Align Putrescine oxidase; EC 1.4.3.10 (uncharacterized)
to candidate RR42_RS24620 RR42_RS24620 amine oxidase
Query= curated2:P40974 (478 letters) >FitnessBrowser__Cup4G11:RR42_RS24620 Length = 498 Score = 187 bits (475), Expect = 7e-52 Identities = 156/473 (32%), Positives = 228/473 (48%), Gaps = 47/473 (9%) Query: 14 ERDVV---VVGAGPAGLMAARTLVAAG-RTVAVLEARDRVGGRTWSKTV-DGAFLEIGGQ 68 ERDV+ ++GAG AGL AAR L AG + VLEARDRVGGRT + + +G F E GGQ Sbjct: 51 ERDVLEVAIIGAGLAGLTAARDLKRAGCESFVVLEARDRVGGRTLNHDLGNGYFSEAGGQ 110 Query: 69 WISPDQTELLALVDELGLETYQRYREGESVYLAPDGTRHTYTGSMFPAGESTIVEMEKLV 128 WI P QT + L ELG+ ++ Y EG++V LA + F KL Sbjct: 111 WIGPGQTAVADLARELGVGSFLTYWEGKAVMLAGNARATIAIDGGFDTD-------PKLR 163 Query: 129 ALLDGLVAEIGATEPWAHPAARELDTISFHHWL-RQHSDDEAACSNIGIFVAGGMLTKPA 187 L+ + + PW P A E D +S WL +H E IG +A + T A Sbjct: 164 RELEEMARSVPTAAPWTSPRAAEFDAMSLADWLATKHLTPE---DQIGWALAAQLTTGTA 220 Query: 188 -HAFSVLQAVLMAASAGSFSNLVD--EDFILDRRVVGGMQSVSETMAAELGEDVVFLDTP 244 S+L + + SA ++ + + R+ GG Q +S MA LG D V L TP Sbjct: 221 PEKLSMLHYLSLINSAECNYRQLEAVKGGAQESRIAGGSQILSIKMAEALG-DKVRLSTP 279 Query: 245 VRTIRWAGDGGTYAEHVPGTPVTVWSDRLTVRAKDVVVAVPPNLYSRISFEPPLPRLQHQ 304 V I E+ PVT+ + + +RA+ ++VA+ P+L ++I+F+PPLP + + Sbjct: 280 VLRI----------ENWQNGPVTLHTAKGVIRARSLIVALSPSLCNQITFDPPLPEKRRE 329 Query: 305 MHQH-QSLGLVIKVHAVYETPFWRDKGLSGTGFGAHELSQEVYDNTNHGDPRGTLVGFV- 362 M + + + K VY+ FWRDKGL+G Q +DN+ G + F Sbjct: 330 MQRRWPAYAPMRKTAHVYKKAFWRDKGLNGMVVQLKGPVQWAFDNSPEDVSFGVISAFAN 389 Query: 363 -----SDERADELFGLPAEERRRLILESLSHYLGEEALHPVVYYESDFGSEEWTRGAYAA 417 SD +A E E R+ ++ G+EALHPV Y+E D+G + + + Sbjct: 390 NGVLPSDPKAAE------AELSRIYAQA----FGDEALHPVAYHEHDWGKADNWSLSCTS 439 Query: 418 SYDLGGLHRYGAHQRTPVGPIRWACSDLAAEGYQHVDGALRQGRLAAAEVLGA 470 G L +YG +G + WA ++ A +DGA+R G AA + L A Sbjct: 440 PIPPGFLTKYGDVLHPSIGRLIWAGTETAEIWITTMDGAIRSGHKAALQALQA 492 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: 615 Number of extensions: 42 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 478 Length of database: 498 Length adjustment: 34 Effective length of query: 444 Effective length of database: 464 Effective search space: 206016 Effective search space used: 206016 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: 52 (24.6 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