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_G03_T7.seq Fgr-S3_1_G03_T7 LENGTH:147bp ;
DIRECTION:5 ; CLONE:Fgr-S3_1_G03 ; CLONELIB: n/a
(147 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
pir||T04112 pol protein homolog - maize retrotransposon Opi... 44 4e-04
gb|AAL35396.1| (AF391808) Opie2a pol [Zea mays] 44 6e-04
gb|AAD09018.1| (AF090446) polyprotein [Zea mays] 43 0.001
gb|AAK00427.2|AC069324_13 (AC069324) Putative copia-type po... 43 0.001
gb|AAC64917.1| (AF053008) gag-pol polyprotein [Glycine max] 43 0.001
gb|AAM08867.1|AC113339_13 (AC113339) Putative retroelement ... 43 0.001
gb|AAL79738.1|AC096687_2 (AC096687) putative polyprotein [O... 42 0.002
gb|AAK52148.1|AC084831_2 (AC084831) putative gag-pol polypr... 42 0.002
gb|AAL25185.1|AC079852_18 (AC079852) Putative polyprotein [... 42 0.002
gb|AAK82436.1|AC091247_3 (AC091247) putative polyprotein [O... 42 0.002
gb|AAM08642.1|AC108883_15 (AC108883) Putative copia-type po... 42 0.002
dbj|BAB10503.1| (AB013391) retroelement pol polyprotein-lik... 42 0.002
gb|AAK72274.1|AC084767_14 (AC084767) putative polyprotein [... 41 0.003
gb|AAK53850.1|AC016781_4 (AC016781) Putative retroelement [... 41 0.003
gb|AAM08718.1|AC116601_11 (AC116601) Putative gag-pol polyp... 41 0.004
gb|AAD20307.1| (AF090447) copia-type pol polyprotein [Zea m... 40 0.006
gb|AAL76004.1|AF466646_12 (AF466646) putative gag-pol polyp... 40 0.006
gb|AAG52949.1| (AY016208) gag/pol polyprotein [Arabidopsis ... 39 0.011
dbj|BAA88531.1| (AP000969) Similar to copia-type pol polypr... 39 0.014
gb|AAF18630.1|AC006228_1 (AC006228) F5J5.1 [Arabidopsis tha... 38 0.024
ref|NP_564465.1| (NM_103299) gag-pol polyprotein, putative ... 38 0.024
gb|AAG10817.1|AC011808_5 (AC011808) Putative retroelement p... 38 0.031
ref|NP_177159.1| (NM_105670) hypothetical protein [Arabidop... 37 0.053
gb|AAC12735.1| (AF053721) putative retrovirus-related polyp... 37 0.069
ref|NP_174020.1| (NM_102462) polyprotein, putative; This ge... 36 0.091
gb|AAF79879.1|AC000348_32 (AC000348) T7N9.5 [Arabidopsis th... 36 0.091
ref|NP_179636.1| (NM_127605) putative retroelement pol poly... 36 0.091
ref|NP_174874.1| (NM_103337) Ty1/copia-element polyprotein ... 36 0.12
ref|NP_176060.1| (NM_104544) hypothetical protein [Arabidop... 36 0.12
pir||T14517 hypothetical protein 1 - wild cabbage transposo... 36 0.12
ref|NP_193714.1| (NM_118099) putative LTR retrotransposon [... 35 0.15
dbj|BAB68043.1| (AP003453) putative copia-type polyprotein ... 35 0.15
pir||T04760 hypothetical protein T16H5.150 - Arabidopsis th... 35 0.15
ref|NP_179011.1| (NM_126967) putative retroelement pol poly... 35 0.15
gb|AAG59661.1|AC084319_19 (AC084319) putative copia-type po... 35 0.20
ref|NP_179187.1| (NM_127147) putative retroelement pol poly... 35 0.26
ref|NP_179914.1| (NM_127897) putative retroelement pol poly... 35 0.26
ref|NP_178718.1| (NM_126677) putative retroelement pol poly... 34 0.34
dbj|BAA97287.1| (AB018120) retroelement pol polyprotein-lik... 34 0.34
ref|NP_180042.1| (NM_128027) putative retroelement pol poly... 34 0.34
ref|NP_179198.1| (NM_127158) putative retroelement pol poly... 34 0.45
ref|NP_189711.1| (NM_113991) hypothetical protein [Arabidop... 33 0.59
gb|AAF79683.1|AC022314_24 (AC022314) F9C16.17 [Arabidopsis ... 33 0.59
gb|AAL55241.1|AF295693_1 (AF295693) polyprotein [Anopheles ... 33 0.59
ref|NP_178851.1| (NM_126810) putative retroelement pol poly... 33 0.59
