Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate GFF1136 PGA1_c11510 gamma-glutamylputrescine oxidoreductase PuuB
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__Phaeo:GFF1136 Length = 436 Score = 164 bits (416), Expect = 4e-45 Identities = 118/392 (30%), Positives = 190/392 (48%), Gaps = 10/392 (2%) Query: 20 PTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIGHGGSGRNVGLVN 79 P L GE +ADVC++GGG TGLSAA+HL E G+SVI+LEA ++G G SGRN G + Sbjct: 26 PLAPFAPLQGEARADVCIVGGGYTGLSAALHLAEAGRSVILLEANRVGFGASGRNGGQLG 85 Query: 80 AGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQHKGTLHMAHNATG 139 +G + D +E+ +G+ ++L + +A V ++I R IDC + G H + + Sbjct: 86 SGQRMEQDGLESLMGEPDAAKLWHLAEDAKDLVKSLIARHDIDCHLK-PGIAHACFSKSD 144 Query: 140 IADLE--ARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTINPMGYTQGLAA 197 ++ H Q R D+ L A Q C + LD AG ++P+ Y GLA Sbjct: 145 VSHEHRYVEHLQTRYGYGDITALDKAALQAICPSPAYVGGSLDMGAGHLHPLAYALGLAR 204 Query: 198 AVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGDWSNLQKQFFR 257 A G +I + S V +E +G R++TA G V A+ ++++ Y G + + Sbjct: 205 AAAAAGVQICEGSEVLDIE-DGAQIRLRTAEGQVTADHLILACNGYLGGLNRQVAARVMP 263 Query: 258 GYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLGRVDNKPAWFV 317 + A++PL G A +VL D++ V++ R GRLL G + + Sbjct: 264 INNFIAATEPL-GADAAQVLARDVAVADSKFVVNYFRLSHDGRLLFGGGESYGYRFPSDI 322 Query: 318 RSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTGYNGRGNTTGT 377 + + + +P L V+ + W G + T + L P +++ +GY+G G T T Sbjct: 323 AATVRKPMTEIFPHLRDVKIDYAWGGTLAITLKRMPYLARLGPNILSASGYSGHGVGTAT 382 Query: 378 VIGRAFAEFLLKGEADSLPIPFSPMSGVSAPS 409 G+ A + G+ D F M+ V AP+ Sbjct: 383 HAGQLMA-LAVAGDGDG----FDTMARVPAPA 409 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: 452 Number of extensions: 23 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: 432 Length of database: 436 Length adjustment: 32 Effective length of query: 400 Effective length of database: 404 Effective search space: 161600 Effective search space used: 161600 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