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= AC121241.10 + phase: 0 /pseudo
         (330 letters)

Database: GMGI 
           63,676 sequences; 37,918,896 total letters

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

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

NP004897 gag-protease polyprotein                                      83  1e-16
TC204438 homologue to UP|Q84VH6 (Q84VH6) Gag-pol polyprotein, co...    82  3e-16
TC204439 UP|Q84VI4 (Q84VI4) Gag-pol polyprotein, complete              79  4e-15
AW704309 weakly similar to GP|6642775|gb| gag-pol polyprotein {V...    72  5e-13
CF920770                                                               59  2e-09
BE805076 weakly similar to GP|9294121|dbj copia-like retrotransp...    50  1e-06
TC227543                                                               30  2.0
TC208581 similar to UP|O64851 (O64851) Expressed protein (At2g26...    28  4.4

>NP004897 gag-protease polyprotein
          Length = 1923

 Score = 83.2 bits (204), Expect = 1e-16
 Identities = 62/195 (31%), Positives = 95/195 (47%), Gaps = 12/195 (6%)
 Frame = +1

Query: 13  PKFDG-HYDHWAMFMENFLRSKEY--WDLIENE-----ILVVEA----GVEQTEAQRKLI 60
           P  DG +Y++W   M  FL+S +   W  +  +     +L  E     G++  E   K  
Sbjct: 40  PILDGTNYEYWKARMVAFLKSLDSRTWKAVIKDWEHPKMLDTEGKPTDGLKPEEDWTKEE 219

Query: 61  KEQKLMNLKTKNYLFQAISHDVLETILNKDTYKNIWDSMKTFF*GSNRVIRAQLQALRRD 120
            E  L N K  N LF  +  ++   I      K+ W+ +KT   G+++V  ++LQ L   
Sbjct: 220 DELALGNSKALNALFNGVDKNIFRLINTCTVAKDAWEILKTTHEGTSKVKMSRLQLLATK 399

Query: 121 FEILHMKEGETINTYFSRTLTIANKMKAHSEIMSQTIITEKILRSMVSKIDYVVCSIEES 180
           FE L MKE E I+ +    L IAN   A  E M+   +  KILRS+  + D  V +IEE+
Sbjct: 400 FENLKMKEEECIHDFHMNILEIANACTALGERMTDEKLVRKILRSLPKRFDMKVTAIEEA 579

Query: 181 NNLDTMTIDELQSSL 195
            ++  + +DEL  SL
Sbjct: 580 QDICNLRVDELIGSL 624


>TC204438 homologue to UP|Q84VH6 (Q84VH6) Gag-pol polyprotein, complete
          Length = 4734

 Score = 82.0 bits (201), Expect = 3e-16
 Identities = 62/195 (31%), Positives = 94/195 (47%), Gaps = 12/195 (6%)
 Frame = +1

Query: 13  PKFDG-HYDHWAMFMENFLRSKEY--WDLI----ENEILVVEAGVEQTEAQ-----RKLI 60
           P  DG +Y++W   M  FL+S +   W  +    E+  ++   G    E +      K  
Sbjct: 40  PILDGTNYEYWKARMVAFLKSLDSRTWKAVIKGWEHPKMLDTEGKPTNELKPEEDWTKEE 219

Query: 61  KEQKLMNLKTKNYLFQAISHDVLETILNKDTYKNIWDSMKTFF*GSNRVIRAQLQALRRD 120
            E  L N K  N LF  +  ++   I      K+ W+ +KT   G+++V  ++LQ L   
Sbjct: 220 DELALGNSKALNALFNGVDKNIFRLINTCTVAKDAWEILKTTHEGTSKVKMSRLQLLATK 399

Query: 121 FEILHMKEGETINTYFSRTLTIANKMKAHSEIMSQTIITEKILRSMVSKIDYVVCSIEES 180
           FE L MKE E I+ +    L IAN   A  E M+   +  KILRS+  + D  V +IEE+
Sbjct: 400 FENLKMKEEECIHDFHMNILEIANACTALGERMTDEKLVRKILRSLPKRFDMKVTAIEEA 579

Query: 181 NNLDTMTIDELQSSL 195
            ++  M +DEL  SL
Sbjct: 580 QDICNMRVDELIGSL 624


>TC204439 UP|Q84VI4 (Q84VI4) Gag-pol polyprotein, complete
          Length = 4731

 Score = 78.6 bits (192), Expect = 4e-15
 Identities = 59/195 (30%), Positives = 96/195 (48%), Gaps = 12/195 (6%)
 Frame = +1

Query: 13  PKFDG-HYDHWAMFMENFLRSKEY--WDLI----ENEILVVEAG--VEQTEAQRKLIKEQ 63
           P  DG +Y++W   M  FL+S +   W  +    E+  ++   G   ++ + +    KE+
Sbjct: 40  PILDGSNYEYWKARMVAFLKSLDSRTWKAVIKGWEHPKMLDTEGKPTDELKPEEDWTKEE 219

Query: 64  K---LMNLKTKNYLFQAISHDVLETILNKDTYKNIWDSMKTFF*GSNRVIRAQLQALRRD 120
               L N K  N LF  +  ++   I      K+ W+ +K    G+++V  ++LQ L   
Sbjct: 220 DELALGNSKALNALFNGVDKNIFRLINTCTVAKDAWEILKITHEGTSKVKMSRLQLLATK 399

Query: 121 FEILHMKEGETINTYFSRTLTIANKMKAHSEIMSQTIITEKILRSMVSKIDYVVCSIEES 180
           FE L MKE E I+ +    L IAN   A  E ++   +  KILRS+  + D  V +IEE+
Sbjct: 400 FENLKMKEEECIHDFHMNILEIANACTALGERITDEKLVRKILRSLPKRFDMKVTAIEEA 579

