Align N-carbamoylputrescine amidohydrolase (EC 3.5.1.53) (characterized)
to candidate WP_007475045.1 CMTB2_RS06920 apolipoprotein acyltransferase
Query= metacyc::MONOMER-17350 (290 letters) >NCBI__GCF_000170735.1:WP_007475045.1 Length = 299 Score = 349 bits (896), Expect = e-101 Identities = 171/300 (57%), Positives = 219/300 (73%), Gaps = 18/300 (6%) Query: 1 MKIALIQQKFHSNKEQTIKKTCEFIEEASKQGAELICLGELHQSEYFCQSENVDFFDYAN 60 MK++LIQQ++ +KE+TI T + I +K EL+ L ELHQ+EYFC+ EN +FDYA Sbjct: 1 MKVSLIQQEYKGSKEKTISHTIKMI---NKSNGELVILQELHQNEYFCKCENTKYFDYAE 57 Query: 61 DYEKDVKFWANIARKNQIVLITSLFEKRSAGLYHNTAVVFEKDGSIAGKYRKMHIPDDPC 120 + +DV+FW ++ IVL+TSLFEK G+Y+NTAVVF+K G IAGKYRK HIPDDP Sbjct: 58 SFNEDVEFWRRVSEDKNIVLVTSLFEKVMDGIYYNTAVVFDK-GKIAGKYRKTHIPDDPG 116 Query: 121 FYEKFYFTPGDLGFEPINTSLGKLGVLICWDQWYPEAARIMALKGAEILIYPTAIGWFDK 180 FYEKFYF PGD EPI+TS+G+LGVL+CWDQWYPE ARIMALKGAEILIYPTAIGW Sbjct: 117 FYEKFYFIPGD-EIEPIDTSIGRLGVLVCWDQWYPEPARIMALKGAEILIYPTAIGWLMC 175 Query: 181 DKD------------EEKQRQLNAWLGVQKGHAIANGLYVVAINRVGFEKDVSGVEEGIR 228 +D EEK++ LNAW+ VQ+GHA+ANG+YV+A+NRVG EKD SGV GI Sbjct: 176 PEDRVDELCEKENTIEEKEKMLNAWMSVQRGHAVANGVYVIAVNRVGKEKDESGVLGGIE 235 Query: 229 FWGNSFVFGPQGEELCLLDSQNECVKIIEIDKKRSENVRRWWPFLRDRRIEYFADLTKRF 288 FWG SF++GPQGE + + + E ++ +ID ++ VR+ WPF RDRRIE + + KR+ Sbjct: 236 FWGRSFIYGPQGEVIKVASDKEEIIE-ADIDLGSAKEVRKIWPFFRDRRIELYDCIKKRY 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: 384 Number of extensions: 18 Number of successful extensions: 6 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: 299 Length adjustment: 26 Effective length of query: 264 Effective length of database: 273 Effective search space: 72072 Effective search space used: 72072 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 24 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