gb|AAM08523.1|AC068654_25 (AC068654) Putative retroelement ... 33 0.59
gb|AAK50413.1|AC021891_14 (AC021891) Putative retroelement ... 33 0.59
gb|AAL31661.1|AC079179_16 (AC079179) Putative copia-type po... 33 0.77
gb|AAF69161.1|AC007915_13 (AC007915) F27F5.19 [Arabidopsis ... 33 0.77
gb|AAL31093.1|AC091749_22 (AC091749) putative retrotranspos... 33 0.77
ref|NP_193935.1| (NM_118325) LTR retrotransposon like prote... 33 1.0
dbj|BAB10743.1| (AB010695) retroelement pol polyprotein-lik... 33 1.0
pir||T49111 hypothetical retrovirus-related pol polyprotein... 33 1.0
gb|AAK51235.1|AF287471_1 (AF287471) polyprotein [Arabidopsi... 33 1.0
pir||T02087 gag/pol polyprotein - maize retrotransposon Hop... 33 1.0
ref|NP_179258.1| (NM_127219) putative retroelement pol poly... 32 1.3
gb|AAL31689.1|AC092390_10 (AC092390) putative polyprotein [... 32 1.3
dbj|BAB03384.1| (AP002538) Similar to Zea mays retrotranspo... 32 1.3
gb|AAK52561.1|AC079853_14 (AC079853) Putative retroelement ... 32 1.7
ref|NP_194451.1| (NM_118855) putative protein [Arabidopsis ... 32 2.2
dbj|BAB90546.1| (AP003791) putative rice retrotransposon re... 32 2.2
pir||T10728 probable gag/pol polyprotein - long-staminate r... 32 2.2
ref|NP_193182.1| (NM_117525) retrovirus-related like polypr... 31 2.9
ref|NP_175784.1| (NM_104258) hypothetical protein [Arabidop... 31 2.9
gb|AAK50412.1|AC021891_13 (AC021891) Putative retroelement ... 31 2.9
dbj|BAB01972.1| (AP002064) copia-like retrotransposable ele... 31 3.8
dbj|BAB63714.1| (AP003289) putative gag/pol polyprotein [Or... 31 3.8
dbj|BAA95819.1| (AP002069) Similar to Zea mays chromosome 4... 31 3.8
ref|NP_176077.1| (NM_104561) polyprotein, putative [Arabido... 31 3.8
gb|AAM08852.1|AC113337_16 (AC113337) Putative retroelement ... 31 3.8
ref|NP_174406.1| (NM_102859) putative reverse transcriptase... 31 3.8
ref|NP_194619.1| (NM_119034) putative protein [Arabidopsis ... 31 3.8
ref|NP_189623.1| (NM_113903) Ty1/Copia-type retroelement po... 31 3.8
ref|NP_189172.1| (NM_113441) hypothetical protein [Arabidop... 31 3.8
ref|NP_193336.1| (NM_117694) reverse transcriptase like pro... 30 5.0
gb|AAL78658.1|AF405555_1 (AF405555) Hopscotch polyprotein [... 30 5.0
dbj|BAB10837.1| (AB016892) retroelement pol polyprotein-lik... 30 5.0
gb|AAF63110.1|AC006423_11 (AC006423) putative retroelement ... 30 5.0
pir||T01956 hypothetical protein T2L5.9 - Arabidopsis thali... 30 5.0
ref|NP_178887.1| (NM_126846) putative retroelement pol poly... 30 5.0
gb|AAK09230.1|AC084320_17 (AC084320) putative copia-like re... 30 6.5
ref|NP_178712.1| (NM_126671) putative retroelement pol poly... 30 6.5
ref|NP_192807.1| (NM_117137) retrotransposon like protein [... 30 6.5
dbj|BAB89929.1| (AP003309) putative gag/pol polyprotein [Or... 30 6.5
gb|AAL75759.1|AC069324_3 (AC069324) Putative pol polyprotei... 30 6.5
pir||T01908 hypothetical protein T12H20.12 - Arabidopsis th... 30 6.5
pir||T31353 polyprotein - Arabidopsis arenosa Evelknievel r... 30 6.5
dbj|BAB02990.1| (AP000736) retroelement pol polyprotein-lik... 30 6.5
gb|AAC02666.1| (AF039372) polyprotein [Arabidopsis thaliana] 30 8.5
gb|AAC02664.1| (AF039371) polyprotein [Arabidopsis thaliana] 30 8.5
gb|AAC02669.1| (AF039373) polyprotein [Arabidopsis thaliana] 30 8.5
dbj|BAB10876.1| (AB010693) polyprotein [Arabidopsis thaliana] 30 8.5
gb|AAL56548.1|AF387862_2 (AF387862) pol polyprotein [Anophe... 30 8.5
