TBLASTN 2.2.2 [Dec-14-2001]


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= TM0185.17
         (469 letters)

Database: LJGI 
           28,460 sequences; 14,692,800 total letters

Searching..................................................done

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

TC12832 weakly similar to UP|POLX_TOBAC (P10978) Retrovirus-rela...    91  5e-19
BP075943                                                               86  1e-17
AV780009                                                               65  2e-11
BP084332                                                               52  3e-07
AV424544                                                               48  4e-06
TC19389 weakly similar to UP|POLX_TOBAC (P10978) Retrovirus-rela...    40  4e-05
AV766665                                                               42  2e-04
TC17611                                                                27  7.1
BP057233                                                               27  7.1
BP043596                                                               27  9.3
BP066094                                                               27  9.3

>TC12832 weakly similar to UP|POLX_TOBAC (P10978) Retrovirus-related Pol
           polyprotein from transposon TNT 1-94 [Contains: Protease
           ; Reverse transcriptase ; Endonuclease] , partial (9%)
          Length = 747

 Score = 90.5 bits (223), Expect = 5e-19
 Identities = 50/120 (41%), Positives = 76/120 (62%), Gaps = 9/120 (7%)
 Frame = +2

Query: 151 VMTCLYVDDMLIFGTDLNEVEKTKSFLSNSFDMKDLGEADVILGIKIIRD--GEIIGLSQ 208
           ++  LYVDDML+ G + + V++ K+ L+  FDMKDLG A+ ILG++I RD     I LSQ
Sbjct: 89  IILLLYVDDMLVVGPNKDRVQELKAQLAREFDMKDLGPANKILGMQIHRDRKDRRIWLSQ 268

Query: 209 SHYIEKVLKKFDHFDCKSVSTPFDQNTKLQPH-------KRCPVAQLEYSKAIRCLMYAM 261
            +Y++KVL++F+  DC  +STP   N KL          +R  ++++ Y+ A+  LMYAM
Sbjct: 269 KNYLQKVLRRFNMQDCNPISTPLPVNYKLSSSMIPSSEAERMEMSRVPYASAVGSLMYAM 448


>BP075943 
          Length = 547

 Score = 85.9 bits (211), Expect = 1e-17
 Identities = 57/170 (33%), Positives = 87/170 (50%), Gaps = 2/170 (1%)
 Frame = -3

Query: 147 SGKAVMTCLYVDDMLIFGTDLNEVEKTKSFLSNSFDMKDLGEADVILGIKIIRDGEIIGL 206
           SG      LYVDD+L+ G D++E++  KS L + F +KDLGEA   LG++I R    I L
Sbjct: 539 SGSFTALLLYVDDVLLAGNDMHEIQLVKSSLHDQFRIKDLGEAKYFLGLEIARSTSGIVL 360

Query: 207 SQSHYIEKVLKKFDHFDCKSVSTPFDQNTK-LQPHKRCPVAQL-EYSKAIRCLMYAMTCT 264
           +Q  Y  +++    HF  +        N++ L  +   P+  +  Y + +  L+Y  T T
Sbjct: 359 NQRKYALQLISDSGHFGFQPRFYSHGTNSQTLGTNTGTPLTDIGSYRRIVGRLLYLNT-T 183

Query: 265 RPDIAYVVGRLSRYTCNPSKDHWHVVNRVLKYLNGTINYSLIYNGYPSVL 314
           RPDI + V +LS++   P+  H   +   LKYL G+    L Y    S L
Sbjct: 182 RPDITFAVNQLSQFLSAPTDIHEQQLTGFLKYL*GSPGSGLFYPASSSTL 33


>AV780009 
          Length = 529

 Score = 65.5 bits (158), Expect = 2e-11
 Identities = 44/151 (29%), Positives = 76/151 (50%), Gaps = 1/151 (0%)
 Frame = -1

