BLASTX 2.2.20 [Feb-08-2009] Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. Query= RLBV_smaller_RNA (1363 letters) Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects 8,994,603 sequences; 3,078,807,967 total letters Searching..................................................done Score E Sequences producing significant alignments: (bits) Value sp|P85309.2|CASPD_HPVKA RecName: Full=Capsid protein; AltName: F... 152 8e-35 sp|P83664.2|CAPSD_HPVCO RecName: Full=Capsid protein; AltName: F... 146 6e-33 gb|AAB03575.1| nucleoprotein 146 6e-33 gb|ABH05070.1| putative nucleocapsid protein [European mountain ... 83 8e-14 gb|AAW12704.1| nucleoprotein [High Plains virus] 73 8e-11 gb|AAW12703.1| nucleoprotein [High Plains virus] 73 8e-11 >sp|P85309.2|CASPD_HPVKA RecName: Full=Capsid protein; AltName: Full=Coat protein gb|ABC58222.1| nucleocapsid [Maize red stripe virus] Length = 288 Score = 152 bits (384), Expect = 8e-35 Identities = 85/265 (32%), Positives = 140/265 (52%), Gaps = 17/265 (6%) Frame = +3 Query: 183 NNNGNLKA--VEPILVNFDQLTT-------------STDAFNIKECISTSNFQLQTCYKC 317 N++G++KA ++ LVN + + T S D F++K +S+ + + Y+C Sbjct: 7 NSSGSIKAKRIKDGLVNANDIETTVIDFSYEKPDLSSVDGFSLKSLLSSDGWHIVVAYQC 66 Query: 318 ITNSLAMXXXXXXXXXXXXXLSDVTYYIVPKVKPGAIKNVISYNRFMAICIAGIRVNLTK 497 +TNS + L ++P +KP KNV+SYNRFMA+CI I + Sbjct: 67 VTNSEQLNNNKKNNKTQKFRLFTFDIIVIPGLKPNKSKNVVSYNRFMALCIGMICYHKKW 126 Query: 498 KIYDWNKHEYVAANTETLQVPDGVG--NKLALSCGMDEGHDLYWFYASGFEYTFDLYPVE 671 K+++W + Y NT T+ + NKLA+S G + H +WFY++GFEYTFD++P E Sbjct: 127 KVFNWTRKSY-EDNTSTIDFNEDEDFMNKLAMSAGFSKEHKYHWFYSTGFEYTFDIFPAE 185 Query: 672 VICCVMLRLANAEEFKLSKVDDLDLVKNLASQIGKKGQIDDVLNSIGIDTISEAYAKYNS 851 VI + R ++ E K+ + DLV+ + Q+ KKG I DV++ IG TI++ Y + Sbjct: 186 VIAMSLFRWSHRVELKIKYTHESDLVEPMVRQLTKKGTISDVMDIIGKSTIAKRYEEIVK 245 Query: 852 TRTDLVSVKRIKDTLSSLQDILKNM 926 R+ + D L ++I+K + Sbjct: 246 DRSSTGIGTKYNDVLDEFKEIIKKI 270 >sp|P83664.2|CAPSD_HPVCO RecName: Full=Capsid protein; AltName: Full=Coat protein sp|P83549.2|CAPSD_HPVID RecName: Full=Capsid protein; AltName: Full=Coat protein sp|P83550.2|CAPSD_HPVKS RecName: Full=Capsid protein; AltName: Full=Coat protein sp|P83666.2|CAPSD_HPVTX RecName: Full=Capsid protein; AltName: Full=Coat protein sp|P83665.2|CAPSD_HPVUT RecName: Full=Capsid protein; AltName: Full=Coat protein Length = 289 Score = 146 bits (368), Expect = 6e-33 Identities = 79/248 (31%), Positives = 127/248 (51%), Gaps = 1/248 (0%) Frame = +3 Query: 243 TSTDAFNIKECISTSNFQLQTCYKCITNSLAMXXXXXXXXXXXXXLSDVTYYIVPKVKPG 422 +S D F++K +S+ + + Y+ +TNS + L ++P +KP Sbjct: 42 SSVDGFSLKSLLSSDGWHIVVAYQSVTNSERLNNNKKNNKTQRFKLFTFDIIVIPGLKPN 101 Query: 423 AIKNVISYNRFMAICIAGIRVNLTKKIYDWNKHEYVA-ANTETLQVPDGVGNKLALSCGM 599 KNV+SYNRFMA+CI I + K+++W+ Y NT D NKLA+S G Sbjct: 102 KSKNVVSYNRFMALCIGMICYHKKWKVFNWSNKRYEDNKNTINFNEDDDFMNKLAMSAGF 161 Query: 600 DEGHDLYWFYASGFEYTFDLYPVEVICCVMLRLANAEEFKLSKVDDLDLVKNLASQIGKK 779 + H +WFY++GFEYTFD++P EVI + R ++ E K+ + DLV + Q+ K+ Sbjct: 162 SKEHKYHWFYSTGFEYTFDIFPAEVIAMSLFRWSHRVELKIKYEHESDLVAPMVRQVTKR 221 Query: 780 GQIDDVLNSIGIDTISEAYAKYNSTRTDLVSVKRIKDTLSSLQDILKNMK*VHIV**VQY 959 G I DV++ +G D I++ Y + R+ + + D L +DI + + Sbjct: 222 GNISDVMDIVGKDIIAKKYEEIVKDRSSIGIGTKYNDILDEFKDIFNKIDSSSL---DST 278 Query: 960 IMSCFNNI 983 I +CFN I Sbjct: 279 IKNCFNKI 286 >gb|AAB03575.1| nucleoprotein Length = 270 Score = 146 bits (368), Expect = 6e-33 