>pir||T04112 pol protein homolog - maize retrotransposon Opie-2
gb|AAC49502.1| (U68408) 5' end not determined experimentally [Zea mays]
Length = 1068
Score = 43.9 bits (102), Expect = 4e-04
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 208 HMDLFGPVAY--LSIGGSKYGLVIVDDFSRFTWVFFLQEKSE 247
>gb|AAL35396.1| (AF391808) Opie2a pol [Zea mays]
Length = 1048
Score = 43.5 bits (101), Expect = 6e-04
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 188 HMDLFGPVAY--LSIGGSKYGLVIVDDFSRFTWVFFLQDKSE 227
>gb|AAD09018.1| (AF090446) polyprotein [Zea mays]
Length = 476
Score = 42.7 bits (99), Expect = 0.001
Identities = 21/41 (51%), Positives = 26/41 (63%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKN 25
HM LFGP Y L+ YG VIVDD+SR+TWV + K+
Sbjct: 188 HMDLFGPVAY--LSIGGSKYGLVIVDDFSRFTWVFFLQDKS 226
>gb|AAK00427.2|AC069324_13 (AC069324) Putative copia-type pol polyprotein [Oryza sativa]
Length = 1377
Score = 42.7 bits (99), Expect = 0.001
Identities = 24/44 (54%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMA-CLYGFVIVDDYSRYTWVHIILYKNDV 19
HM LFGPT Y ++ + CL VIVDDYSRYTWV + K+ V
Sbjct: 692 HMDLFGPTTYKSIGGNSHCL---VIVDDYSRYTWVFFLHDKSIV 732
>gb|AAC64917.1| (AF053008) gag-pol polyprotein [Glycine max]
Length = 1550
Score = 42.7 bits (99), Expect = 0.001
Identities = 20/42 (47%), Positives = 27/42 (63%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM L GP Q +L Y +V+VDD+SR+TWV+ I K+D
Sbjct: 730 HMDLMGPMQVESLGRKR--YAYVVVDDFSRFTWVNFIREKSD 769
>gb|AAM08867.1|AC113339_13 (AC113339) Putative retroelement [Oryza sativa] [Oryza sativa
(japonica cultivar-group)]
Length = 1061
Score = 42.7 bits (99), Expect = 0.001
Identities = 24/44 (54%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMA-CLYGFVIVDDYSRYTWVHIILYKNDV 19
HM LFGPT Y ++ + CL VIVDDYSRYTWV + K+ V
Sbjct: 675 HMDLFGPTTYKSIGGNSHCL---VIVDDYSRYTWVFFLHDKSIV 715
>gb|AAL79738.1|AC096687_2 (AC096687) putative polyprotein [Oryza sativa]
Length = 890
Score = 42.0 bits (97), Expect = 0.002
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 767 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFFLHDKSE 806
>gb|AAK52148.1|AC084831_2 (AC084831) putative gag-pol polyprotein, 3'-partial [Oryza sativa]
Length = 1074
Score = 42.0 bits (97), Expect = 0.002
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 872 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFFLHDKSE 911
>gb|AAL25185.1|AC079852_18 (AC079852) Putative polyprotein [Oryza sativa]
Length = 1407
Score = 42.0 bits (97), Expect = 0.002
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 897 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFFLHDKSE 936
>gb|AAK82436.1|AC091247_3 (AC091247) putative polyprotein [Oryza sativa]
Length = 928
Score = 42.0 bits (97), Expect = 0.002
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 805 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFFLHDKSE 844
>gb|AAM08642.1|AC108883_15 (AC108883) Putative copia-type pol polyprotein [Oryza sativa]
[Oryza sativa (japonica cultivar-group)]
Length = 1866
Score = 42.0 bits (97), Expect = 0.002
Identities = 21/42 (50%), Positives = 27/42 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+SR+TWV + K++
Sbjct: 667 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFFLHDKSE 706
>dbj|BAB10503.1| (AB013391) retroelement pol polyprotein-like [Arabidopsis thaliana]
Length = 1475
Score = 42.0 bits (97), Expect = 0.002
