Align gamma-glutamylputrescine oxidase (EC 1.4.3.-) (characterized)
to candidate PP_4548 PP_4548 putative Oxidoreductase
Query= reanno::pseudo5_N2C3_1:AO356_21495 (427 letters) >FitnessBrowser__Putida:PP_4548 Length = 435 Score = 332 bits (850), Expect = 2e-95 Identities = 171/421 (40%), Positives = 254/421 (60%), Gaps = 5/421 (1%) Query: 9 SYYAASANPVPPRPALQDDVETDVCVIGAGYTGLSSALFLLENGFKVTVLEAAKVGFGAS 68 SYY+A+ N P L+ V+ DV +IG G+TG+++A+ L E G KV ++E ++G+GAS Sbjct: 15 SYYSATLNDHTAYPQLKGTVQVDVAIIGGGFTGVATAVELAERGLKVAIVETNRIGWGAS 74 Query: 69 GRNGGQIVNSYSRDIDV---IERSVGPQQAQLLGNMAFEGGRIIRERVAKYQIQCDLKDG 125 GRNGGQ+ S S D + + +G + + ++ + G ++I +RVA+Y I CDLK G Sbjct: 75 GRNGGQVTGSLSGDEAMRSQMRNHLGAEVDDFIWHLRWRGHQVIEQRVARYGIDCDLKRG 134 Query: 126 GVFAALTAKQMGHLESQKRLWERFGH-TQLELLDQRRIREVVACEEYVGGMLDMSGGHIH 184 + AA+ M L + + R G Q++LLD+ + E + Y+G + ++ H+H Sbjct: 135 HLHAAMKPSHMNELRAFEAEARRRGMGDQVQLLDRAAVAEHLQSPLYLGALKNLRNLHLH 194 Query: 185 PLNLALGEAAAVESLGGVIYEQSPAVRIERGASPVVHTPQGKVRAKFIIVAGNAYLGNLV 244 PLNL LGEA A LG +I+E S + I G P V T G+V A+ +++AG+ Y Sbjct: 195 PLNLCLGEARAAHGLGALIFENSEVLDIVHGPRPAVVTAHGRVEARQVMLAGDVYHKLEK 254 Query: 245 PELAAKSMPCGTQVIATEPLGDELAHSLLPQDYCVEDCNYLLDYYRLTGDKRLIFGGGVV 304 +L K P ++ T PLG ELA + PQD V DC ++LDYYRLT DKRL+FGGG Sbjct: 255 RQLKGKIFPAMGGIVTTAPLG-ELAEQINPQDLAVYDCRFVLDYYRLTADKRLLFGGGAN 313 Query: 305 YGARDPANIEAIIRPKMLKAFPQLKDVKIDYAWTGNFLLTLSRLPQVGRLGDNIYYSQGC 364 Y +D +IE +RP + + FP LK V I++ W+ + ++R+PQ+G+L DN++Y QG Sbjct: 314 YSGKDSRDIEGELRPCIERTFPALKGVPIEFQWSCAMGIVVNRIPQLGKLSDNVWYCQGY 373 Query: 365 SGHGVTYTHLAGKVLAEALRGQAERFDAFADLPHYPFPGGQLLRTPFAAMGAWYYGLRDK 424 SGHG+ +H+ G+++AEAL G E+FD FA H P G LL P A G WYY + +K Sbjct: 374 SGHGIATSHIMGEIMAEALTGTLEKFDTFAQCRHVRVPMGDLLGNPLLAAGMWYYQMLEK 433 Query: 425 L 425 L Sbjct: 434 L 434 Lambda K H 0.320 0.139 0.421 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: 581 Number of extensions: 25 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: 427 Length of database: 435 Length adjustment: 32 Effective length of query: 395 Effective length of database: 403 Effective search space: 159185 Effective search space used: 159185 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 (21.8 bits) S2: 51 (24.3 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