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= TM0003.6
         (1307 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...   148  5e-36
BP066094                                                               96  3e-22
BP084332                                                               88  8e-18
BP063694                                                               82  5e-16
AV780009                                                               76  4e-14
TC8301                                                                 71  1e-12
BP043850                                                               66  3e-11
TC15664 weakly similar to UP|O81617 (O81617) F8M12.17 protein, p...    64  1e-10
AU088980                                                               64  2e-10
AV424544                                                               63  3e-10
AV766088                                                               62  8e-10
TC8302                                                                 62  8e-10
BP075943                                                               61  1e-09
AV427921                                                               59  6e-09
TC19389 weakly similar to UP|POLX_TOBAC (P10978) Retrovirus-rela...    55  5e-08
TC16929 weakly similar to UP|Q9LFY6 (Q9LFY6) T7N9.5, partial (4%)      55  7e-08
BP057233                                                               54  2e-07
TC9039                                                                 53  3e-07
BP033602                                                               52  5e-07
TC8952 similar to UP|O82607 (O82607) T2L5.9 protein, partial (3%)      46  4e-05

>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 =  148 bits (374), Expect = 5e-36
 Identities = 71/139 (51%), Positives = 95/139 (68%)
 Frame = +2

Query: 956  FDSYMLRIGYRRCDYDCCVYVMSLDDGSFIFLLLYVDDMLIAANHLHDVNELKTKLGKEF 1015
            FDS+++ +GY R   D C Y    DD  FI LLLYVDDML+   +   V ELK +L +EF
Sbjct: 2    FDSFIMSLGYNRLSSDHCTYHKRFDDNDFIILLLYVDDMLVVGPNKDRVQELKAQLAREF 181

Query: 1016 DMKDLGAAKKILGMEIHKDRGAKKLWLSQKSYVEGVLSRFDMSKANHVSTPLTNHFKLSL 1075
            DMKDLG A KILGM+IH+DR  +++WLSQK+Y++ VL RF+M   N +STPL  ++KLS 
Sbjct: 182  DMKDLGPANKILGMQIHRDRKDRRIWLSQKNYLQKVLRRFNMQDCNPISTPLPVNYKLSS 361

Query: 1076 EQSPKIDSEIEGMSKIPYA 1094
               P  ++E   MS++PYA
Sbjct: 362  SMIPSSEAERMEMSRVPYA 418


>BP066094 
          Length = 532

 Score = 95.5 bits (236), Expect(2) = 3e-22
 Identities = 47/146 (32%), Positives = 86/146 (58%)
 Frame = +2

Query: 885  SIRVVLALVASMDMHLEQMDVKTTFLHGNLEEQIYIEQPEGFSETGDGRLVCKLKRSLYG 944
            +IR++++   + ++ L QM+VK+ FL+G + E++Y+ QP G  +  +   + KLK+SLYG
Sbjct: 98   AIRLLISFSVNHNIILHQMNVKSAFLNGYISEEVYVHQPPGXEDEKNSDHIFKLKKSLYG 277

Query: 945  LKQSPRQWYKRFDSYMLRIGYRRCDYDCCVYVMSLDDGSFIFLLLYVDDMLIAANHLHDV 1004
            LKQ+PR WY+R  S++L     R   D  ++  +  D   + + +YVDD++  + +    
Sbjct: 278  LKQAPRAWYERLSSFLLENEXVRGKVDTTLFCKTYKD-DILIVQIYVDDIIFGSANPSLC 454

Query: 1005 NELKTKLGKEFDMKDLGAAKKILGME 1030
             E    +  EF+M+ +G  K  LG++
Sbjct: 455  KEFSEMMQAEFEMRMMGELKYFLGIQ 532



 Score = 28.1 bits (61), Expect(2) = 3e-22
 Identities = 12/18 (66%), Positives = 13/18 (71%)
 Frame = +3

Query: 865 YSQHKGIDYDEIFSPVVR 882
           YSQ  GIDY E F+PV R
Sbjct: 39  YSQQ*GIDYTETFAPVAR 92


>BP084332 
          Length = 368

 Score = 88.2 bits (217), Expect = 8e-18
 Identities = 38/107 (35%), Positives = 68/107 (63%)
 Frame = +2

Query: 1194 QSTVAMSTTEAEYMAVAEAAKEALWLTGLVKELGVEQGGVQLHCDSQSAIYLTNNQVYHA 1253
            QST+A+ST EAEY++ A  + + LW+   +++  + +  + ++CD+ +AI L+ N + H+
Sbjct: 32   QSTIALSTAEAEYISAAICSTQMLWMKHQLEDYQILESNIPIYCDNTAAISLSKNPILHS 211

