WORKLIST ENTRIES (1):
SPUMVIRPTASE View alignment Spumavirus aspartic protease (A9) signature
Type of fingerprint: COMPOUND with 7 elements
Links:
PRINTS; PR00792 PEPSIN; PR00731 CAULIMOPTASE; PR00977 SCYTLDPTASE
PRINTS; PR00863 NODAVIRPTASE; PR00781 LIPOSIGPTASE
INTERPRO; IPR001641
Creation date 18-JUN-1998; UPDATE 07-JUN-1999
1. RAWLINGS, N.D. AND BARRETT A.J.
Families of aspartic peptidases, and those of unkown catalytic mechanism.
METHODS ENZYMOL. 248 183-228 (1995).
2. RAWLINGS, N.D. AND BARRETT, A.J.
Evolutionary families of peptidases.
BIOCHEM.J. 290 205-218 (1993).
3. BAIROCH, A. AND RAWLINGS, N.
Classification of peptidase families and index of peptidase entries in
SWISS-PROT.
http://expasy.hcuge.ch/cgi-bin/lists?peptidas.txt
4. MAURER, B., BANNERT, H., DARAI, G. AND FLUGEL, R.M.
Analysis of the primary structure of the long terminal repeat and the
gag and pol genes of the human spumaretrovirus.
J.VIROL. 62(5) 1590-1597 (1998).
5. KUPIEC, J.J., KAY, A., HAYAT, M., RAVIER, R., PERIES, J.
AND GALIBERT, F.
Sequence analysis of the simian foamy virus type 1 genome.
GENE 101(2) 185-194 (1991).
6. LAMPE, J., MARINO, S., RETHWILM, A. AND AGUZZI, A.
Degeneration of the cerebellar granule cell layer in transgenic mice
expressing genes of human foamy virus.
NEUROPATHOL.APPL.NEUROBIOL. 24(1) 36-38 (1998).
Aspartic proteases have a catalytic aspartate residue at their active site.
More than 8 families (denoted A1-A9) have been identified, three of which
(pepsin, retropepsin and cauliflower mosaic virus) have been grouped into
a single clan (AA), as they are thought to share a common ancestry. The
remaining five families have not yet been assigned to clans [1-3].
Foamy virus (spumavirus) proteases belong to the A9 family of aspartic
proteases [3]. At the moment, it is not clear whether they share a common
evolutionary origin with other aspartic proteases. Foamy viruses are single-
stranded enveloped retroviruses that have been noted to infect monkeys, cats
and humans. In the human virus, the aspartic protease is encoded by the
retroviral gag gene [4], and in monkeys by the pol gene [5]. At present,
the virus has not been proven to cause any particular disease. However,
studies have shown human foamy virus causes neurological disorders in
infected mice [6].
SPUMVIRPTASE is a 7-element fingerprint that provides a signature for the
aspartic protease of foamy viruses (spumavirus). The fingerprint was derived
from an initial alignment of 6 sequences: the motifs were drawn from
conserved regions spanning the C-terminal portion the gag polyprotein and
the N-terminal portion of the pol polyprotein - motif 1 encodes the
catalytic aspartate residue. Two iterations of OWL30.1 were required to
reach convergence, at which point a true set comprising 9 sequences was
identified. A single partial match was also found, FVPROPOL, a feline foamy
virus fragment that matches motifs 1 and 2.
An update on SPTR37_9f identified a true set of 6 sequences.
SUMMARY INFORMATION
6 codes involving 7 elements
0 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
7| 6 6 6 6 6 6 6
6| 0 0 0 0 0 0 0
5| 0 0 0 0 0 0 0
4| 0 0 0 0 0 0 0
3| 0 0 0 0 0 0 0
2| 0 0 0 0 0 0 0
--+------------------------------------
| 1 2 3 4 5 6 7
True positives..
POL_SFV1 O93209 POL_SFV3L P90458
GAG_FOAMV O41894
PROTEIN TITLES
POL_SFV1 POL POLYPROTEIN [CONTAINS: PROTEASE (EC 3.4.23.-); REVERSE T
O93209 POL PROTEIN - FELINE FOAMY VIRUS.
POL_SFV3L POL POLYPROTEIN [CONTAINS: PROTEASE (EC 3.4.23.-); REVERSE T
P90458 REVERSE TRANSCRIPTASE - FELINE SYNCYTIAL VIRUS.
