Align 4-guanidinobutyramide hydrolase; SubName: Full=Carbon-nitrogen hydrolase (characterized, see rationale)
to candidate PP_0382 PP_0382 5-aminopentanamidase
Query= uniprot:A0A291T0X0 (265 letters) >FitnessBrowser__Putida:PP_0382 Length = 264 Score = 221 bits (564), Expect = 9e-63 Identities = 122/264 (46%), Positives = 161/264 (60%), Gaps = 2/264 (0%) Query: 4 LRTALLQNSGHPGDPAGNLKVLDEAAARAAADGAGLLVTAEMFLTGYAIG-GGVRDLAEP 62 +R AL Q + P D GNL+ L A AA GA LLV EMFL+GY IG V LAE Sbjct: 1 MRIALYQGAPKPLDVPGNLQRLRHQAQLAADRGAQLLVCPEMFLSGYNIGLAQVERLAEA 60 Query: 63 ADGPSGRAVADIAAAHGLAILYGYPER-HAGAVHNSARLVGADGTELANYRKTHLYGCFE 121 ADGP+ V +IA AH +AI+YGYPER GA++NS +L+ A G L+NYRKTHL+G + Sbjct: 61 ADGPAAMTVVEIAQAHRIAIVYGYPERGDDGAIYNSVQLIDAHGRSLSNYRKTHLFGELD 120 Query: 122 RASFTPGETPVVQATVGELTVGILVCYDVEFPENVRAHALAGTDLLLVPTAQMHPFEFVA 181 R+ F+PG + VG+L+CYD+EFPEN R AL G +L+LVPTA M P++F Sbjct: 121 RSMFSPGADHFPVVELEGWKVGLLICYDIEFPENARRLALDGAELILVPTANMTPYDFTC 180 Query: 182 ESLIPVRAFESQMYIAYVNRSGPEGEFDFVGLSCLAGPDGATCLRAGRGEELLLGDVDPK 241 + + RA E+Q Y+ Y N G E E ++ G S + GPDG+ AGR E LL +++ + Sbjct: 181 QVTVRARAQENQCYLVYANYCGAEDEIEYCGQSSIIGPDGSLLAMAGRDECQLLAELEHE 240 Query: 242 LLTTSRRINPYLRDRRPGLYTSLG 265 + RR PYL D R L+ G Sbjct: 241 RVVQGRRAFPYLTDLRQELHLRKG 264 Lambda K H 0.319 0.138 0.414 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: 218 Number of extensions: 10 Number of successful extensions: 4 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: 265 Length of database: 264 Length adjustment: 25 Effective length of query: 240 Effective length of database: 239 Effective search space: 57360 Effective search space used: 57360 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 (21.7 bits) S2: 47 (22.7 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