective length of query: 425 Effective length of database: 427 Effective search space: 181475 Effective search space used: 181475 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