Align N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) (characterized)
to candidate 350403 BT0875 beta-ureidopropionase (NCBI ptt file)
Query= metacyc::MONOMER-17350 (290 letters) >FitnessBrowser__Btheta:350403 Length = 294 Score = 381 bits (978), Expect = e-110 Identities = 181/291 (62%), Positives = 221/291 (75%), Gaps = 1/291 (0%) Query: 1 MKIALIQQKFHSNKEQTIKKTCEFIEEASKQGAELICLGELHQSEYFCQSENVDFFDYAN 60 +K+ LIQQ ++ + + IE + GA+LI L ELH S YFCQ+EN + FD A Sbjct: 4 IKVGLIQQSNTADIRVNLMNLAKSIEACAAHGAQLIVLQELHNSLYFCQTENTNLFDLAE 63 Query: 61 DYE-KDVKFWANIARKNQIVLITSLFEKRSAGLYHNTAVVFEKDGSIAGKYRKMHIPDDP 119 F++ +A N++VL+ SLFEKR+ GLYHNTAVVF++DGSIAGKYRKMHIPDDP Sbjct: 64 PIPGPSTGFYSELAAANKVVLVASLFEKRAPGLYHNTAVVFDRDGSIAGKYRKMHIPDDP 123 Query: 120 CFYEKFYFTPGDLGFEPINTSLGKLGVLICWDQWYPEAARIMALKGAEILIYPTAIGWFD 179 +YEKFYFTPGD+GFEPI TSLGKLGVL+CWDQWYPEAAR+MALKGAE+LIYPTAIGW Sbjct: 124 AYYEKFYFTPGDIGFEPIQTSLGKLGVLVCWDQWYPEAARLMALKGAELLIYPTAIGWES 183 Query: 180 KDKDEEKQRQLNAWLGVQKGHAIANGLYVVAINRVGFEKDVSGVEEGIRFWGNSFVFGPQ 239 D D+EK RQLNAW+ Q+ HA+ANGL V+++NRVG E D SG GI+FWGNSFV GPQ Sbjct: 184 SDTDDEKARQLNAWIISQRAHAVANGLPVISVNRVGHEPDPSGQTNGIQFWGNSFVAGPQ 243 Query: 240 GEELCLLDSQNECVKIIEIDKKRSENVRRWWPFLRDRRIEYFADLTKRFID 290 GE L + + ++EID +RSENVRRWWPFLRDRRI+ + LTKRF+D Sbjct: 244 GEFLAQASNDHPENMVVEIDMERSENVRRWWPFLRDRRIDEYDGLTKRFLD 294 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: 327 Number of extensions: 15 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: 294 Length adjustment: 26 Effective length of query: 264 Effective length of database: 268 Effective search space: 70752 Effective search space used: 70752 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