Align Gamma-glutamyl-putrescine synthetase (EC 6.3.1.11) (characterized)
to candidate CCNA_03240 CCNA_03240 glutamine synthetase
Query= reanno::pseudo5_N2C3_1:AO356_13135 (458 letters) >FitnessBrowser__Caulo:CCNA_03240 Length = 460 Score = 384 bits (985), Expect = e-111 Identities = 198/450 (44%), Positives = 278/450 (61%), Gaps = 4/450 (0%) Query: 10 LNEANAFLKEHPEVLYVDLLIADMNGVVRGKRIERTSLHKVYEKGINLPASLFALDINGS 69 + E FL HP+V +V++ M GV RGKR+ L +YE G LP S+ +D NG+ Sbjct: 8 IQECRDFLAAHPQVKFVEVFFTSMTGVPRGKRLRVHELEAIYEYGRFLPGSVLVVDTNGA 67 Query: 70 TVESTGLGLDIGDADRICYPIPDTLCNEPWQKRPTAQLLMTMHELEGEPFFADPREVLRQ 129 E TGL + GDADR P+P TL PW AQ++++++EL+G P DPR VL++ Sbjct: 68 DCEDTGLVWEDGDADRRARPVPGTLTLAPWLGPDVAQVMLSLYELDGTPNDLDPRHVLQR 127 Query: 130 VVTKFDELGLTICAAFELEFYLID-QENVNGRPQPPRSPISGKRPHSTQVYLIDDLDEYV 188 V+ ++ GLT AA ELE+YL+D Q NG P +S +G RP QVY + +L+ + Sbjct: 128 VLDRYAADGLTPVAACELEYYLVDLQRGPNGELLPAKSLQTGLRPTGIQVYGLPELEAHA 187 Query: 189 DCLQDILEGAKEQGIPADAIVKESAPAQFEVNLHHVADPIKACDYAVLLKRLIKNIAYDH 248 L+++ + A G+P + + E APAQ E+ L H D ++A D AVL KR K +A H Sbjct: 188 PFLRELWDVADTLGVPLEGAISEFAPAQVELTLKHKPDALRAADDAVLYKRAAKGVALRH 247 Query: 249 EMDTTFMAKPYPGQAGNGLHVHISILDKDGKNIFASEDPEQNAALRHAIGGVLETLPAQM 308 M+ TFMAKP+ +AGNG HVH+S+ D G N+ ASED E + L+HAIGG+ L M Sbjct: 248 GMEATFMAKPWSDRAGNGFHVHLSVNDAAGNNLCASEDIEGSDLLKHAIGGMKVLLGEGM 307 Query: 309 AFLCPNVNSYRRFGAQFYVPNSPTWGLDNRTVALRVPTGSADAVRLEHRVAGADANPYLL 368 A L PN NSYRRF A Y P +PTWG++NRTV+LRVP G +EHRVAGAD NPYL+ Sbjct: 308 AILAPNANSYRRFKANSYAPVAPTWGVNNRTVSLRVPAGPPKTRHVEHRVAGADGNPYLV 367 Query: 369 MAAVLAGVHHGLVNKIEPGAPVEGNSY---EQNEQSLPNNLRDALRELDDSEVMAKYIDP 425 +A +LA HHG+ NKI+PG V G+ Y + LPNN A+ + S V+ Y+ Sbjct: 368 LAVLLASAHHGITNKIDPGPAVIGDGYAAAAKENIRLPNNWFAAVDLFEQSSVLRDYLGD 427 Query: 426 KYIDIFVACKESELEEFEHSISDLEYNWYL 455 +++D+FV+ K +E F +++L+++WYL Sbjct: 428 RFVDMFVSVKRTEQARFFEVVTELDFDWYL 457 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: 629 Number of extensions: 30 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