Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate Pf1N1B4_4356 Gamma-glutamyl-putrescine oxidase (EC1.4.3.-)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__pseudo1_N1B4:Pf1N1B4_4356 Length = 432 Score = 139 bits (349), Expect = 2e-37 Identities = 116/379 (30%), Positives = 176/379 (46%), Gaps = 13/379 (3%) Query: 34 DVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVG-LVNAGTWIRPDDV-EA 91 DVCVIG G TGLS+A+ L E G SV VLEA K+G G SGRN G LVN ++ R DV E Sbjct: 35 DVCVIGAGYTGLSSALFLSEAGYSVTVLEAAKVGFGASGRNGGQLVN--SYSRDVDVIEE 92 Query: 92 TLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATGIADLEARHEQWR 151 G K L ++ E + + I+ I C G + A N + L + W Sbjct: 93 RYGDKTAEVLGSMIFEGADIIRSRIKEYDIQCD-YRPGGIFAALNKKQLNGLAEQKSSWE 151 Query: 152 RRG-ADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAAAVTRLGGKIFQQS 210 R G ++ +L A + G D LLD + G I+P+ G AAA+ RLGGKI++QS Sbjct: 152 RYGNKNLRMLDAADIKREVGCDNYVGGLLDMQGGHIHPLNLALGEAAAIIRLGGKIYEQS 211 Query: 211 SVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSN-LQKQFFRGYYYQVASKPLQ 269 + + G+ V+TA+G VRA+ ++I+ AY D N + ++ V ++PL Sbjct: 212 AAVEI-TYGEPITVRTAKGVVRAKYLLIAGNAYLPQDLDNRVTRKSMPCGSQIVVTEPLS 270 Query: 270 GIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFVRSWADRIQSHYY 329 A ++ + D +L R RLL G + + + Sbjct: 271 EKVARSLIANNYCVEDCNYLLDYYRLTADNRLLYGGGVVYGAREPDDIEQLIRPKILKTF 330 Query: 330 PELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGTVIGRAFAEFLLK 389 P+L V+ + WTG T + + + GY+G G T + G+ +E +++ Sbjct: 331 PQLKDVKIDYRWTGNFLLTMSRMPQFGRIEKNAYYMQGYSGHGVTCSHLAGKLISE-MIR 389 Query: 390 GEADSL----PIPFSPMSG 404 G+A+ +P PM G Sbjct: 390 GDAERFDAFASLPHMPMLG 408 Lambda K H 0.319 0.135 0.419 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: 424 Number of extensions: 21 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: 432 Length of database: 432 Length adjustment: 32 Effective length of query: 400 Effective length of database: 400 Effective search space: 160000 Effective search space used: 160000 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: 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