Query: 1254 RTKHIDVRFHKIRELLASRQILLQKIHTSENTTDKLTKPVTSDKFMF 1300
            R KHI+V++H IR+ +    +LL+ + T     D  TKP+  D+F F
Sbjct: 212  RAKHIEVKYHFIRDYVQKGVLLLKFVDTDHQWADIFTKPLAEDRFNF 352


>BP063694 
          Length = 511

 Score = 82.0 bits (201), Expect = 5e-16
 Identities = 45/119 (37%), Positives = 65/119 (53%), Gaps = 2/119 (1%)
 Frame = -2

Query: 418 KLWHMRLGHLSERGMMELHKRNMLKGVRSCIIG--LCKYCVLGKQCRVRFKTGHHKTKGI 475
           +LWH RLGH++   + +LHK   L  V S +     C  C + K  R+ F   + +   +
Sbjct: 363 ELWHSRLGHVNFDIIKQLHKHGCLD-VSSILPKPICCTSCQMAKSKRLVFHDNNKRASAV 187

Query: 476 LDYVHSDVRGPTKEPSV*GFRYFVTFTDDFSRKVWVYFMKYKSEVFAKFKLWKAEVENQ 534
           LD +H D+RGP+   S+ GF YFV F DDFSR  W Y +K KS+       +K  +EN+
Sbjct: 186 LDLIHCDLRGPSPVASIDGFSYFVIFVDDFSRFTWFYPLKRKSDFSDVLLRFKVFMENR 10


>AV780009 
          Length = 529

 Score = 75.9 bits (185), Expect = 4e-14
 Identities = 42/107 (39%), Positives = 62/107 (57%), Gaps = 1/107 (0%)
 Frame = -1

Query: 1187 ICWKSSVQSTVAMSTTEAEYMAVAEAAKEALWLTGLVKELGVEQG-GVQLHCDSQSAIYL 1245
            I W++  Q+TV+ S++EAEY A+A    E  WL+ L + L +     V L CD+QSA+++
Sbjct: 358  ISWRTKKQTTVSRSSSEAEYRALAATVCEVQWLSYLFQFLKLNVPLPVPLFCDNQSALHI 179

Query: 1246 TNNQVYHARTKHIDVRFHKIRELLASRQILLQKIHTSENTTDKLTKP 1292
             +N  +H RTKHI++  H +R  L +  I L  I T     D  TKP
Sbjct: 178  AHNPTFHERTKHIELDCHVVRAKLQAGLIHLLPISTHHQLADIFTKP 38


>TC8301 
          Length = 1243

 Score = 71.2 bits (173), Expect = 1e-12
 Identities = 41/123 (33%), Positives = 67/123 (54%)
 Frame = +2

Query: 4   AKFEVTRFDGTGNFGLWQRMAKDLLAQKSLQKALRDEKPADIATVDWNEMKEKAAGLITL 63
           AKFE+ +F G+ NF LW+   K +L + +   A+ D +PADI    W EM + A   + L
Sbjct: 506 AKFEIPKFSGS-NFSLWKLKIKAILRKDNCLPAI-DGRPADITDDKWKEMDDNAVANLHL 679

Query: 64  CVSDDVMNHILDLTTLKDVWDKLESLYMSKTPMNKLFAKQRLYSLKMQEGGDLQAHVYAF 123
            V+D V++ I +  T K++WD L  LY  K+  N++  ++ L S       D  +H  + 
Sbjct: 680 AVADSVLSSIAEKKTAKEIWDTLIQLYEVKSLHNRILKEETLNSSNE*IHFDAGSHQQSE 859

Query: 124 NNI 126
           +N+
Sbjct: 860 HNV 868


>BP043850 
          Length = 515

 Score = 66.2 bits (160), Expect = 3e-11
 Identities = 37/87 (42%), Positives = 47/87 (53%), Gaps = 1/87 (1%)
 Frame = -1

Query: 1215 EALWLTGLVKELGVEQGG-VQLHCDSQSAIYLTNNQVYHARTKHIDVRFHKIRELLASRQ 1273
            E +WL GL+ ELG  Q     LH D+ SAI +  N VYH  T+HI+V  H +RE    R 
Sbjct: 512  EIIWLRGLLSELGFLQSQPTPLHADNTSAIQIAANPVYHEWTRHIEVDCHSVREAYDRRV 333

Query: 1274 ILLQKIHTSENTTDKLTKPVTSDKFMF 1300
            I L  + TS    D LTK +T  +  F
Sbjct: 332  ITLPHVSTSVQIADILTKSLTRQRHNF 252


