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= AC140773.4 + phase: 0 /pseudo
         (1194 letters)

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

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

                                                                   Score     E
Sequences producing significant alignments:                        (bits)  Value

TC223727 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, part...    46  5e-08
CF922488                                                               50  8e-06
TC232528 weakly similar to UP|Q6WAY5 (Q6WAY5) Gag/pol polyprotei...    43  7e-04
NP334778 reverse transcriptase [Glycine max]                           39  0.018
TC219643 weakly similar to UP|Q6WAY7 (Q6WAY7) Gag/pol polyprotei...    33  0.57
TC233837 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, part...    33  0.98
BI316922                                                               32  1.7
CD487724                                                               31  2.8
BI321666                                                               31  3.7
NP395548 reverse transcriptase [Glycine max]                           30  8.3

>TC223727 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, partial (9%)
          Length = 843

 Score = 46.2 bits (108), Expect(2) = 5e-08
 Identities = 21/41 (51%), Positives = 27/41 (65%)
 Frame = +1

Query: 1154 FTKWIEAIPLKDVTQEEVISFIQKFIIYRFGIPETITTDQG 1194
            FTKW+EA    DV +  V+ FI+K II R+G+P  I TD G
Sbjct: 613  FTKWVEAASYTDVMRGVVVRFIKKEIICRYGLPRKIITDNG 735



 Score = 30.4 bits (67), Expect(2) = 5e-08
 Identities = 26/92 (28%), Positives = 42/92 (45%), Gaps = 3/92 (3%)
 Frame = +3

Query: 1066 WNMRDTPSRPQNEMALISTRFVLANYAQRLHRIRKRMPK---IRRNSTRPSK*TPCNNQT 1122
            WN R      Q +     +R +LA + + L    + MP+   +RR    P+  + C+   
Sbjct: 348  WNARQRACYGQEDP---KSRLLLAYHGK*LLCPCEEMPQMSSVRR*CQCPTASSECHVLP 518

Query: 1123 VAI*RRGLRCNRGD*TYFIEMIQIYLSRDRLF 1154
            +A    G RC+RG *   +E   ++   DRLF
Sbjct: 519  LAFLHVGNRCHRGH*AQGLEWSSLHPRSDRLF 614


>CF922488 
          Length = 741

 Score = 49.7 bits (117), Expect = 8e-06
 Identities = 46/157 (29%), Positives = 71/157 (44%)
 Frame = +2

Query: 473 WVLWL*SNLYCRRRYRQDRISMPGGIRML*MDSDAIWSEKCWCYVPEGDEFDVP*LHREL 532
           W+  L* +    R Y +D      G  +L*     +W+E+CW  +P G    +     + 
Sbjct: 146 WIFRL*PDKDSTRGYGKDNFHYSMGNLLL*--GYVVWAEECWGNIPAGHGGIILGHDAQG 319

Query: 533 YAGLYR*HCSEIFFGRKTLGTFTPIIRKDEAIWIENESIKMCIWGLCR*FLRFRCAQKRN 592
             GL+ *H  EI  G  T   F  ++     I +E ES K+ + G  +   R     +RN
Sbjct: 320 DRGLHG*HDREIKNGGGTPCQFAKVV*ATT*IQVETESRKVYV*GKIQKVARLY**LERN 499

Query: 593 RDQPEQNQSNN*DQGSFYKERITVSIRENQLSPKIYI 629
           R   EQ +S+ *D  + Y+E     + E +L  KI+I
Sbjct: 500 RGGFEQGESDP*DGQATYREASPRFLGEVELHRKIHI 610


>TC232528 weakly similar to UP|Q6WAY5 (Q6WAY5) Gag/pol polyprotein
           (Fragment), partial (3%)
          Length = 449

 Score = 43.1 bits (100), Expect = 7e-04
 Identities = 20/58 (34%), Positives = 36/58 (61%)
 Frame = +1

Query: 13  VNKVLVDGGATVNLLPQSFLGKIGLYDSDLKPHNVILTNYEGSSGNSLGAIKLELMVG 70
           V KVL+D G ++N++P+S L K+    S LKP ++++  ++G+     G I L + +G
Sbjct: 265 VAKVLIDNGYSLNVMPKSTLDKLPFNASHLKPSSMVVRAFDGTRREVRGEIDLPVQIG 438


>NP334778 reverse transcriptase [Glycine max]
          Length = 431

 Score = 38.5 bits (88), Expect = 0.018
 Identities = 32/113 (28%), Positives = 50/113 (43%)
 Frame = +2

Query: 463 GGFRLLEYARWVLWL*SNLYCRRRYRQDRISMPGGIRML*MDSDAIWSEKCWCYVPEGDE 522
           G F  + +  W+  L*S+    R Y +D      G  +L*   D +W+E+ W  +P G  
Sbjct: 92  GQFCPILFHGWIFGL*SDKDGTRGYGKDNFHYSMGNLLL*--GDVVWAEEFWGNLPSGHG 265

Query: 523 FDVP*LHRELYAGLYR*HCSEIFFGRKTLGTFTPIIRKDEAIWIENESIKMCI 575
             +P    +   GL  *+  EI  G  T   F   +     I +E ES ++C+
Sbjct: 266 GIIPGHDAQGDRGLCG*NDREIKNGGGTPSQFAKFVWATT*IQVETESQEVCV 424


