Align Primary amine oxidase; Monamine oxidase; Tyramine oxidase; EC 1.4.3.21 (characterized)
to candidate BWI76_RS13080 BWI76_RS13080 tyramine oxidase
Query= SwissProt::P80695 (752 letters) >FitnessBrowser__Koxy:BWI76_RS13080 Length = 752 Score = 1524 bits (3946), Expect = 0.0 Identities = 740/752 (98%), Positives = 745/752 (99%) Query: 1 MAILSPRKTALALAVALSCAWQSPAFAHGGEAHMVPMDKTLQDFGADVQWDDYAQMFTLI 60 MAILSPRKTALALAVAL CAWQSPAFAHGGEAHMVPMDKTLQDFG DVQWDDYAQMFTLI Sbjct: 1 MAILSPRKTALALAVALFCAWQSPAFAHGGEAHMVPMDKTLQDFGVDVQWDDYAQMFTLI 60 Query: 61 KDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVEKRP 120 KDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVEKRP Sbjct: 61 KDGAYVKVKPGAKTAIVNGKTLELQVPVVMKDGKAWVSDTFINDVFQSGLDQTFQVEKRP 120 Query: 121 HPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPRAAD 180 HPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPR AD Sbjct: 121 HPLNSLSAAEISAAVAIVKAAADFKPNTRFTEISLREPDKKAVWDFALNGTPVNAPRTAD 180 Query: 181 VIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLKKHG 240 VIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLKKHG Sbjct: 181 VIMLDGKHVIEAVVDLQNKKVLSWTPIKDAHGMVLLDDFASVQNIINASSEFAEVLKKHG 240 Query: 241 IDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLEQK 300 IDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLEQK Sbjct: 241 IDDPSKVITTPLTVGYFDGKDGLKQDARLLKVVSYLDVGDGNYWAHPIENLVAVVDLEQK 300 Query: 301 KIIKIEEGPTIPVPMAARPYDGRDRVAPKIKPLDIIEPEGKNYTITGDMIHWQNWDFHLR 360 KIIKIEEGPTIPVPMAARPYDGRDRVAP +KPL+IIEPEGKNYTITGDMIHW+NWDFHLR Sbjct: 301 KIIKIEEGPTIPVPMAARPYDGRDRVAPTVKPLEIIEPEGKNYTITGDMIHWRNWDFHLR 360 Query: 361 MNSRVGPILSTVTYNDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMGTLT 420 MNSRVGPILSTVT+NDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMGTLT Sbjct: 361 MNSRVGPILSTVTWNDNGKKRQVMYEGSLGGMIVPYGDPDVGWYFKAYLDSGDYGMGTLT 420 Query: 421 SPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKHQEMGKPNVSTERR 480 SPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKH EMGKPNVSTERR Sbjct: 421 SPIVRGKDAPSNAVLLDETIADYTGTPTTIPRAIAIFERYAGPEYKHLEMGKPNVSTERR 480 Query: 481 ELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTRYGT 540 ELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTRYGT Sbjct: 481 ELVVRWISTVGNYDYIFDWVFHENGTIGIDAGATGIEAVKGVQAKTMHDPSAKEDTRYGT 540 Query: 541 LIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTIDSE 600 LIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTI SE Sbjct: 541 LIDHNIVGTTHQHIYNFRLDLDVDGENNTLVAMDPEVKPNTAGGPRTSTMQINQYTIASE 600 Query: 601 QKAAQKFDPGTIRLLSNITKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHRLSF 660 QKAAQKFDPGTIRLLSN TKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHRLSF Sbjct: 601 QKAAQKFDPGTIRLLSNTTKENRMGNPVSYQIIPYAGGTHPVATGAKFAPDEWIYHRLSF 660 Query: 661 MDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHVARA 720 MDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHVARA Sbjct: 661 MDKQLWVTRYHPTERFPEGKYPNRSIHDTGLGQYAKDDESLDNHDDVVWITTGTTHVARA 720 Query: 721 EEWPIMPTEWAHALLKPWNFFDETPTLGEKKE 752 EEWPIMPTEWAHALLKPWNFFDETPTLGEKK+ Sbjct: 721 EEWPIMPTEWAHALLKPWNFFDETPTLGEKKQ 752 Lambda K H 0.317 0.135 0.412 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: 2346 Number of extensions: 104 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: 752 Length of database: 752 Length adjustment: 40 Effective length of query: 712 Effective length of database: 712 Effective search space: 506944 Effective search space used: 506944 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 (21.6 bits) S2: 55 (25.8 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