>TC15664 weakly similar to UP|O81617 (O81617) F8M12.17 protein, partial (4%)
          Length = 670

 Score = 64.3 bits (155), Expect = 1e-10
 Identities = 34/82 (41%), Positives = 50/82 (60%), Gaps = 1/82 (1%)
 Frame = +1

Query: 1218 WLTGLVKELGVEQGGVQL-HCDSQSAIYLTNNQVYHARTKHIDVRFHKIRELLASRQILL 1276
            WLT ++++L V      L +CDSQSA ++  N V+H RTKH+D+  H +RE L ++   L
Sbjct: 13   WLTYILQDLRVPFISPSLLYCDSQSARHIATNAVFHERTKHLDIDCHVVREKLQAKLFHL 192

Query: 1277 QKIHTSENTTDKLTKPVTSDKF 1298
              I + + T D LTKP+ S  F
Sbjct: 193  LPISSVDQTADILTKPLESGPF 258


>AU088980 
          Length = 360

 Score = 63.5 bits (153), Expect = 2e-10
 Identities = 31/109 (28%), Positives = 53/109 (48%)
 Frame = +2

Query: 577 NGVAERMNRTLTEKARCLRLNACLSKCLWAATINMACYLVNRSPRASLDGKVAEEVWTGN 636
           N + ER +R +    R L  ++ L K LW   +  A YL+N  P   L G+   +    +
Sbjct: 2   NSIVERKHRHILNVTRALMFHSYLPKNLWTFAVKHAAYLINXLPSPLLKGQCPYQFLNND 181

Query: 637 PIDLSNLRIFWRPAYVHISSEDRSKLDPKSK*CIIIGYNKGVKGYKLWD 685
              L +L++F    Y    + +  KLDP+++ C+ +G+  G  GY + D
Sbjct: 182 SPTLLDLKVFGTLCYSSTLTHNXQKLDPRARKCVFLGFKTGTXGYIVMD 328


>AV424544 
          Length = 276

 Score = 63.2 bits (152), Expect = 3e-10
 Identities = 34/93 (36%), Positives = 57/93 (60%)
 Frame = +3

Query: 955  RFDSYMLRIGYRRCDYDCCVYVMSLDDGSFIFLLLYVDDMLIAANHLHDVNELKTKLGKE 1014
            +  SY+  +GY +  +D  ++     D SF  +L+YVDD+++A N L+++  +K KL  +
Sbjct: 6    KLSSYLHILGYIQSAHDHSLFT-KFRDASFTVILVYVDDLILAGNDLNEIQCVKNKLDIQ 182

Query: 1015 FDMKDLGAAKKILGMEIHKDRGAKKLWLSQKSY 1047
            F +KDLG  K  LG+E+   R +  L+LSQ+ Y
Sbjct: 183  FRIKDLGTLKYFLGLEV--ARSSCGLFLSQRKY 275


>AV766088 
          Length = 501

 Score = 61.6 bits (148), Expect = 8e-10
 Identities = 35/106 (33%), Positives = 52/106 (49%)
 Frame = -3

Query: 416 ATKLWHMRLGHLSERGMMELHKRNMLKGVRSCIIGLCKYCVLGKQCRVRFKTGHHKTKGI 475
           A  LWH RLGH S   +  L     +         +C+ CV GK  R+ F + ++ T   
Sbjct: 316 AQSLWHSRLGHPSSSALRYLRSNKFISYELLNYSPVCESCVFGKHVRLPFVSSNNVTVMP 137

Query: 476 LDYVHSDVRGPTKEPSV*GFRYFVTFTDDFSRKVWVYFMKYKSEVF 521
            D +HSD+       S  G R++V F DDF+  +W + +  KS+VF
Sbjct: 136 FDILHSDLWTSPVLSSA-GHRFYVLFLDDFTDFLWTFPLSNKSQVF 2


>TC8302 
          Length = 494

 Score = 61.6 bits (148), Expect = 8e-10
 Identities = 42/145 (28%), Positives = 68/145 (45%), Gaps = 2/145 (1%)
 Frame = +3

Query: 103 QRLYSLKMQEGGDLQAHVYAFNNILADMTRLGVTVDDEDKAIILLCSLPGSYDHLVTTLT 162
           +RLY+L+M E   +  H+   N + A ++    T+ + ++A +LL SLP SYD LV  + 
Sbjct: 3   KRLYTLRMSESTSMSDHIDHMNTLFAQLSASNFTIGENERAELLLESLPDSYDQLVINIK 182