Query: 292 RVLKYLNGTINYSLIYNG-YPSVLEGYTYASWVTCVKDHASTSG*IFNLGGGAVSWGSKK 350
           RVL+Y+ G     L ++   P  L+ Y+ + W  C     S +G    LG   +SW +KK
Sbjct: 517 RVLRYVKGAPAQGLFFSADSPLKLQAYSDSDWAGCPDTRRSVTGYSIFLGTSLISWRTKK 338

Query: 351 QTCIADSTMAAEFIALAACSKETV*LRNLLYEILIWPKLMRQVSIHCDSQCTLSKAYSQV 410
           QT ++ S+  AE+ ALAA   E   L  L   + +   +   V + CD+Q  L  A++  
Sbjct: 337 QTTVSRSSSEAEYRALAATVCEVQWLSYLFQFLKL--NVPLPVPLFCDNQSALHIAHNPT 164

Query: 411 YNGKSRHIVLRHSHVKDLITNGVISIVFVRT 441
           ++ +++HI L    V+  +  G+I ++ + T
Sbjct: 163 FHERTKHIELDCHVVRAKLQAGLIHLLPIST 71


>BP084332 
          Length = 368

 Score = 51.6 bits (122), Expect = 3e-07
 Identities = 26/91 (28%), Positives = 54/91 (58%)
 Frame = +2

Query: 351 QTCIADSTMAAEFIALAACSKETV*LRNLLYEILIWPKLMRQVSIHCDSQCTLSKAYSQV 410
           Q+ IA ST  AE+I+ A CS + + +++ L +  I   L   + I+CD+   +S + + +
Sbjct: 32  QSTIALSTAEAEYISAAICSTQMLWMKHQLEDYQI---LESNIPIYCDNTAAISLSKNPI 202

Query: 411 YNGKSRHIVLRHSHVKDLITNGVISIVFVRT 441
            + +++HI +++  ++D +  GV+ + FV T
Sbjct: 203 LHSRAKHIEVKYHFIRDYVQKGVLLLKFVDT 295


>AV424544 
          Length = 276

 Score = 47.8 bits (112), Expect = 4e-06
 Identities = 23/57 (40%), Positives = 35/57 (61%)
 Frame = +3

Query: 155 LYVDDMLIFGTDLNEVEKTKSFLSNSFDMKDLGEADVILGIKIIRDGEIIGLSQSHY 211
           +YVDD+++ G DLNE++  K+ L   F +KDLG     LG+++ R    + LSQ  Y
Sbjct: 105 VYVDDLILAGNDLNEIQCVKNKLDIQFRIKDLGTLKYFLGLEVARSSCGLFLSQRKY 275


>TC19389 weakly similar to UP|POLX_TOBAC (P10978) Retrovirus-related Pol
           polyprotein from transposon TNT 1-94 [Contains: Protease
           ; Reverse transcriptase ; Endonuclease] , partial (6%)
          Length = 498

 Score = 40.0 bits (92), Expect(2) = 4e-05
 Identities = 19/45 (42%), Positives = 26/45 (57%)
 Frame = +3

Query: 336 IFNLGGGAVSWGSKKQTCIADSTMAAEFIALAACSKETV*LRNLL 380
           +    GGAV+W S+ Q C+A ST  AEFIA      E + ++N L
Sbjct: 3   LVTFAGGAVAWPSRLQKCVALSTAEAEFIAATEACHELLWMKNFL 137



 Score = 23.5 bits (49), Expect(2) = 4e-05
 Identities = 7/28 (25%), Positives = 18/28 (64%)
 Frame = +2

Query: 395 IHCDSQCTLSKAYSQVYNGKSRHIVLRH 422
           ++CD+Q  +    +  ++ +S+HI +R+
Sbjct: 173 LYCDNQGAIYLGQNSTFHSRSKHIDVRY 256


>AV766665 
          Length = 601

 Score = 42.0 bits (97), Expect = 2e-04
 Identities = 22/54 (40%), Positives = 31/54 (56%)
 Frame = +3