Identities = 21/43 (48%), Positives = 28/43 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP ++T TT Y IVDDYSR TWV+++ KNDV
Sbjct: 646 HIDTWGP--FATPTTEGYKYFLTIVDDYSRATWVYLMKAKNDV 686
>gb|AAK72274.1|AC084767_14 (AC084767) putative polyprotein [Oryza sativa (japonica
cultivar-group)]
Length = 454
Score = 41.2 bits (95), Expect = 0.003
Identities = 20/36 (55%), Positives = 24/36 (66%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHI 40
HM LFGP Y L+ YG VIVDD+SR+TWV +
Sbjct: 393 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFL 426
>gb|AAK53850.1|AC016781_4 (AC016781) Putative retroelement [Oryza sativa]
Length = 916
Score = 41.2 bits (95), Expect = 0.003
Identities = 20/36 (55%), Positives = 24/36 (66%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHI 40
HM LFGP Y L+ YG VIVDD+SR+TWV +
Sbjct: 417 HMDLFGPIAY--LSIGGNKYGLVIVDDFSRFTWVFL 450
>gb|AAM08718.1|AC116601_11 (AC116601) Putative gag-pol polyprotein [Oryza sativa]
Length = 1627
Score = 40.8 bits (94), Expect = 0.004
Identities = 22/44 (50%), Positives = 29/44 (65%), Gaps = 1/44 (2%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMA-CLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ LFGPT Y ++ + CL VI+DDYSRYTWV + K+ V
Sbjct: 682 HIDLFGPTTYKSIGGNSHCL---VIIDDYSRYTWVFFLHDKSIV 722
>gb|AAD20307.1| (AF090447) copia-type pol polyprotein [Zea mays]
Length = 1063
Score = 40.0 bits (92), Expect = 0.006
Identities = 20/41 (48%), Positives = 25/41 (60%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKN 25
HM LFGP Y ++ Y VIVDDYSR+TWV + K+
Sbjct: 186 HMDLFGPIAYISIG--GSKYCLVIVDDYSRFTWVFFLQEKS 224
>gb|AAL76004.1|AF466646_12 (AF466646) putative gag-pol polyprotein [Zea mays]
Length = 1694
Score = 40.0 bits (92), Expect = 0.006
Identities = 20/41 (48%), Positives = 25/41 (60%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKN 25
HM LFGP Y ++ Y VIVDDYSR+TWV + K+
Sbjct: 1025 HMDLFGPIAYISIG--GSKYCLVIVDDYSRFTWVFFLQEKS 1063
>gb|AAG52949.1| (AY016208) gag/pol polyprotein [Arabidopsis thaliana]
Length = 1643
Score = 39.3 bits (90), Expect = 0.011
Identities = 19/42 (45%), Positives = 25/42 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM L GP Q ++ Y FV+VDD+SRY WV I K++
Sbjct: 803 HMDLMGPMQTESIAGKR--YVFVLVDDFSRYAWVRFIREKSE 842
>dbj|BAA88531.1| (AP000969) Similar to copia-type pol polyprotein. (AF105716) [Oryza
sativa (japonica cultivar-group)]
Length = 940
Score = 38.9 bits (89), Expect = 0.014
Identities = 20/42 (47%), Positives = 26/42 (61%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM LFGP Y L+ YG VIVDD+S +TWV + K++
Sbjct: 85 HMDLFGPIAY--LSIGGNKYGLVIVDDFSCFTWVFFLHDKSE 124
>gb|AAF18630.1|AC006228_1 (AC006228) F5J5.1 [Arabidopsis thaliana]
Length = 1463
Score = 38.1 bits (87), Expect = 0.024
Identities = 19/40 (47%), Positives = 24/40 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYK 28
HM L GP Q +L+ Y V+VDDYSR+TWV + K
Sbjct: 752 HMDLMGPVQTESLSGKK--YILVLVDDYSRFTWVRFLREK 789
>ref|NP_564465.1| (NM_103299) gag-pol polyprotein, putative [Arabidopsis thaliana]
Length = 1418
Score = 38.1 bits (87), Expect = 0.024
Identities = 19/40 (47%), Positives = 24/40 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYK 28
HM L GP Q +L+ Y V+VDDYSR+TWV + K
Sbjct: 780 HMDLMGPVQTESLSGKK--YILVLVDDYSRFTWVRFLREK 817
>gb|AAG10817.1|AC011808_5 (AC011808) Putative retroelement polyprotein [Arabidopsis thaliana]
Length = 1413