Query: 163 YGK--DSITLDSISSTLLPHAQRRQSVEEGGGSSGEGLFVKGGQDRGRGKGKAVDSGKKK 220
                + + L  +S  LL    +R + E+   SS               K     +  + 
Sbjct: 183 NNNIVNHLPLMMLSEVLLEEDSQR*NKEDR*DSS---------------KPMEALTMTRG 317

Query: 221 RSKSKDRKTTECYSCKQIGHWKRDC 245
           RSKS+ +   +CY C Q  H K+DC
Sbjct: 318 RSKSRKKINLKCYHCGQR*HLKKDC 392


>BP075943 
          Length = 547

 Score = 61.2 bits (147), Expect = 1e-09
 Identities = 32/72 (44%), Positives = 47/72 (64%)
 Frame = -3

Query: 982  GSFIFLLLYVDDMLIAANHLHDVNELKTKLGKEFDMKDLGAAKKILGMEIHKDRGAKKLW 1041
            GSF  LLLYVDD+L+A N +H++  +K+ L  +F +KDLG AK  LG+EI   R    + 
Sbjct: 536  GSFTALLLYVDDVLLAGNDMHEIQLVKSSLHDQFRIKDLGEAKYFLGLEI--ARSTSGIV 363

Query: 1042 LSQKSYVEGVLS 1053
            L+Q+ Y   ++S
Sbjct: 362  LNQRKYALQLIS 327


>AV427921 
          Length = 284

 Score = 58.5 bits (140), Expect = 6e-09
 Identities = 30/87 (34%), Positives = 45/87 (51%)
 Frame = +1

Query: 573 TPQQNGVAERMNRTLTEKARCLRLNACLSKCLWAATINMACYLVNRSPRASLDGKVAEEV 632
           TPQQNGV+ER NRT+    R L   + L K      +  + +++NRSP   +   + EE 
Sbjct: 22  TPQQNGVSERKNRTILNMVRSLLTMSGLPKSFLPEAVMWSLHILNRSPTLVVQNMMPEEA 201

Query: 633 WTGNPIDLSNLRIFWRPAYVHISSEDR 659
           W+G    + + RI    AY H+  + R
Sbjct: 202 WSGRQPAVDHFRISRCLAYAHVPDQKR 282


>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 = 55.5 bits (132), Expect = 5e-08
 Identities = 32/115 (27%), Positives = 57/115 (48%), Gaps = 1/115 (0%)
 Frame = +3

Query: 1184 GGPICWKSSVQSTVAMSTTEAEYMAVAEAAKEALWLTGLVKELGVEQGGVQLHCDSQSAI 1243
            GG + W S +Q  VA+ST EAE++A  EA  E LW+   ++        +        A+
Sbjct: 18   GGAVAWPSRLQKCVALSTAEAEFIAATEACHELLWMKNFLQNAWFHSHPILCCIVITKAL 197

Query: 1244 Y-LTNNQVYHARTKHIDVRFHKIRELLASRQILLQKIHTSENTTDKLTKPVTSDK 1297
            + L    ++      +      +R++L S+ + L+KIHT ++  D +TK +  +K
Sbjct: 198  FTLARILLFIQDPSTLMFVIIGLRDVLNSKLLELEKIHTDDDGADMMTKSLPREK 362


>TC16929 weakly similar to UP|Q9LFY6 (Q9LFY6) T7N9.5, partial (4%)
          Length = 553

 Score = 55.1 bits (131), Expect = 7e-08
 Identities = 32/83 (38%), Positives = 49/83 (58%), Gaps = 2/83 (2%)
 Frame = +1

Query: 1218 WLTGLVKELGV--EQGGVQLHCDSQSAIYLTNNQVYHARTKHIDVRFHKIRELLASRQIL 1275
            WLT L+++L V  EQ  + ++CD+ SA ++  N V+H RTKHI++  H +RE +    I 
Sbjct: 4    WLTYLLQDLKVPFEQPAL-VYCDNNSARHIAANPVFHERTKHIEIDCHIVRERIQKGLIH 180

Query: 1276 LQKIHTSENTTDKLTKPVTSDKF 1298
            L  I +SE   D  TK ++   F
Sbjct: 181  LLPISSSEPLADIYTKALSPQNF 249


>BP057233 
          Length = 473

 Score = 53.9 bits (128), Expect = 2e-07
 Identities = 24/64 (37%), Positives = 41/64 (63%)
 Frame = -2

Query: 1235 LHCDSQSAIYLTNNQVYHARTKHIDVRFHKIRELLASRQILLQKIHTSENTTDKLTKPVT 1294
            L CD+ SA  L +N V HAR+KHI++  H IR+ +   ++++  + T++   D LTKP++
Sbjct: 445  LWCDNLSAKALASNPVLHARSKHIEIDVHYIRDQVLQNEVVVAYVPTTDQIADCLTKPLS 266

