Align Putrescine oxidase; EC 1.4.3.10 (uncharacterized)
to candidate RR42_RS24640 RR42_RS24640 amine oxidase
Query= curated2:P40974 (478 letters) >FitnessBrowser__Cup4G11:RR42_RS24640 Length = 498 Score = 189 bits (479), Expect = 2e-52 Identities = 152/465 (32%), Positives = 229/465 (49%), Gaps = 38/465 (8%) Query: 16 DVVVVGAGPAGLMAARTLVAAG-RTVAVLEARDRVGGRTWSKTV-DGAFLEIGGQWISPD 73 +VVV+GAG AGL AAR L AG + VLEARDRVGGRT + + +G F E GGQWI P Sbjct: 56 EVVVIGAGLAGLTAARDLKRAGCESFVVLEARDRVGGRTLNHDLGNGYFSESGGQWIGPG 115 Query: 74 QTELLALVDELGLETYQRYREGESVYLAPDGTRHTYTGSMFPAGESTIVEMEKLVALLDG 133 QT + L ELG+ T+ Y +G+++ LA D T F E+E+ Sbjct: 116 QTAVADLARELGVGTFPTYWQGKTMMLAGDAHAAVDTEGGFGTDPKIAHELEE------- 168 Query: 134 LVAEIGATEPWAHPAARELDTISFHHWL--RQHSDDEAACSNIGIFVAGGMLTKPAHAFS 191 L + PW P A E D +S WL + ++ + + G+ + GG PA S Sbjct: 169 LAKSVPCGAPWKSPRAAEFDAMSVGDWLVKKNIANADQIGWSTGLAITGG--ASPAR-LS 225 Query: 192 VLQAVLMAASAGSFSNLVD--EDFILDRRVVGGMQSVSETMAAELGEDVVFLDTPVRTIR 249 +L + M SA + ++ + R+ GG Q +S MA LG D V L TPV + Sbjct: 226 LLHWLSMVNSAECNYDRLEAVKGGAQQTRISGGSQILSIKMAQALG-DKVRLSTPVLRV- 283 Query: 250 WAGDGGTYAEHVPGTPVTVWSDRLTVRAKDVVVAVPPNLYSRISFEPPLPRLQHQMHQH- 308 E+ PV + + VRA++V+VA+ P L ++I+F+PPLP +H+M + Sbjct: 284 ---------ENWQNGPVAIHTANGVVRARNVIVALAPMLCNQIAFDPPLPEKRHEMQRRW 334 Query: 309 QSLGLVIKVHAVYETPFWRDKGLSGTGFGAHELSQEVYDNTNHGDPRGTLVGFVSDERAD 368 + K VY+ FWRD+GL+G F YDN+ G + FV Sbjct: 335 PAFAPGRKTTHVYKKAFWRDRGLNGWIFQPGGPVLWAYDNSPEDVSFGVINAFV------ 388 Query: 369 ELFGLPAE--ERRRLILESLSHYLGEEALHPVVYYESDF-GSEEWTRGAYAASYDLGGLH 425 + LPA+ E + + + G++ALHP+ +++ D+ +++WT + G L Sbjct: 389 HISMLPADPKEAEAQLSQIYAQAFGDQALHPIAFHQRDWLKADKWTLSC-VSPMPPGFLT 447 Query: 426 RYGAHQRTPVGPIRWACSDLAAEGYQHVDGALRQGRLAAAEVLGA 470 YG VG + W+ ++ A ++DGA+R G AA + L A Sbjct: 448 TYGEALHPSVGKLIWSGTETAEIWAGYMDGAVRSGHKAALQALQA 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: 663 Number of extensions: 47 Number of successful extensions: 8 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: 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