Score = 37.7 bits (86), Expect = 0.031
Identities = 18/43 (41%), Positives = 28/43 (64%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ ++GP +S T Y IVDD++R TWV+++ YK+DV
Sbjct: 594 HIDVWGP--FSEPTQEGYHYFLTIVDDHTRVTWVYLMKYKSDV 634
>ref|NP_177159.1| (NM_105670) hypothetical protein [Arabidopsis thaliana]
gb|AAB61111.1| (AC002062) Strong similarity to Zea mays retrotransposon Hopscotch
polyprotein (gb|U12626). [Arabidopsis thaliana]
Length = 1315
Score = 37.0 bits (84), Expect = 0.053
Identities = 19/43 (44%), Positives = 26/43 (60%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP +S T Y IVDDYSR TWV+++ K+DV
Sbjct: 467 HIDTWGP--FSVQTHDGYRYFLTIVDDYSRATWVYLLRNKSDV 507
>gb|AAC12735.1| (AF053721) putative retrovirus-related polyprotein [Lithospermum
erythrorhizon]
Length = 244
Score = 36.6 bits (83), Expect = 0.069
Identities = 16/43 (37%), Positives = 25/43 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H L+GP + ++ Y VDDYSRY W++ + +KN+V
Sbjct: 171 HTDLWGPAKVNSKD--GSWYFVTFVDDYSRYAWIYFLKHKNEV 211
>ref|NP_174020.1| (NM_102462) polyprotein, putative; This gene structure is
inaccurate, likely due to discrepancies within
overlapping bac sequences. This will be resolved asap.
In the meantime, an either full or partial translation
is provided. [Arabidopsis thaliana]
Length = 1425
Score = 36.2 bits (82), Expect = 0.091
Identities = 17/43 (39%), Positives = 27/43 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP +S T + Y IVDD+SR TW++++ K+DV
Sbjct: 608 HIDTWGP--FSVPTVDSYRYFLTIVDDFSRATWIYLLKQKSDV 648
>gb|AAF79879.1|AC000348_32 (AC000348) T7N9.5 [Arabidopsis thaliana]
Length = 1436
Score = 36.2 bits (82), Expect = 0.091
Identities = 17/43 (39%), Positives = 27/43 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP +S T + Y IVDD+SR TW++++ K+DV
Sbjct: 619 HIDTWGP--FSVPTVDSYRYFLTIVDDFSRATWIYLLKQKSDV 659
>ref|NP_179636.1| (NM_127605) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD25646.1| (AC007109) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1461
Score = 36.2 bits (82), Expect = 0.091
Identities = 17/43 (39%), Positives = 27/43 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ ++GP +S T Y IVDD+SR TW++++ K+DV
Sbjct: 629 HIDVWGP--FSVETVEGYKYFLTIVDDHSRATWIYLLKSKSDV 669
>ref|NP_174874.1| (NM_103337) Ty1/copia-element polyprotein [Arabidopsis thaliana]
gb|AAG51258.1|AC025782_3 (AC025782) Ty1/copia-element polyprotein [Arabidopsis thaliana]
Length = 1152
Score = 35.8 bits (81), Expect = 0.12
Identities = 16/43 (37%), Positives = 26/43 (60%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP Y ++ Y IVDD+SR W+H++L K++V
Sbjct: 575 HYDVWGP--YKHASSCGAHYFLTIVDDHSRAVWIHLMLAKSEV 615
>ref|NP_176060.1| (NM_104544) hypothetical protein [Arabidopsis thaliana]
gb|AAG09097.1|AC009323_8 (AC009323) Putative retroelement polyprotein [Arabidopsis thaliana]
Length = 1486
Score = 35.8 bits (81), Expect = 0.12
Identities = 16/45 (35%), Positives = 25/45 (55%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
H L+GP Y T + Y +VDDYSR W++++ K + P+
Sbjct: 565 HCDLWGP--YRTTSICGSRYFLTLVDDYSRAVWLYLLPSKQEAPK 607
>pir||T14517 hypothetical protein 1 - wild cabbage transposon Melmoth
emb|CAA72989.1| (Y12321) open reading frame 1 [Brassica oleracea]
Length = 1131
Score = 35.8 bits (81), Expect = 0.12
Identities = 17/43 (39%), Positives = 27/43 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ ++GP +S T Y IVDD+SR TW++++ K+DV
