Align Putrescine oxidase; EC 1.4.3.10 (uncharacterized)
to candidate Synpcc7942_0369 Synpcc7942_0369 putative flavin-containing monoamine oxidase
Query= curated2:P40974 (478 letters) >FitnessBrowser__SynE:Synpcc7942_0369 Length = 484 Score = 254 bits (648), Expect = 6e-72 Identities = 169/473 (35%), Positives = 242/473 (51%), Gaps = 28/473 (5%) Query: 5 RTLGSETAIERDVVVVGAGPAGLMAARTLVAAGRTVAVLEARDRVGGRTWSKTVDGA-FL 63 R + DVVVVGAG AGL AA L AG V VLEARDRVGGR WS + G +L Sbjct: 26 RAQAQSKSTRADVVVVGAGYAGLAAAWQLQKAGLKVVVLEARDRVGGRVWSIDLKGGGWL 85 Query: 64 EIGGQWISPDQTELLALVDELGLETYQRYREGESVYLAPDGT---RHTYTGSMFPA--GE 118 ++GGQW+ Q AL+ E+G +TY G+++Y + R GS + + G Sbjct: 86 DLGGQWLGATQDRFAALIQEMGCQTYPTPNFGDTLYRGVTSSGYYRVKADGSNWESVPGS 145 Query: 119 STIVEM-EKLVALLDGLVAEIGATEPWAHPAARELDTISFHHWLRQHSDDEAACSNIGIF 177 I E EKL A++D +I PW HP A D ++F WL Q+ D A + + Sbjct: 146 DLIDEADEKLSAMVD----QIDPKAPWQHPQAAIWDGLTFGQWLDQNVPD--ANARRFLI 199 Query: 178 VAGGMLTKPAHAFSVLQAVLMAASAGSFSNLVD-EDFILDRRVVGGMQSVSETMAAELGE 236 + S+LQ + + + G + L E R++GG Q V++ +A LG Sbjct: 200 ASVSYACASPQEISMLQLLFIIRACGGLAMLDGFEGAAQQDRIIGGAQVVAKRLAERLGS 259 Query: 237 DVVFLDTPVRTIRWAGDGGTYAEHVPGTPVTVWSDRLTVRAKDVVVAVPPNLYSRISFEP 296 + F + PVR IRW+ G VTV++D+ + A+ VV+AVPP L I +EP Sbjct: 260 RIQF-NQPVRKIRWSDRG-----------VTVFTDQQAIAAQSVVIAVPPTLAGSIEYEP 307 Query: 297 PLPRLQHQMHQHQSLGLVIKVHAVYETPFWRDKGLSGTGFGAHELSQEVYDNTNHGD--P 354 LP + Q+ Q G VIKV V+E PFWR GLSG L E D++ + Sbjct: 308 SLPTDRAQITQRWPQGCVIKVGMVFEEPFWRKDGLSGASIDYGSLVGETADSSTPPEYSK 367 Query: 355 RGTLVGFVSDERADELFGLPAEERRRLILESLSHYLGEEALHPVVYYESDFGSEEWTRGA 414 +G L GFV E A ++ L A +RR+ +L SL G+ L PV Y E ++ + WT+G Sbjct: 368 QGILTGFVYAETARQVLRLSASDRRQQLLASLQGRFGDRILKPVFYQEMNWAMQPWTKGC 427 Query: 415 YAASYDLGGLHRYGAHQRTPVGPIRWACSDLAAEGYQHVDGALRQGRLAAAEV 467 YA G + + + R P+GP+ WA ++ A++ +DGA+R G AA + Sbjct: 428 YAGYLAPGATYLFKSAVRDPIGPLHWAGTETASQWPTFIDGAIRSGERAAQAI 480 Lambda K H 0.318 0.135 0.406 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: 662 Number of extensions: 32 Number of successful extensions: 7 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: 478 Length of database: 484 Length adjustment: 34 Effective length of query: 444 Effective length of database: 450 Effective search space: 199800 Effective search space used: 199800 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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