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= TM0013.3
         (324 letters)

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

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

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

BP075943                                                              145  7e-36
AV424544                                                              106  6e-24
BP066094                                                               91  7e-21
AV411594                                                               59  2e-10
TC12832 weakly similar to UP|POLX_TOBAC (P10978) Retrovirus-rela...    59  1e-09
TC18909                                                                29  0.002
AV767042                                                               38  0.002
AV777643                                                               29  0.94
TC9278                                                                 28  1.6
TC13668                                                                28  2.7
AV410378                                                               27  3.6
BP057980                                                               27  3.6
TC10523                                                                27  6.1
AV774371                                                               27  6.1
AV781245                                                               26  8.0

>BP075943 
          Length = 547

 Score =  145 bits (367), Expect = 7e-36
 Identities = 82/156 (52%), Positives = 102/156 (64%), Gaps = 1/156 (0%)
 Frame = -3

Query: 170 FAGLLVYVDDVILFGNCLAEFQVVKDSLHTAFGIKDLVILKYFLGLEVAHSSLGISLCQR 229
           F  LL+YVDDV+L GN + E Q+VK SLH  F IKDL   KYFLGLE+A S+ GI L QR
Sbjct: 530 FTALLLYVDDVLLAGNDMHEIQLVKSSLHDQFRIKDLGEAKYFLGLEIARSTSGIVLNQR 351

Query: 230 KYCLDLLTETGTLGSKP-VSTPLDPSCKLVVNQGEPYSDATAYRRLVGRLLYLTTTRPDI 288
           KY L L++++G  G +P   +    S  L  N G P +D  +YRR+VGRLLYL TTRPDI
Sbjct: 350 KYALQLISDSGHFGFQPRFYSHGTNSQTLGTNTGTPLTDIGSYRRIVGRLLYLNTTRPDI 171

Query: 289 SFATQQLSQFMSNPMTDHYKAALRVLRFLKTSPGLG 324
           +FA  QLSQF+S P   H +     L++L  SPG G
Sbjct: 170 TFAVNQLSQFLSAPTDIHEQQLTGFLKYL*GSPGSG 63


>AV424544 
          Length = 276

 Score =  106 bits (264), Expect = 6e-24
 Identities = 57/90 (63%), Positives = 64/90 (70%)
 Frame = +3

Query: 142 KLSSHLRNLGYSQATSDHSLFVKFQDTLFAGLLVYVDDVILFGNCLAEFQVVKDSLHTAF 201
           KLSS+L  LGY Q+  DHSLF KF+D  F  +LVYVDD+IL GN L E Q VK+ L   F
Sbjct: 6   KLSSYLHILGYIQSAHDHSLFTKFRDASFTVILVYVDDLILAGNDLNEIQCVKNKLDIQF 185

Query: 202 GIKDLVILKYFLGLEVAHSSLGISLCQRKY 231
            IKDL  LKYFLGLEVA SS G+ L QRKY
Sbjct: 186 RIKDLGTLKYFLGLEVARSSCGLFLSQRKY 275


>BP066094 
          Length = 532

 Score = 90.5 bits (223), Expect(2) = 7e-21
 Identities = 52/149 (34%), Positives = 85/149 (56%), Gaps = 1/149 (0%)
 Frame = +2

Query: 69  AKLTTVRMVLALAAAQNWHLHQLDVDNAFLHGTLDEDVYMNIPAGVPTMK-PNQVCKLQK 127
           +K   +R++++ +   N  LHQ++V +AFL+G + E+VY++ P G    K  + + KL+K
Sbjct: 86  SKTEAIRLLISFSVNHNIILHQMNVKSAFLNGYISEEVYVHQPPGXEDEKNSDHIFKLKK 265

Query: 128 SLYGLKQASRKWYEKLSSHLRNLGYSQATSDHSLFVKFQDTLFAGLLVYVDDVILFGNCL 187
           SLYGLKQA R WYE+LSS L      +   D +LF K        + +YVDD+I      
Sbjct: 266 SLYGLKQAPRAWYERLSSFLLENEXVRGKVDTTLFCKTYKDDILIVQIYVDDIIFGSANP 445