Sbjct: 578 HVDVWGP--FSVETLEGYKYFLTIVDDHSRATWIYLLQSKSDV 618
>ref|NP_193714.1| (NM_118099) putative LTR retrotransposon [Arabidopsis thaliana]
Length = 183
Score = 35.4 bits (80), Expect = 0.15
Identities = 17/43 (39%), Positives = 26/43 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP +S T Y IVDD+SR TW++++ K+DV
Sbjct: 110 HIDTWGP--FSVPTNDGFKYFLTIVDDFSRATWIYLLKNKSDV 150
>dbj|BAB68043.1| (AP003453) putative copia-type polyprotein [Oryza sativa (japonica
cultivar-group)]
dbj|BAB89833.1| (AP003288) putative copia-type polyprotein [Oryza sativa (japonica
cultivar-group)]
Length = 1433
Score = 35.4 bits (80), Expect = 0.15
Identities = 18/41 (43%), Positives = 26/41 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKN 25
H+ L GP ST++ Y F+IVDDYSR+ WV ++ K+
Sbjct: 560 HIDLCGPITPSTMSGNR--YFFLIVDDYSRWMWVFVLKTKD 598
>pir||T04760 hypothetical protein T16H5.150 - Arabidopsis thaliana (fragment)
emb|CAA19696.1| (AL024486) putative LTR retrotransposon (fragment) [Arabidopsis
thaliana]
emb|CAB78981.1| (AL161551) putative LTR retrotransposon (fragment) [Arabidopsis
thaliana]
Length = 281
Score = 35.4 bits (80), Expect = 0.15
Identities = 17/43 (39%), Positives = 26/43 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP +S T Y IVDD+SR TW++++ K+DV
Sbjct: 208 HIDTWGP--FSVPTNDGFKYFLTIVDDFSRATWIYLLKNKSDV 248
>ref|NP_179011.1| (NM_126967) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD19784.1| (AC006528) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1501
Score = 35.4 bits (80), Expect = 0.15
Identities = 16/43 (37%), Positives = 25/43 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP Y + +Y IVDDYSR W +++L K++V
Sbjct: 588 HCDVWGP--YRVPASCGAVYFLTIVDDYSRAVWTYLLLEKSEV 628
>gb|AAG59661.1|AC084319_19 (AC084319) putative copia-type pol polyprotein [Oryza sativa]
Length = 1778
Score = 35.0 bits (79), Expect = 0.20
Identities = 13/23 (56%), Positives = 20/23 (86%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKND 22
YGFVIVD++SR+TWV+ + K++
Sbjct: 788 YGFVIVDNFSRFTWVYFLHDKSE 810
>ref|NP_179187.1| (NM_127147) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD41979.1| (AC006438) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1264
Score = 34.7 bits (78), Expect = 0.26
Identities = 16/43 (37%), Positives = 27/43 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ ++GP +S T Y IVDD+SR TW++++ K++V
Sbjct: 477 HIDIWGP--FSVETVDGYQYFLTIVDDHSRATWIYLLKTKSEV 517
>ref|NP_179914.1| (NM_127897) putative retroelement pol polyprotein [Arabidopsis
thaliana]
pir||T00499 hypothetical protein T20D16.4 - Arabidopsis thaliana
gb|AAB87099.1| (AC002391) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1496
Score = 34.7 bits (78), Expect = 0.26
Identities = 16/43 (37%), Positives = 25/43 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP Y T +T +Y +VDDYSR W +++ K +V
Sbjct: 561 HGDVWGP--YRTPSTTGAVYFLTLVDDYSRSVWTYLMSSKTEV 601
>ref|NP_178718.1| (NM_126677) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAC67205.1| (AC005171) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1413
Score = 34.3 bits (77), Expect = 0.34
Identities = 15/43 (34%), Positives = 26/43 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP Y ++ +Y IVDD+SR W +++L K++V
Sbjct: 571 HCDVWGP--YRVPSSCGAVYFLTIVDDFSRSVWTYLLLAKSEV 611
>dbj|BAA97287.1| (AB018120) retroelement pol polyprotein-like [Arabidopsis thaliana]
Length = 1491
Score = 34.3 bits (77), Expect = 0.34
