The query sequence for this search has been filtered. Filtering
eliminates low complexity regions that commonly give spuriously high
scores that reflect compositional bias rather than significant
position-by-position alignment. Filtering can eliminate these potentially
confounding matches (e.g., hits against proline-rich regions or poly-A
tails) from the blast reports, leaving regions whose blast statistics
reflect the specificity of their pairwise alignment.
BLASTX 2.2.3 [Apr-24-2002]
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= Fgr-S3_1_A16_T7.seq Fgr-S3_1_A16_T7 LENGTH:154bp ;
DIRECTION:5 ; CLONE:Fgr-S3_1_A16 ; CLONELIB: n/a
(154 letters)
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
922,381 sequences; 289,601,141 total letters
Score E
Sequences producing significant alignments: (bits) Value
dbj|BAA22288.1| (D85597) polyprotein [Oryza australiensis] 45 2e-04
pir||T17429 gag-pol polyprotein - maize copia-like retrotra... 34 0.45
gb|AAD12994.1| (AF082130) gag-pol polyprotein [Zea mays] 34 0.45
dbj|BAB89089.1| (AP003372) putative gag-pol polyprotein [Or... 31 2.9
gb|AAK70633.1|AC091238_11 (AC091238) Putative gag-pol polyp... 30 4.9
gb|AAD08711.1| (AF115482) topoisomerase I [Nicotiana tabacu... 30 6.5
emb|CAD19427.1| (AL359716) possible mitochondrial endonucle... 30 6.5
gb|AAM00995.1|AC090482_24 (AC090482) Hypothetical protein w... 30 6.5
>dbj|BAA22288.1| (D85597) polyprotein [Oryza australiensis]
Length = 1317
Score = 45.1 bits (105), Expect = 2e-04
Identities = 20/38 (52%), Positives = 27/38 (70%)
Frame = +2
Query: 20 CNSKQGLRIKRRLAKDEVTMRVGNGSKVDVIAVGTLPV 133
C S QG+R R L + EV +RVGNG+ V +AVGT+P+
Sbjct: 313 CKSLQGMRRSRGLRRGEVNLRVGNGASVATVAVGTVPL 350
>pir||T17429 gag-pol polyprotein - maize copia-like retrotransposon Sto-4
gb|AAD12997.1| (AF082133) gag-pol polyprotein [Zea mays]
Length = 1406
Score = 33.9 bits (76), Expect = 0.45
Identities = 17/35 (48%), Positives = 22/35 (62%)
Frame = +2
Query: 23 NSKQGLRIKRRLAKDEVTMRVGNGSKVDVIAVGTL 127
NS QGLR +RL K T+RV NG + V A+G +
Sbjct: 313 NSLQGLRTSQRLPKGRRTIRVANGVEAAVEAIGDI 347
>gb|AAD12994.1| (AF082130) gag-pol polyprotein [Zea mays]
Length = 595
Score = 33.9 bits (76), Expect = 0.45
Identities = 17/35 (48%), Positives = 22/35 (62%)
Frame = +2
Query: 23 NSKQGLRIKRRLAKDEVTMRVGNGSKVDVIAVGTL 127
NS QGLR +RL K T+RV NG + V A+G +
Sbjct: 313 NSLQGLRTSQRLPKGRRTIRVANGVEAAVEAIGDI 347
>dbj|BAB89089.1| (AP003372) putative gag-pol polyprotein [Oryza sativa (japonica
cultivar-group)]
Length = 1397
Score = 31.2 bits (69), Expect = 2.9
Identities = 16/38 (42%), Positives = 21/38 (55%)
Frame = +2
Query: 20 CNSKQGLRIKRRLAKDEVTMRVGNGSKVDVIAVGTLPV 133
CN + R R + E T+RV NG + V AVG LP+
Sbjct: 320 CNCLKAFRSTRTTQRRESTIRVANGVEEKVEAVGDLPL 357
>gb|AAK70633.1|AC091238_11 (AC091238) Putative gag-pol polyprotein [Oryza sativa]
Length = 1225
Score = 30.4 bits (67), Expect = 4.9
Identities = 14/33 (42%), Positives = 21/33 (63%)
Frame = +2
Query: 23 NSKQGLRIKRRLAKDEVTMRVGNGSKVDVIAVG 121
NS QG ++R L + E +RV NG + +V A+G
Sbjct: 333 NSLQGFAMRRTLRRGERRIRVANGVETEVEAIG 365
>gb|AAD08711.1| (AF115482) topoisomerase I [Nicotiana tabacum]
gb|AAK69776.1| (AY038803) topoisomerase I [Nicotiana tabacum]
Length = 852
Score = 30.0 bits (66), Expect = 6.5
Identities = 12/32 (37%), Positives = 23/32 (71%)
Frame = +2
Query: 8 RGRGCNSKQGLRIKRRLAKDEVTMRVGNGSKV 103
RGRG + K G ++KRR+ +++T+ +G G+ +
Sbjct: 476 RGRGEHPKMG-KLKRRIRPNDITINIGKGAPI 506
>emb|CAD19427.1| (AL359716) possible mitochondrial endonuclease [Leishmania major]
Length = 859
Score = 30.0 bits (66), Expect = 6.5
Identities = 15/41 (36%), Positives = 21/41 (50%)
Frame = +3
Query: 24 TRNRDYGLSEDWLRTR*RCAWGMVPKSM*SPSARYLYLPGR 146
TR DYG + +WL C W +P+ + P+ LY P R
Sbjct: 222 TRRLDYGHAAEWLAACTGCRW--LPQRLSRPTLLKLYSPAR 260
>gb|AAM00995.1|AC090482_24 (AC090482) Hypothetical protein with similarity to putative
retroelement [Oryza sativa] [Oryza sativa (japonica
cultivar-group)]
Length = 371
Score = 30.0 bits (66), Expect = 6.5
Identities = 15/36 (41%), Positives = 20/36 (54%)
Frame = +2
Query: 20 CNSKQGLRIKRRLAKDEVTMRVGNGSKVDVIAVGTL 127
CN +G R R + E ++RV NG + V AVG L
Sbjct: 312 CNCLKGFRSMRTTQRSERSIRVANGVEAKVEAVGDL 347
Database: All non-redundant GenBank CDS
translations+PDB+SwissProt+PIR+PRF
Posted date: May 11, 2002 4:54 AM
Number of letters in database: 289,601,141
Number of sequences in database: 922,381
Lambda K H
0.318 0.135 0.00
Gapped
Lambda K H
0.267 0.0410 4.94e-324
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 88,989,598
Number of Sequences: 922381
Number of extensions: 1299792
Number of successful extensions: 3596
Number of sequences better than 10.0: 16
Number of HSP's better than 10.0 without gapping: 3549
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): 3595
length of database: 289,601,141
effective HSP length: 26
effective length of database: 265,619,235
effective search space used: 6374861640
frameshift window, decay const: 50, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)