Align N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) (characterized)
to candidate GFF2084 PS417_10630 hydratase
Query= metacyc::MONOMER-17350 (290 letters) >FitnessBrowser__WCS417:GFF2084 Length = 295 Score = 128 bits (322), Expect = 1e-34 Identities = 92/289 (31%), Positives = 148/289 (51%), Gaps = 25/289 (8%) Query: 2 KIALIQ---QKFHSNKEQTIKKTCEFIEEASKQGAELICLGELHQSEYFCQSENVDFFDY 58 ++A+IQ Q +N+ + ++ EA+ GA LI L EL YF S D FD+ Sbjct: 9 RVAVIQLDPQVGMNNRSSNLHQSLALATEAANGGANLIVLPELTNCGYFFSSRQ-DAFDH 67 Query: 59 ANDYE--KDVKFWANIARKNQIVLITSLFEKRSAGLYHNTAVVFEKDGSIAGKYRKMHIP 116 A + V+ W + A K+Q+ L+T L E L+ NTAV+ DG I GKYRK H+ Sbjct: 68 AELIPGGESVRAWIDFACKHQVYLVTGLCEIDGMQLF-NTAVLLGPDGFI-GKYRKAHLW 125 Query: 117 DDPCFYEKFYFTPGDLGFEPINTSLGKLGVLICWDQWYPEAARIMALKGAEILIYPTAIG 176 + EK +FTPGD GF T +G++G+LICWD W+PE RI++ +GA+I+ Sbjct: 126 N----LEKLWFTPGDTGFPVFETPIGRIGLLICWDIWFPEVPRILSQQGADIICSLNNWV 181 Query: 177 WFDKDKDEEKQRQLNAWLGVQKGHAIANGLYVVAINRVGFEKDVSGVEEGIRFWGNSFVF 236 W +E + + ++L + H N +++ A +R+G E++ R+ G S + Sbjct: 182 WTPPPLFDEAGKCMASYLTMTAAH--VNNVFIAAASRIGEEREA-------RYLGCSLIA 232 Query: 237 GPQGEELCLLDSQN-ECVKIIEIDKKRSENVRRW---WPFLRDRRIEYF 281 G G + + S N + + ++D + + W RDRRI+ + Sbjct: 233 GTNGWPIGAVASANRQEILFADVDITSARSAPIWNSLNDLQRDRRIDLY 281 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: 200 Number of extensions: 13 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: 290 Length of database: 295 Length adjustment: 26 Effective length of query: 264 Effective length of database: 269 Effective search space: 71016 Effective search space used: 71016 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