Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate PfGW456L13_4498 glutamine synthetase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_925 (458 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4498 Length = 460 Score = 392 bits (1008), Expect = e-113 Identities = 200/447 (44%), Positives = 276/447 (61%), Gaps = 3/447 (0%) Query: 12 EANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGSTV 71 EA FL+++P++ +L I D NGV RGK + R L VYE G LP+++ L ING V Sbjct: 13 EALTFLEQNPDIEMFELFILDNNGVPRGKLLHRDELLAVYESGRPLPSTILGLTINGDDV 72 Query: 72 ESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPF-FADPREVLANV 130 E++GL D+GD D YPI +L PW+ PTA + ++MH EG P ADPR +LA V Sbjct: 73 ENSGLVWDVGDIDCRAYPISGSLTRMPWRLIPTAAVQVSMHPTEGMPATIADPRHLLAKV 132 Query: 131 VRKFDEMGLTICAAFELEFYLIDQE-NVNGRPQPPRSPVSGKRPHSTQVYLIDDLDEYVD 189 + G A ELEFYL+DQ+ + NGRPQP R V G RP+ TQVY + +L++ Sbjct: 133 IEGLQADGYYPVMAAELEFYLLDQQRDSNGRPQPARD-VDGGRPYGTQVYGLRELEQIEP 191 Query: 190 CLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDHE 249 L D+ K QGIPA + E AP Q E+ L H D ++A D AV KRL+K +A+ H Sbjct: 192 FLADLYSACKLQGIPARTAISEYAPGQVEITLEHRTDALQAMDEAVRYKRLVKGVAHKHG 251 Query: 250 MDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQMA 309 M FMAKP+ AG G+H+H+S+ DKDG N+FASE + L+ A+ G+L TL + Sbjct: 252 MTACFMAKPFDDLAGTGMHMHVSLADKDGNNLFASEAADGTPLLKQAVAGMLSTLLDSLL 311 Query: 310 FLCPNVNSYRRFGAQFYVPNSPCWGLDNRTVAIRVPTGSADAVRIEHRVAGADANPYLLM 369 CPN NSYRRF A Y P + WG+DNRTV++RVP G A + IEHR+ GADANPYL Sbjct: 312 LFCPNANSYRRFQANSYAPLAATWGVDNRTVSLRVPGGPAYSRHIEHRICGADANPYLAA 371 Query: 370 ASVLAGVHHGLTNKIEPGAPVEGNSYEQNEQSLPNNLRDALRELDDSEVMAKYIDPKYID 429 A++LAG+H G+ +++PGAPVEGN Y Q + LP + LR L+ S + +++ Sbjct: 372 AAILAGIHRGIREQLDPGAPVEGNGYAQATKLLPTDWLTTLRSLEGSSWAREAFGGEFLG 431 Query: 430 IFVACKESELEEFEHSISDLEYNWYLH 456 +++A K +E +F + + ++ WYLH Sbjct: 432 VYLAVKRAEYRQFMGEVGEQDWRWYLH 458 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: 608 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: 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