Align N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) (characterized)
to candidate GFF2120 HP15_2074 carbon-nitrogen hydrolase family protein
Query= metacyc::MONOMER-17350 (290 letters) >FitnessBrowser__Marino:GFF2120 Length = 307 Score = 344 bits (882), Expect = 2e-99 Identities = 171/298 (57%), Positives = 215/298 (72%), Gaps = 8/298 (2%) Query: 1 MKIALIQQKFHSNKEQTIKKTCEFIEEASKQGAELICLGELHQSEYFCQSENVDFFDYAN 60 + +A+IQQ S+K ++ T + + EA GA L+ L ELH + YFCQ+E F+ A Sbjct: 10 INVAVIQQACSSDKAASLATTEKLVREAVASGANLVILQELHATLYFCQTEETSVFELAE 69 Query: 61 DYEKDV-KFWANIARKNQIVLITSLFEKRSAGLYHNTAVVFEKDGSIAGKYRKMHIPDDP 119 K +++AR+ IVL+ S+FE+R G+YHNTAVVFEKDGS+AG YRKMHIPDDP Sbjct: 70 PIPGPTSKRLSDLARELGIVLVGSIFERRMNGVYHNTAVVFEKDGSLAGLYRKMHIPDDP 129 Query: 120 CFYEKFYFTPGDL-------GFEPINTSLGKLGVLICWDQWYPEAARIMALKGAEILIYP 172 FYEKFYFTPGD GF PI+TS+G+LGVL+CWDQWYPEAAR+MAL GAEILIYP Sbjct: 130 GFYEKFYFTPGDAQFNDGRSGFTPIDTSVGRLGVLVCWDQWYPEAARLMALAGAEILIYP 189 Query: 173 TAIGWFDKDKDEEKQRQLNAWLGVQKGHAIANGLYVVAINRVGFEKDVSGVEEGIRFWGN 232 TAIGW D +E+ RQL+AW+ VQ+GHA+AN L VVA NRVG E D SG +GIRFWGN Sbjct: 190 TAIGWDVTDDPDEQARQLDAWVTVQRGHAVANNLPVVAPNRVGTEPDPSGHSDGIRFWGN 249 Query: 233 SFVFGPQGEELCLLDSQNECVKIIEIDKKRSENVRRWWPFLRDRRIEYFADLTKRFID 290 SF+ GPQGE L D +EC+ + +D+ RSE+VRR WP+LRDRRI+ + D+ KR D Sbjct: 250 SFICGPQGELLARGDDSSECILAVTLDRSRSESVRRIWPYLRDRRIDAYGDILKRVRD 307 Lambda K H 0.322 0.140 0.438 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: 297 Number of extensions: 14 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: 290 Length of database: 307 Length adjustment: 27 Effective length of query: 263 Effective length of database: 280 Effective search space: 73640 Effective search space used: 73640 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 48 (23.1 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