Query: 188 AEFQVVKDSLHTAFGIKDLVILKYFLGLE 216
           +  +   + +   F ++ +  LKYFLG++
Sbjct: 446 SLCKEFSEMMQAEFEMRMMGELKYFLGIQ 532



 Score = 26.2 bits (56), Expect(2) = 7e-21
 Identities = 10/18 (55%), Positives = 15/18 (82%)
 Frame = +3

Query: 53 YNQIEGLDYFDTFSPVAK 70
          Y+Q  G+DY +TF+PVA+
Sbjct: 39 YSQQ*GIDYTETFAPVAR 92


>AV411594 
          Length = 244

 Score = 58.5 bits (140), Expect(2) = 2e-10
 Identities = 32/65 (49%), Positives = 37/65 (56%)
 Frame = +2

Query: 212 FLGLEVAHSSLGISLCQRKYCLDLLTETGTLGSKPVSTPLDPSCKLVVNQGEPYSDATAY 271
           FL   +A S  GI L +RKY L LL +T  +G KP   PLDPS KL    GE  SD T Y
Sbjct: 50  FLRT*IAKSKKGILLSRRKYALQLLDDTRNMGCKPPPFPLDPSIKLNSTDGELLSDVTLY 229

Query: 272 RRLVG 276
            R +G
Sbjct: 230 IRFIG 244



 Score = 22.7 bits (47), Expect(2) = 2e-10
 Identities = 11/20 (55%), Positives = 14/20 (70%)
 Frame = +3

Query: 197 LHTAFGIKDLVILKYFLGLE 216
           L  +F +K L  +KYFLGLE
Sbjct: 6   LAKSFKLKVLDDMKYFLGLE 65


>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 = 58.5 bits (140), Expect = 1e-09
 Identities = 47/146 (32%), Positives = 69/146 (47%), Gaps = 10/146 (6%)
 Frame = +2

Query: 145 SHLRNLGYSQATSDHSLFVK-FQDTLFAGLLVYVDDVILFGNCLAEFQVVKDSLHTAFGI 203
           S + +LGY++ +SDH  + K F D  F  LL+YVDD+++ G      Q +K  L   F +
Sbjct: 8   SFIMSLGYNRLSSDHCTYHKRFDDNDFIILLLYVDDMLVVGPNKDRVQELKAQLAREFDM 187

Query: 204 KDLVILKYFLGLEV--AHSSLGISLCQRKYCLDLLTETGTLGSKPVSTPLDPSCKLVVNQ 261
           KDL      LG+++        I L Q+ Y   +L         P+STPL  + KL  + 
Sbjct: 188 KDLGPANKILGMQIHRDRKDRRIWLSQKNYLQKVLRRFNMQDCNPISTPLPVNYKLSSSM 367

Query: 262 GEPYSDA-------TAYRRLVGRLLY 280
             P S+A         Y   VG L+Y
Sbjct: 368 -IPSSEAERMEMSRVPYASAVGSLMY 442


>TC18909 
          Length = 621

 Score = 28.9 bits (63), Expect(2) = 0.002
 Identities = 13/22 (59%), Positives = 17/22 (77%)
 Frame = +2

Query: 60 DYFDTFSPVAKLTTVRMVLALA 81
          DY +T SPV K  TVR++L+LA
Sbjct: 62 DYTETVSPVVKPVTVRILLSLA 127



 Score = 28.5 bits (62), Expect(2) = 0.002
 Identities = 11/17 (64%), Positives = 16/17 (93%)
 Frame = +1

Query: 39 GTLARYKARLVAKGYNQ 55
          G++ +YKARLVAKG++Q
Sbjct: 1  GSINKYKARLVAKGFHQ 51


>AV767042 
          Length = 444

 Score = 38.1 bits (87), Expect = 0.002
 Identities = 17/44 (38%), Positives = 27/44 (60%)
 Frame = -3

Query: 55  QIEGLDYFDTFSPVAKLTTVRMVLALAAAQNWHLHQLDVDNAFL 98
           Q  G+D   TFSPV K   +R V  +A +++W + QL+V N ++
Sbjct: 349 QTAGVDCNKTFSPVVKPAPIRTVFTIALSRSWPIPQLNVQNLWI 218