GAG_FOAMV GAG POLYPROTEIN (CORE POLYPROTEIN) [CONTAINS: PROTEASE (EC 3
O41894 POL POLYPROTEIN - BOVINE SYNCYTIAL VIRUS.
SCAN HISTORY
OWL30_1 2 50 NSINGLE
SPTR37_9f 2 7 NSINGLE
INITIAL MOTIF SETS
SPUMVIRPTASE1 Length of motif = 21 Motif number = 1
Foamy virus aspartate protease motif I - 1
PCODE ST INT
IKGTKLLAHWDSGATITCIPE GAG_FOAMV 645 645
IKGTKLKAHWDSGATITCVPE POL_SFV1 26 26
IKGTKLKAHWDSGATITCVPQ POL_SFV3L 28 28
IKGNHLKGYWDSGAEITCVPA BSU945141 11 11
RKGVKIKGYWDSQADITCVPK FFVY088511 11 11
RKGVKIKGYWDSQADVTCVPK FSU78765 11 11
SPUMVIRPTASE2 Length of motif = 21 Motif number = 2
Foamy virus aspartate protease motif II - 1
PCODE ST INT
FLEDEQPIKKTLIKTIHGEKQ GAG_FOAMV 667 1
FLEDERPIQTMLIKTIHGEKQ POL_SFV1 48 1
FLEEEVPIKNIWIKTIHGEKE POL_SFV3L 50 1
YIIEEQPVGKKLITTIHNEKE BSU945141 33 1
LLQGEEPVRQQNVTTIHGTQE FFVY088511 33 1
LLQGEEPVRQQNVTTIHGTQE FSU78765 33 1
SPUMVIRPTASE3 Length of motif = 22 Motif number = 3
Foamy virus aspartate protease motif III - 1
PCODE ST INT
VYYVTFKVKGRKVEAEVIASPY GAG_FOAMV 690 2
VYYLTFKVQGRKVEAEVLASPY POL_SFV1 71 2
VYYLTFKIQGRKVEAEVISSPY POL_SFV3L 73 2
VYYVEMKIEKRKVQCEVIATAL BSU945141 56 2
VYYVNLKIDGRRINTEVIGTTL FFVY088511 56 2
VYYVNLKIDGRRINTEVIGTTL FSU78765 56 2
SPUMVIRPTASE4 Length of motif = 22 Motif number = 4
Foamy virus aspartate protease motif IV - 1
PCODE ST INT
LLSPTDVPWLTQQPLQLTILVP GAG_FOAMV 715 3
LLNPSDVPWLMKKPLQLTVLVP POL_SFV1 96 3
LVSPSDIPWLMKKPLQLTTLVP POL_SFV3L 98 3
LVAPVDIPWYKPGPLELTIKID BSU945141 81 3
IITPGDVPWILKKPLELTIKLD FFVY088511 81 3
IITPGDVPWILKKPLELTIKLD FSU78765 81 3
SPUMVIRPTASE5 Length of motif = 22 Motif number = 5
Foamy virus aspartate protease motif V - 1
PCODE ST INT
QEYQEKILSKTALPEDQKQQLK GAG_FOAMV 738 1
HEYQERLLQQTALPKEQKELLQ POL_SFV1 119 1
QEYEERLLKQTMLTGSYKEKLQ POL_SFV3L 121 1
ESQKHTLITESTLSPQGQMRLK BSU945141 104 1
EEQQGTLLNNSILSKKGKEELK FFVY088511 104 1
EEQQRTLLNNSILSKKGKEELK FSU78765 104 1
SPUMVIRPTASE6 Length of motif = 21 Motif number = 6
Foamy virus aspartate protease motif VI - 1
PCODE ST INT
VKYDNLWQHWENQVGHRKIRP GAG_FOAMV 763 3
LKYDALWQHWENQVGHRRIKP POL_SFV1 144 3
LKYDALWQHWENQVGHRRIKP POL_SFV3L 146 3
DQYQALWQCWENQVGHRRIEP BSU945141 129 3
EKYSALWQSWENQVGHRRIRP FFVY088511 129 3
DKYNALWQSWENQVGHRKIRP FSU78765 129 3
SPUMVIRPTASE7 Length of motif = 22 Motif number = 7
Foamy virus aspartate protease motif VII - 1
PCODE ST INT
IATGDYPPRPQKQYPINPKAKP GAG_FOAMV 786 2
IATGTLAPRPQKQYPINPKAKP POL_SFV1 167 2
IATGTVNPRPQKQYPINPKAKA POL_SFV3L 169 2
IATGALKPRPQKQYHINPRAKA BSU945141 152 2