Query: 1295 SDKF 1298
              +F
Sbjct: 265  HTRF 254


>TC9039 
          Length = 1218

 Score = 53.1 bits (126), Expect = 3e-07
 Identities = 38/172 (22%), Positives = 72/172 (41%), Gaps = 6/172 (3%)
 Frame = +2

Query: 80  KDVWDKLESLYMSKTPMNKLFAKQRLYSLKMQEGGDLQAHVYAFNNILADMTRLGVTVDD 139
           KD   ++E  +            Q L S+K Q  G+++ ++   +NI + +  L + + D
Sbjct: 398 KDFLAEIEKRFAKSDKAETSTLLQNLISMKYQGKGNIREYIMGMSNIASKLKALKLELSD 577

Query: 140 EDKAIILLCSLPGSYDHLVTTLTYGKDSITLDSISSTLLPHAQRRQSVEEGGGSSGEGLF 199
           +    ++L SLP  +     +    K+  +L+ + S  +   +R +   +         F
Sbjct: 578 DLLIHLVLLSLPAQFSQFKISYNCPKEKWSLNELISFCVQEEERLKQERKESAH-----F 742

Query: 200 VKGGQDRGRGK------GKAVDSGKKKRSKSKDRKTTECYSCKQIGHWKRDC 245
           V   +D+G+ K       +A D+   K+ K  D     CY C   GH K+ C
Sbjct: 743 VSTSKDKGKRKKTVEPKNEAADAPAPKKQKEDDT----CYFCNVSGHMKKKC 886



 Score = 33.5 bits (75), Expect = 0.22
 Identities = 17/55 (30%), Positives = 28/55 (50%)
 Frame = +3

Query: 312  YVYLGDDKPCIIKGMRQVKIALDDGGVRTLSQVRYVLEVMKNLISLGTLHENGYS 366
            Y+Y+GD K   ++ +   ++ L  G    L     V    +NLIS+  L ++GYS
Sbjct: 957  YIYVGDGKTVEVEAIGHFRLLLCTGFYLDLKDTFVVPSFRRNLISVSNLDKSGYS 1121


>BP033602 
          Length = 533

 Score = 52.4 bits (124), Expect = 5e-07
 Identities = 33/90 (36%), Positives = 47/90 (51%)
 Frame = +3

Query: 415 DATKLWHMRLGHLSERGMMELHKRNMLKGVRSCIIGLCKYCVLGKQCRVRFKTGHHKTKG 474
           D   LWH RLGH + + +  L   ++ K V +C    C+ CVL K  R  + +  +    
Sbjct: 264 DQIMLWHNRLGHPNFQYLRHLFP-DLFKNV-NCSSLECESCVLAKNQRAPYYSQPYHASR 437

Query: 475 ILDYVHSDVRGPTKEPSV*GFRYFVTFTDD 504
               +HSDV GP+K  +  G R+FVTF DD
Sbjct: 438 PFYLIHSDVWGPSKITTQFGKRWFVTFIDD 527


>TC8952 similar to UP|O82607 (O82607) T2L5.9 protein, partial (3%)
          Length = 550

 Score = 45.8 bits (107), Expect = 4e-05
 Identities = 25/81 (30%), Positives = 47/81 (57%), Gaps = 1/81 (1%)
 Frame = +3

Query: 1215 EALWLTGLVKELGVEQGG-VQLHCDSQSAIYLTNNQVYHARTKHIDVRFHKIRELLASRQ 1273
            EALWLT  + +L +     V ++CD++SA++L  N V+H RT++I++  H +   +    
Sbjct: 21   EALWLTYALADLRIASLLLVVIYCDNRSALHLAANSVFHKRTENIEIDCHIV*VKVLFGI 200

Query: 1274 ILLQKIHTSENTTDKLTKPVT 1294
            + L  + +S+   D  TK ++
Sbjct: 201  LHLLHVPSSDQVADVFTKTIS 263


  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
   0.323    0.138    0.419 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,439,372
Number of Sequences: 28460
Number of extensions: 319328
Number of successful extensions: 1691
Number of sequences better than 10.0: 79
Number of HSP's better than 10.0 without gapping: 1645
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): 1671
length of query: 1307
length of database: 4,897,600
effective HSP length: 101
effective length of query: 1206
effective length of database: 2,023,140
effective search space: 2439906840
effective search space used: 2439906840
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 61 (28.1 bits)