>TC219643 weakly similar to UP|Q6WAY7 (Q6WAY7) Gag/pol polyprotein
           (Fragment), partial (8%)
          Length = 1320

 Score = 33.5 bits (75), Expect = 0.57
 Identities = 14/25 (56%), Positives = 17/25 (68%)
 Frame = +1

Query: 95  WIHGVGAVPSTVHQRIAIWKEDGLV 119
           WIH VG VPST+HQ++    E  LV
Sbjct: 4   WIHSVGVVPSTLHQKLKFVVEGHLV 78


>TC233837 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, partial (6%)
          Length = 402

 Score = 32.7 bits (73), Expect = 0.98
 Identities = 37/128 (28%), Positives = 56/128 (42%)
 Frame = +1

Query: 473 WVLWL*SNLYCRRRYRQDRISMPGGIRML*MDSDAIWSEKCWCYVPEGDEFDVP*LHREL 532
           W L +*SN+    R R+D    P G   L*  SD + +EK W  +       VP*     
Sbjct: 16  WFLGV*SNIDGT*RCREDHFRHPMGDIQL*--SDGLRAEKYWGNLSACHGGVVP*YDA*G 189

Query: 533 YAGLYR*HCSEIFFGRKTLGTFTPIIRKDEAIWIENESIKMCIWGLCR*FLRFRCAQKRN 592
             GL R*H  ++    +T       + K   I I+ +  +M IWG      R     +R+
Sbjct: 190 NRGLRR*HDCQVSD*DRTPCQSV*AVWKVAEIPIKTKPNQMHIWGEVGEAARIYRKSERD 369

Query: 593 RDQPEQNQ 600
           RD+  +++
Sbjct: 370 RDRSRESE 393


>BI316922 
          Length = 405

 Score = 32.0 bits (71), Expect = 1.7
 Identities = 15/39 (38%), Positives = 23/39 (58%)
 Frame = +3

Query: 1154 FTKWIEAIPLKDVTQEEVISFIQKFIIYRFGIPETITTD 1192
            FTKWIE   +  ++   V  F+ + I+  FGIP T+ +D
Sbjct: 285  FTKWIETEHIAIISIANVRKFV*RNIVC*FGIPNTLISD 401


>CD487724 
          Length = 676

 Score = 31.2 bits (69), Expect = 2.8
 Identities = 20/86 (23%), Positives = 42/86 (48%)
 Frame = +3

Query: 17  LVDGGATVNLLPQSFLGKIGLYDSDLKPHNVILTNYEGSSGNSLGAIKLELMVGSTKRIT 76
           LVDGG+T N + Q  + ++GL      P  V++ N       ++    + + + + + + 
Sbjct: 33  LVDGGSTHNFVQQPLVSQLGLPCRSTPPLRVMVGNGHHLKCTTI-CEAIPISIQNIEFLV 209

Query: 77  TFMVVPSKANFNVLLGREWIHGVGAV 102
              V+P     N++LG +W+  +G +
Sbjct: 210 HLYVLPI-VGANIVLGVQWLKTLGPI 284


>BI321666 
          Length = 430

 Score = 30.8 bits (68), Expect = 3.7
 Identities = 13/40 (32%), Positives = 23/40 (57%)
 Frame = +2

Query: 1155 TKWIEAIPLKDVTQEEVISFIQKFIIYRFGIPETITTDQG 1194
            +KW+EA+  +    + VI F++K I  R G+P  +  + G
Sbjct: 239  SKWVEAVACQKSDAKIVIKFLKKQIFSRLGVPWVLIDNGG 358


>NP395548 reverse transcriptase [Glycine max]
          Length = 762

 Score = 29.6 bits (65), Expect = 8.3
 Identities = 23/84 (27%), Positives = 40/84 (47%)
 Frame = +3

Query: 435 MHRF*RSKSRYPQRRIPNAGSRNASRFSGGFRLLEYARWVLWL*SNLYCRRRYRQDRISM 494
           MHR  +++  + +R  P+    +    +   RLL     +LW+*S+    +   +D + M
Sbjct: 168 MHRLPQAQRSHKERPFPSTLHGSDVGETCRTRLLLLLGCILWI*SDCCRPQGSGEDGLHM 347

Query: 495 PGGIRML*MDSDAIWSEKCWCYVP 518
           P     L* DS  IW  +C  ++P
Sbjct: 348 PFWCLCL*TDS--IWVVQCTYHIP 413


  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
   0.348    0.153    0.528 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 51,934,826
Number of Sequences: 63676
Number of extensions: 720002
Number of successful extensions: 5584
Number of sequences better than 10.0: 20
Number of HSP's better than 10.0 without gapping: 4097
Number of HSP's successfully gapped in prelim test: 142
Number of HSP's that attempted gapping in prelim test: 1409
Number of HSP's gapped (non-prelim): 4363
length of query: 1194
length of database: 12,639,632
effective HSP length: 108
effective length of query: 1086
effective length of database: 5,762,624
effective search space: 6258209664
effective search space used: 6258209664
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 14 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 38 (21.8 bits)
S2: 64 (29.3 bits)