Identities = 79/248 (31%), Positives = 127/248 (51%), Gaps = 1/248 (0%) Frame = +3 Query: 243 TSTDAFNIKECISTSNFQLQTCYKCITNSLAMXXXXXXXXXXXXXLSDVTYYIVPKVKPG 422 +S D F++K +S+ + + Y+ +TNS + L ++P +KP Sbjct: 23 SSVDGFSLKSLLSSDGWHIVVAYQSVTNSERLNNNKKNNKTQRFKLFTFDIIVIPGLKPN 82 Query: 423 AIKNVISYNRFMAICIAGIRVNLTKKIYDWNKHEYVA-ANTETLQVPDGVGNKLALSCGM 599 KNV+SYNRFMA+CI I + K+++W+ Y NT D NKLA+S G Sbjct: 83 KSKNVVSYNRFMALCIGMICYHKKWKVFNWSNKRYEDNKNTINFNEDDDFMNKLAMSAGF 142 Query: 600 DEGHDLYWFYASGFEYTFDLYPVEVICCVMLRLANAEEFKLSKVDDLDLVKNLASQIGKK 779 + H +WFY++GFEYTFD++P EVI + R ++ E K+ + DLV + Q+ K+ Sbjct: 143 SKEHKYHWFYSTGFEYTFDIFPAEVIAMSLFRWSHRVELKIKYEHESDLVAPMVRQVTKR 202 Query: 780 GQIDDVLNSIGIDTISEAYAKYNSTRTDLVSVKRIKDTLSSLQDILKNMK*VHIV**VQY 959 G I DV++ +G D I++ Y + R+ + + D L +DI + + Sbjct: 203 GNISDVMDIVGKDIIAKKYEEIVKDRSSIGIGTKYNDILDEFKDIFNKIDSSSL---DST 259 Query: 960 IMSCFNNI 983 I +CFN I Sbjct: 260 IKNCFNKI 267 >gb|ABH05070.1| putative nucleocapsid protein [European mountain ash ringspot-associated virus] Length = 314 Score = 82.8 bits (203), Expect = 8e-14 Identities = 61/247 (24%), Positives = 109/247 (44%), Gaps = 13/247 (5%) Frame = +3 Query: 135 KTYNINDVKDGITKDFNNNGNLK----AVEPILVNFDQLTTSTDAFNIKECISTSNFQLQ 302 KT D++ I N+ N+ AV P L T + D FNI + N + Sbjct: 40 KTIKFLDMRGNIATSARNSLNISPGVFAVNPFLGE----TLAEDTFNILDYAGLGN--VD 93 Query: 303 TCYKCITNSLAMXXXXXXXXXXXXXLSD-VTYYIVPKVKPGAIKNVISYNRFMAICIAGI 479 C ++ S + +SD +V ++ ++NV+S+N+ A+ I Sbjct: 94 ACASHLSRSQELREQVTEKTLREVPISDSYVLKVVSNLQATTVQNVVSFNKACAVMSFNI 153 Query: 480 RVNLTKKIYDWNKHEYVA--ANTETLQVPDGVGNKLALSCGMDEGHDLYWFYASGFEYTF 653 + T ++YDW K+EYV+ + +V + N+LA + Y+ G+E+ + Sbjct: 154 LRHTTDEMYDWTKNEYVSLGLKEKAAKVNPNIINRLAGQINLSPQSPYYYLVTPGYEFLY 213 Query: 654 DLYPVEVICCVMLRLANAEEFKL-SKVDDLDLVKNLASQIGKK-----GQIDDVLNSIGI 815 D YP E I ++++A + L + D D+ +L ++I K+ IDD++ IG Sbjct: 214 DAYPAETIAMTLVKMAYRKTMNLPDSMKDSDICSSLNAKINKRHNLAVNNIDDIIKQIGK 273 Query: 816 DTISEAY 836 I + Y Sbjct: 274 KHIEDMY 280 >gb|AAW12704.1| nucleoprotein [High Plains virus] Length = 100 Score = 72.8 bits (177), Expect = 8e-11 Identities = 34/92 (36%), Positives = 52/92 (56%), Gaps = 1/92 (1%) Frame = +3 Query: 498 KIYDWNKHEYVA-ANTETLQVPDGVGNKLALSCGMDEGHDLYWFYASGFEYTFDLYPVEV 674 K+++W+ Y NT D NKLA+S G + H +WFY++GFEYTFD++P EV Sbjct: 9 KVFNWSNKRYEDNKNTINFNEDDDFMNKLAMSAGFSKEHKYHWFYSTGFEYTFDIFPAEV 68 Query: 675 ICCVMLRLANAEEFKLSKVDDLDLVKNLASQI 770 I + R ++ E K+ + DLV + Q+ Sbjct: 69 IAMSLFRWSHRVELKIKYEHESDLVAPMVRQV 100 Database: All non-redundant GenBank CDS translations+PDB+SwissProt+PIR+PRF excluding environmental samples from WGS projects Posted date: Jun 4, 2009 5:40 PM Number of letters in database: 3,078,807,967 Number of sequences in database: 8,994,603 Lambda K H 0.318 0.134 0.401 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 8994603 Number of Hits to DB: 5,492,690,251 Number of extensions: 101053918 Number of successful extensions: 250509 Number of sequences better than 1.0e-04: 6 Number of HSP's gapped: 250209 Number of HSP's successfully gapped: 6 Length of query: 454 Length of database: 3,078,807,967 Length adjustment: 139 Effective length of query: 315 Effective length of database: 1,828,558,150 Effective search space: 575995817250 Effective search space used: 575995817250 Neighboring words threshold: 12 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: 33 (17.3 bits)