Align pipecolate oxidase (EC 1.5.3.7) (characterized)
to candidate Pf6N2E2_3581 L-pipecolate oxidase (1.5.3.7)
Query= metacyc::G1G01-5614-MONOMER (432 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_3581 Length = 427 Score = 588 bits (1517), Expect = e-173 Identities = 281/425 (66%), Positives = 335/425 (78%) Query: 8 LRQQCLWEHVSKPTVAAQALAGEHKADVCVIGGGITGLSAAIHLLEQGKSVIVLEAWKIG 67 LR++CLWE ++ L GE ADVCVIG G TGLSAA+HLLEQGK V+VLEA + G Sbjct: 3 LREECLWEKLTPQRPENSGLTGEVTADVCVIGAGFTGLSAAVHLLEQGKRVVVLEAHRAG 62 Query: 68 HGGSGRNVGLVNAGTWIRPDDVEATLGQKQGSRLNKVLGEAPAEVFAMIERLGIDCQAQH 127 HGGSGRNVGLVNAG WI PDD+EA G+ GS+LN++LG APA VF++I++ IDCQ + Sbjct: 63 HGGSGRNVGLVNAGLWIPPDDIEAGFGEAVGSQLNRMLGAAPALVFSLIDKYNIDCQLRR 122 Query: 128 KGTLHMAHNATGIADLEARHEQWRRRGADVELLTGAQCQEYCGTDKISAALLDRRAGTIN 187 +GTLHMAHNA G ADL +R EQW+RRGA VELLTG C + GT KI+AALLDRRAGT+N Sbjct: 123 EGTLHMAHNARGEADLRSREEQWKRRGAPVELLTGQACVDATGTSKIAAALLDRRAGTLN 182 Query: 188 PMGYTQGLAAAVTRLGGKIFQQSSVEGLEREGDGWRVKTARGAVRAEKVVISTGAYTEGD 247 PM YT GLA A T LGG++F S V LER+G W V+TA+GAV AE+VVI++ AYTEGD Sbjct: 183 PMAYTSGLAKAATDLGGQLFDHSPVTHLERQGQRWSVQTAQGAVLAEQVVIASNAYTEGD 242 Query: 248 WSNLQKQFFRGYYYQVASKPLQGIAADKVLPHGQGSWDTRTVLSSIRRDDQGRLLLGSLG 307 W+ L++ FF GYYYQVAS PL AA ++LP GQGSWDTR VLSSIRRD GRLLLGSLG Sbjct: 243 WTELRRNFFPGYYYQVASVPLTDEAARRILPGGQGSWDTRQVLSSIRRDKDGRLLLGSLG 302 Query: 308 RVDNKPAWFVRSWADRIQSHYYPELGKVEWEMHWTGCIDFTPDHLMRLFEPAPGLVAVTG 367 + KP WF+++WADR+Q HY+P L VEWE WTGCI FTPDHLMRLFEPAPGLVAVTG Sbjct: 303 NGNRKPTWFLKAWADRVQQHYFPYLKSVEWECTWTGCIAFTPDHLMRLFEPAPGLVAVTG 362 Query: 368 YNGRGNTTGTVIGRAFAEFLLKGEADSLPIPFSPMSGVSAPSLRTAFYESGFSLYHAGQC 427 YNGRG TTGTV+G+AFA++L G A +LPIPF+PM ++ LR+ YE+GFSLYHAGQC Sbjct: 363 YNGRGVTTGTVVGKAFADYLCHGNAQALPIPFAPMQPLAGVGLRSCLYEAGFSLYHAGQC 422 Query: 428 LRVVL 432 LR+V+ Sbjct: 423 LRIVI 427 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: 661 Number of extensions: 22 Number of successful extensions: 1 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: 427 Length adjustment: 32 Effective length of query: 400 Effective length of database: 395 Effective search space: 158000 Effective search space used: 158000 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