Query: 312 SVLEGYTYASWVTCVKDHASTSG*IFNLGGGAVSWGSKKQTCIADSTMAAEFIA 365
           S ++G+TYA ++  + D  ST G    L G  V+W SK+Q  IA S+  AE  A
Sbjct: 435 SSMDGFTYADYLGSIVDRLSTMGYYMFLSGNLVTWRSKQQNIIARSSGEAELRA 596



 Score = 30.0 bits (66), Expect = 0.84
 Identities = 16/39 (41%), Positives = 21/39 (53%)
 Frame = +1

Query: 154 CLYVDDMLIFGTDLNEVEKTKSFLSNSFDMKDLGEADVI 192
           C+YVD M I G D  E +  +  L+  FD+K L    VI
Sbjct: 118 CVYVDHMTIVGDDEVEKQILREKLAPQFDLKKLKYISVI 234


>TC17611 
          Length = 409

 Score = 26.9 bits (58), Expect = 7.1
 Identities = 10/32 (31%), Positives = 19/32 (59%)
 Frame = -1

Query: 212 IEKVLKKFDHFDCKSVSTPFDQNTKLQPHKRC 243
           I K +++ +HFD K +     +N ++QP + C
Sbjct: 247 ISKKVRRTNHFDSKDLHRIL*KNIQIQPQRTC 152


>BP057233 
          Length = 473

 Score = 26.9 bits (58), Expect = 7.1
 Identities = 11/54 (20%), Positives = 28/54 (51%)
 Frame = -2

Query: 391 RQVSIHCDSQCTLSKAYSQVYNGKSRHIVLRHSHVKDLITNGVISIVFVRTVKE 444
           R+  + CD+    + A + V + +S+HI +   +++D +    + + +V T  +
Sbjct: 457 RKPILWCDNLSAKALASNPVLHARSKHIEIDVHYIRDQVLQNEVVVAYVPTTDQ 296


>BP043596 
          Length = 569

 Score = 26.6 bits (57), Expect = 9.3
 Identities = 20/81 (24%), Positives = 32/81 (38%)
 Frame = +3

Query: 389 LMRQVSIHCDSQCTLSKAYSQVYNGKSRHIVLRHSHVKDLITNGVISIVFVRTVKESCRS 448
           L+ +V       C+L      ++    +HI     H +  I N  +S       K  CRS
Sbjct: 327 LLSKVRYDIGDSCSLDYLIDSIFPLFRKHIEPDLHHAQIRINNSFVSSFREAIYKVKCRS 506

Query: 449 FDERSDKGNGVEDIVGDESQT 469
               S +G+      G+E+QT
Sbjct: 507 ---ESSEGHSDSVFQGNETQT 560


>BP066094 
          Length = 532

 Score = 26.6 bits (57), Expect = 9.3
 Identities = 11/42 (26%), Positives = 23/42 (54%)
 Frame = +2

Query: 155 LYVDDMLIFGTDLNEVEKTKSFLSNSFDMKDLGEADVILGIK 196
           +YVDD++    + +  ++    +   F+M+ +GE    LGI+
Sbjct: 407 IYVDDIIFGSANPSLCKEFSEMMQAEFEMRMMGELKYFLGIQ 532


  Database: LJGI
    Posted date:  Jul 30, 2004 11:16 AM
  Number of letters in database: 14,692,800
  Number of sequences in database:  28,460
  
Lambda     K      H
   0.351    0.154    0.546 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,612,997
Number of Sequences: 28460
Number of extensions: 126128
Number of successful extensions: 1023
Number of sequences better than 10.0: 23
Number of HSP's better than 10.0 without gapping: 1012
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1020
length of query: 469
length of database: 4,897,600
effective HSP length: 94
effective length of query: 375
effective length of database: 2,222,360
effective search space: 833385000
effective search space used: 833385000
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 14 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (21.9 bits)
S2: 57 (26.6 bits)