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= AC148154.9 + phase: 0 /pseudo
         (481 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...    52  2e-14
TC224482 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, part...    61  1e-09
AW184779                                                               43  9e-06
TC212032 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, part...    32  0.82

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

 Score = 52.4 bits (124), Expect(2) = 2e-14
 Identities = 44/129 (34%), Positives = 67/129 (51%)
 Frame = +3

Query: 66  *TLVLRHQTVLAEP*VSAGCFQARQEDLEKIGQ*IPVRWRYSVQEKL*HGIVKMC**T*S 125
           * LV RHQ +  +  + A   +   ED+EK+G       +++V EK  H    +C     
Sbjct: 132 *ALVFRHQAICHKQRIPARDCRQ**EDIEKVGGRFLHERKHTV*EKPRHETSAVCGCQGG 311

Query: 126 GAVNA*CT*RYLRDPCYRAYYVKEVVTSRLLLDDHGA*LLPIRQKMPQMSNLC**DSCAS 185
            + +    *  + +   RA Y +E   SRLLL  HG *LL   ++MPQMS++  *  C +
Sbjct: 312 KSHDRGSP*GLVWNARQRACYGQEDPKSRLLLAYHGK*LLCPCEEMPQMSSVRR*CQCPT 491

Query: 186 ACSQCYVIP 194
           A S+C+V+P
Sbjct: 492 ASSECHVLP 518



 Score = 44.7 bits (104), Expect(2) = 2e-14
 Identities = 39/104 (37%), Positives = 47/104 (44%)
 Frame = +2

Query: 194 PQGRSQCGAST*LEELNRRLQMVIVSS*WQLTTSPSGLKQHLIPM*PSKW*LSSSKTTSS 253
           P G S CG       L+ R +MVI SS  +   SPSG +Q  IP     W   S +  SS
Sbjct: 515 PLGLSPCGE*MSSGPLSPRPRMVIASSS*R*IISPSGSRQLPIPTS*GVWWSGSLRKRSS 694

Query: 254 VDMVFPARLLPTMVPT*TIMWCKLFVKNSKLSIITLLPIDLR*M 297
            DMV   RL  T  PT*       F ++ K SI    P   R*+
Sbjct: 695 ADMVCQGRLSRTTAPT*ITR*WGKFARSLKSSITIPXPTGQR*I 826


>TC224482 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, partial (6%)
          Length = 669

 Score = 60.8 bits (146), Expect = 1e-09
 Identities = 60/165 (36%), Positives = 80/165 (48%), Gaps = 1/165 (0%)
 Frame = +2

Query: 303 PTRISRELSKRW*PLTRTGMRCYPMLCMVTVLQCAVQPGQPLFLLYMVWKQFFLWK*RSR 362
           P RIS+ LSKR    TR G RC      VT LQC  Q GQ     YM W+  +  +*+SR
Sbjct: 8   PIRISKRLSKR*PCHTRIGTRCSHSRYTVTGLQCERQLGQRRSHWYMGWRLCYRLR*KSR 187

Query: 363 LSG*SWKQSYLR-LNGAKAGMIS*I*LRKNVWMPWLVDIHIKQE*RLLLTRKFILENSR* 421
             G SW+    R  +G K  MIS   LR +   P ++     +E*R+  TR++   +S  
Sbjct: 188 H*G-SWQNPD*RNQSGLKRAMISSTSLRVSA*RP*VMGACTSKE*RVHSTRRYACASSMR 364

Query: 422 GNLY*KEG*ASNPTQGASGHLTMKVLMLSRRPSPVVL*SLHTWMV 466
             L *++    + T   +G  T K L+L R   P     L TWMV
Sbjct: 365 ETLC*RKCPMLSRTIEGNGPRTTKGLLL*RGLFPEEPWCLPTWMV 499


>AW184779 
          Length = 432

 Score = 42.7 bits (99), Expect(2) = 9e-06
 Identities = 27/46 (58%), Positives = 31/46 (66%)
 Frame = +1

Query: 200 CGAST*LEELNRRLQMVIVSS*WQLTTSPSGLKQHLIPM*PSKW*L 245
           CGA T* E L+ RLQM I S * QLTTSP+G KQ  + +*   W*L
Sbjct: 292 CGA*T*SEPLSPRLQMDITSF*SQLTTSPNGSKQFRMLV*LGVW*L 429



 Score = 24.6 bits (52), Expect(2) = 9e-06
 Identities = 24/69 (34%), Positives = 33/69 (47%), Gaps = 1/69 (1%)
 Frame = +3

Query: 105 RYSVQEKL*HGIVKMC**T*SGAVNA-*CT*RYLRDPCYRAYYVKEVVTSRLLLDDHGA* 163
           +Y +QE+ *HG+  MC   * G  NA    *  L + C    +  E   S +LL  +G  
Sbjct: 9   KYPIQEEP*HGVASMC-GC*GG*ANAGRGA*GILWNTCQHTCHGPEDSESGVLLAHYGER 185

Query: 164 LLPIRQKMP 172
           LL    +MP
Sbjct: 186 LLHPCVEMP 212


>TC212032 similar to UP|Q6WAY3 (Q6WAY3) Gag/pol polyprotein, partial (3%)
          Length = 803

 Score = 31.6 bits (70), Expect = 0.82
 Identities = 30/101 (29%), Positives = 48/101 (46%)
 Frame = +1

Query: 15  NG*CSCYSIFHVPSKPLE*RAINQSTTPRKTFACVCYWGCDRSGW*KCG*L*TLVLRHQT 74
           NG C+C+   HVP+       ++      +T   +       SG    G  * LV  +Q 
Sbjct: 397 NGRCACHFSVHVPANTAWGPTVH*V*VSWQTRTLL-------SGGRGTG-R*ALVF*YQA 552

Query: 75  VLAEP*VSAGCFQARQEDLEKIGQ*IPVRWRYSVQEKL*HG 115
           +  +  V  G F+ RQ++ E+IG  +    +++VQEK *HG
Sbjct: 553 IR*KQRVPTGGFRQRQKEKEEIGSRLLHERKHTVQEKP*HG 675


  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
   0.364    0.161    0.620 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,571,793
Number of Sequences: 63676
Number of extensions: 336856
Number of successful extensions: 4613
Number of sequences better than 10.0: 8
Number of HSP's better than 10.0 without gapping: 2522
Number of HSP's successfully gapped in prelim test: 156
Number of HSP's that attempted gapping in prelim test: 2050
Number of HSP's gapped (non-prelim): 2768
length of query: 481
length of database: 12,639,632
effective HSP length: 101
effective length of query: 380
effective length of database: 6,208,356
effective search space: 2359175280
effective search space used: 2359175280
frameshift window, decay const: 50,  0.1
T: 13
A: 40
X1: 14 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 36 (21.6 bits)
S2: 61 (28.1 bits)