Query: 181 NNLDTMTIDELQSSL 195
            ++  M +DEL  SL
Sbjct: 580 QDICNMRVDELIGSL 624


>AW704309 weakly similar to GP|6642775|gb| gag-pol polyprotein {Vitis
           vinifera}, partial (23%)
          Length = 423

 Score = 71.6 bits (174), Expect = 5e-13
 Identities = 42/131 (32%), Positives = 72/131 (54%), Gaps = 1/131 (0%)
 Frame = -1

Query: 71  KNYLFQAISHDVLETILNKDTYKNIWDSMKTFF*GSNRVIRAQLQALRRDFEILHMKEGE 130
           ++ LF  +S  +   I+   + K IWD +K  + G +R+   Q+  LRR+FE+  MKE E
Sbjct: 420 RSCLFTGVSQMIFIRIMTLKSPKAIWDCLKEEYAGDDRIRSMQVLNLRREFEL*RMKESE 241

Query: 131 TINTYFSRTLTIANKMKAHSEIMSQTIITEKILRSMVSKIDYVVCSIEESNNLDTMTIDE 190
           TI  Y ++ L I NK+K      + + I EK L ++  + +  + S+E + +L  +T+ E
Sbjct: 240 TIKEYSNKLLGIVNKIKLLGSDFADSRIVEKNLVTVPERYEAFIASLENTKDLSKITLAE 61

Query: 191 LQSSL-VHEQR 200
           +  +L   EQR
Sbjct: 60  VLHALQAQEQR 28


>CF920770 
          Length = 581

 Score = 59.3 bits (142), Expect = 2e-09
 Identities = 40/150 (26%), Positives = 70/150 (46%), Gaps = 1/150 (0%)
 Frame = -2

Query: 53  TEAQRKLIKEQKLMNLKTKNYLFQAISHDVLETILNKDTYKNIWDSMKTFF*GSNRVIRA 112
           +E  RK ++     NLK KN +  A+  D    + N  + K +WD+++    G+  V R+
Sbjct: 451 SEEDRKRVQ----YNLKAKNIITSALGMDEYFRVSNCKSAKEMWDTLRLTHEGTTDVKRS 284

Query: 113 QLQALRRDFEILHMKEGETINTYFSRTLTIANKMKAHSEIMSQTIITEKILRSMVSKIDY 172
           ++ AL  ++E+  M   E I +   R   I N + A  +      +  K+LR +  +   
Sbjct: 283 RINALTHEYELFRMNTNENIQSMQKRFTHIVNHLAALGKEFQNEDLINKVLRCLSREWQP 104

Query: 173 VVCSIEESNNLDTMTIDELQSSL-VHEQRI 201
            V +I ES +L  M++  L   L  HE  +
Sbjct: 103 KVTAISESRDLSNMSLATLFGKLQEHEMEL 14


>BE805076 weakly similar to GP|9294121|dbj copia-like retrotransposable
           element {Arabidopsis thaliana}, partial (2%)
          Length = 388

 Score = 50.4 bits (119), Expect = 1e-06
 Identities = 27/86 (31%), Positives = 43/86 (49%), Gaps = 1/86 (1%)
 Frame = +1

Query: 12  IPKFDG-HYDHWAMFMENFLRSKEYWDLIENEILVVEAGVEQTEAQRKLIKEQKLMNLKT 70
           +P F+G +YD W + ME +L S++ WD++E    +         +Q K +K+ K  N KT
Sbjct: 130 VPIFNGENYDFWRVKMETYLSSQDLWDIVEEGFTIPADTSALNASQEKELKKNKQKNSKT 309

Query: 71  KNYLFQAISHDVLETILNKDTYKNIW 96
              L QA +  +   I+   T K  W
Sbjct: 310 LFTLQQAETDPIFPRIMGAKTAKEAW 387


>TC227543 
          Length = 1489

 Score = 29.6 bits (65), Expect = 2.0
 Identities = 15/38 (39%), Positives = 26/38 (67%), Gaps = 1/38 (2%)
 Frame = +2

Query: 159 TEKILRSMVS-KIDYVVCSIEESNNLDTMTIDELQSSL 195
           TE +LRS+ S KID+   ++E  NN+++  I+ + +SL
Sbjct: 221 TEDLLRSLPSSKIDWSAFAMENKNNVNSSAIENIGASL 334


>TC208581 similar to UP|O64851 (O64851) Expressed protein (At2g26190/T1D16.17),
            partial (46%)
          Length = 1304

 Score = 28.5 bits (62), Expect = 4.4
 Identities = 16/34 (47%), Positives = 18/34 (52%)
 Frame = -2

Query: 243  TMLNLK*KKKKRYYCCPMLKTNMGRKKKCGFLTP 276
            T L  K KKKK Y+C P  K   GRK   G + P
Sbjct: 1279 TPLTAKKKKKKEYFCIP--KKERGRKMVKGPICP 1184


  Database: GMGI
    Posted date:  Oct 22, 2004  4:58 PM
  Number of letters in database: 37,918,896
  Number of sequences in database:  63,676
  
Lambda     K      H
   0.334    0.144    0.439 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,870,235
Number of Sequences: 63676
Number of extensions: 142597
Number of successful extensions: 1194
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 1187
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): 1194
length of query: 330
length of database: 12,639,632
effective HSP length: 98
effective length of query: 232
effective length of database: 6,399,384
effective search space: 1484657088
effective search space used: 1484657088
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 59 (27.3 bits)