IATGTVKPTPQKQYHINPKAKP FFVY088511 152 2
IATGTVKPTPQKQYHINPKAKP FSU78765 152 2
FINAL MOTIF SETS
SPUMVIRPTASE1 Length of motif = 21 Motif number = 1
Foamy virus aspartate protease motif I - 2
PCODE ST INT
IKGTKLKAHWDSGATITCVPE POL_SFV1 26 26
RKGVKIKGYWDSQADITCVPK O93209 11 11
IKGTKLKAHWDSGATITCVPQ POL_SFV3L 28 28
RKGVKIKGYWDSQADVTCVPK P90458 11 11
IKGTKLLAHWDSGATITCIPE GAG_FOAMV 645 645
IKGNHLKGYWDSGAEITCVPA O41894 11 11
SPUMVIRPTASE2 Length of motif = 21 Motif number = 2
Foamy virus aspartate protease motif II - 2
PCODE ST INT
FLEDERPIQTMLIKTIHGEKQ POL_SFV1 48 1
LLQGEEPVRQQNVTTIHGTQE O93209 33 1
FLEEEVPIKNIWIKTIHGEKE POL_SFV3L 50 1
LLQGEEPVRQQNVTTIHGTQE P90458 33 1
FLEDEQPIKKTLIKTIHGEKQ GAG_FOAMV 667 1
YIIEEQPVGKKLITTIHNEKE O41894 33 1
SPUMVIRPTASE3 Length of motif = 22 Motif number = 3
Foamy virus aspartate protease motif III - 2
PCODE ST INT
VYYLTFKVQGRKVEAEVLASPY POL_SFV1 71 2
VYYVNLKIDGRRINTEVIGTTL O93209 56 2
VYYLTFKIQGRKVEAEVISSPY POL_SFV3L 73 2
VYYVNLKIDGRRINTEVIGTTL P90458 56 2
VYYVTFKVKGRKVEAEVIASPY GAG_FOAMV 690 2
VYYVEMKIEKRKVQCEVIATAL O41894 56 2
SPUMVIRPTASE4 Length of motif = 22 Motif number = 4
Foamy virus aspartate protease motif IV - 2
PCODE ST INT
LLNPSDVPWLMKKPLQLTVLVP POL_SFV1 96 3
IITPGDVPWILKKPLELTIKLD O93209 81 3
LVSPSDIPWLMKKPLQLTTLVP POL_SFV3L 98 3
IITPGDVPWILKKPLELTIKLD P90458 81 3
LLSPTDVPWLTQQPLQLTILVP GAG_FOAMV 715 3
LVAPVDIPWYKPGPLELTIKID O41894 81 3
SPUMVIRPTASE5 Length of motif = 22 Motif number = 5
Foamy virus aspartate protease motif V - 2
PCODE ST INT
HEYQERLLQQTALPKEQKELLQ POL_SFV1 119 1
EEQQGTLLNNSILSKKGKEELK O93209 104 1
QEYEERLLKQTMLTGSYKEKLQ POL_SFV3L 121 1
EEQQRTLLNNSILSKKGKEELK P90458 104 1
QEYQEKILSKTALPEDQKQQLK GAG_FOAMV 738 1
ESQKHTLITESTLSPQGQMRLK O41894 104 1
SPUMVIRPTASE6 Length of motif = 21 Motif number = 6
Foamy virus aspartate protease motif VI - 2
PCODE ST INT
LKYDALWQHWENQVGHRRIKP POL_SFV1 144 3
EKYSALWQSWENQVGHRRIRP O93209 129 3
LKYDALWQHWENQVGHRRIKP POL_SFV3L 146 3
DKYNALWQSWENQVGHRKIRP P90458 129 3
VKYDNLWQHWENQVGHRKIRP GAG_FOAMV 763 3
DQYQALWQCWENQVGHRRIEP O41894 129 3
SPUMVIRPTASE7 Length of motif = 22 Motif number = 7
Foamy virus aspartate protease motif VII - 2
PCODE ST INT
IATGTLAPRPQKQYPINPKAKP POL_SFV1 167 2
IATGTVKPTPQKQYHINPKAKP O93209 152 2
IATGTVNPRPQKQYPINPKAKA POL_SFV3L 169 2
IATGTVKPTPQKQYHINPKAKP P90458 152 2
IATGDYPPRPQKQYPINPKAKP GAG_FOAMV 786 2
IATGALKPRPQKQYHINPRAKA O41894 152 2
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