>AV777643 
          Length = 423

 Score = 29.3 bits (64), Expect = 0.94
 Identities = 12/29 (41%), Positives = 19/29 (65%)
 Frame = +3

Query: 154 QATSDHSLFVKFQDTLFAGLLVYVDDVIL 182
           Q+ +DHS+F +        L+VYVDD+I+
Sbjct: 300 QSEADHSIFYRNSGAACIYLIVYVDDIII 386


>TC9278 
          Length = 743

 Score = 28.5 bits (62), Expect = 1.6
 Identities = 13/30 (43%), Positives = 19/30 (63%)
 Frame = +1

Query: 3   EIAALEKNETWKIVDLPQGVKAIGNKWVYR 32
           EI  +EKNET ++ DL    + I  KWV++
Sbjct: 622 EIHVIEKNET*ELTDLLGDQRLISVKWVHK 711


>TC13668 
          Length = 662

 Score = 27.7 bits (60), Expect = 2.7
 Identities = 12/24 (50%), Positives = 15/24 (62%)
 Frame = +2

Query: 275 VGRLLYLTTTRPDISFATQQLSQF 298
           + RLLYLTT RPDI +     + F
Sbjct: 167 IRRLLYLTTIRPDIIYVLMVYNNF 238


>AV410378 
          Length = 358

 Score = 27.3 bits (59), Expect = 3.6
 Identities = 11/17 (64%), Positives = 13/17 (75%)
 Frame = +1

Query: 3   EIAALEKNETWKIVDLP 19
           EI ALE+N TW +VD P
Sbjct: 298 EIEALERNHTWILVDKP 348


>BP057980 
          Length = 491

 Score = 27.3 bits (59), Expect = 3.6
 Identities = 14/41 (34%), Positives = 22/41 (53%)
 Frame = -1

Query: 214 GLEVAHSSLGISLCQRKYCLDLLTETGTLGSKPVSTPLDPS 254
           G+ V+  S  ISL  +KY    L +  +LG+  +S+   PS
Sbjct: 269 GVHVSKQSFPISLLHKKYLDPRLLQFQSLGNSSISSSFPPS 147


>TC10523 
          Length = 501

 Score = 26.6 bits (57), Expect = 6.1
 Identities = 20/65 (30%), Positives = 27/65 (40%)
 Frame = +2

Query: 132 LKQASRKWYEKLSSHLRNLGYSQATSDHSLFVKFQDTLFAGLLVYVDDVILFGNCLAEFQ 191
           L Q   K+YEK +SH  +   SQ    +  FV   D   A      DD I+    +    
Sbjct: 86  LDQLHDKYYEKTASHWFDAPSSQVWWGYKKFVPLSDLHKAAKGYLKDDAIVVNVEILTVS 265

Query: 192 VVKDS 196
           +VK S
Sbjct: 266 IVKIS 280


>AV774371 
          Length = 492

 Score = 26.6 bits (57), Expect = 6.1
 Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
 Frame = -3

Query: 232 CLD-LLTETGTLGSKPVSTPLDPSCKL 257
           CL+  +T +GTL  +P S+P  P C L
Sbjct: 367 CLNHCITSSGTLTHRPASSP*QPRCNL 287


>AV781245 
          Length = 523

 Score = 26.2 bits (56), Expect = 8.0
 Identities = 16/53 (30%), Positives = 25/53 (46%)
 Frame = +2

Query: 211 YFLGLEVAHSSLGISLCQRKYCLDLLTETGTLGSKPVSTPLDPSCKLVVNQGE 263
           Y   + + H   G+  C R++   L  E     +KPV++PL  SC  +   GE
Sbjct: 332 YLFTISLVHV-YGVGACPRQFISLLHQE*WVSPNKPVASPLSRSCHGIPA*GE 487


  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
   0.321    0.137    0.405 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,131,064
Number of Sequences: 28460
Number of extensions: 64642
Number of successful extensions: 306
Number of sequences better than 10.0: 30
Number of HSP's better than 10.0 without gapping: 302
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): 302
length of query: 324
length of database: 4,897,600
effective HSP length: 90
effective length of query: 234
effective length of database: 2,336,200
effective search space: 546670800
effective search space used: 546670800
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)