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)