Identities = 15/43 (34%), Positives = 26/43 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP Y ++ +Y IVDD+SR W +++L K++V
Sbjct: 571 HCDVWGP--YRVPSSCGAVYFLTIVDDFSRSVWTYLLLAKSEV 611
>ref|NP_180042.1| (NM_128027) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD23883.1| (AC006954) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1156
Score = 34.3 bits (77), Expect = 0.34
Identities = 15/43 (34%), Positives = 26/43 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP Y ++ +Y IVDD+SR W +++L K++V
Sbjct: 149 HCDVWGP--YRVPSSCGAVYFLTIVDDFSRAVWTYLLLAKSEV 189
>ref|NP_179198.1| (NM_127158) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD26943.1| (AC007134) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1454
Score = 33.9 bits (76), Expect = 0.45
Identities = 16/43 (37%), Positives = 27/43 (62%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ ++GP +S T Y IVDD+SR TW++++ K++V
Sbjct: 618 HIDVWGP--FSVETVEGYKYFLTIVDDHSRATWMYLLKTKSEV 658
>ref|NP_189711.1| (NM_113991) hypothetical protein [Arabidopsis thaliana]
dbj|BAA97099.1| (AP002461) retroelement pol polyprotein-like [Arabidopsis thaliana]
Length = 1098
Score = 33.5 bits (75), Expect = 0.59
Identities = 16/45 (35%), Positives = 25/45 (55%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
H ++GP Y T + +Y IVDD+SR W ++ K++V R
Sbjct: 564 HCDVWGP--YRTPASCGSVYFLTIVDDFSRSVWTFLMAEKSEVSR 606
>gb|AAF79683.1|AC022314_24 (AC022314) F9C16.17 [Arabidopsis thaliana]
Length = 873
Score = 33.5 bits (75), Expect = 0.59
Identities = 16/34 (47%), Positives = 20/34 (58%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWV 46
HM L GP + Y FV+VDD++RYTWV
Sbjct: 221 HMDLMGPINVQSRAGKT--YIFVMVDDFTRYTWV 252
>gb|AAL55241.1|AF295693_1 (AF295693) polyprotein [Anopheles gambiae]
Length = 786
Score = 33.5 bits (75), Expect = 0.59
Identities = 15/42 (35%), Positives = 26/42 (61%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H + GP + +TL C Y ++DD+SRYT+V+ + K++
Sbjct: 343 HSDVCGPMEETTLG--GCRYYMTLIDDHSRYTFVYFLKKKSE 382
>ref|NP_178851.1| (NM_126810) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAM15219.1| (AC006250) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 767
Score = 33.5 bits (75), Expect = 0.59
Identities = 17/42 (40%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L GP + T++ Y FV++DDYSRY W ++ K D
Sbjct: 265 HGDLCGPI--TPKTSVGNRYIFVLIDDYSRYMWTVLLKEKGD 304
>gb|AAM08523.1|AC068654_25 (AC068654) Putative retroelement [Oryza sativa] [Oryza sativa
(japonica cultivar-group)]
Length = 1522
Score = 33.5 bits (75), Expect = 0.59
Identities = 17/42 (40%), Positives = 25/42 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM GP + ++ Y VIVDD+SRY+WV I+ K++
Sbjct: 742 HMDTVGPARVQSVGEK--WYVLVIVDDFSRYSWVFIMETKDE 781
>gb|AAK50413.1|AC021891_14 (AC021891) Putative retroelement [Oryza sativa]
Length = 1232
Score = 33.5 bits (75), Expect = 0.59
Identities = 16/42 (38%), Positives = 25/42 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM + GP + ++ Y VIVDD+SRY+WV + K++
Sbjct: 617 HMDIVGPARVQSVGGK--WYVLVIVDDFSRYSWVFFMATKDE 656
>gb|AAL31661.1|AC079179_16 (AC079179) Putative copia-type pol polyprotein [Oryza sativa]
gb|AAM08715.1|AC116601_8 (AC116601) Putative copia-type pol polyprotein [Oryza sativa]
Length = 998
Score = 33.1 bits (74), Expect = 0.77
Identities = 16/42 (38%), Positives = 24/42 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM GP + ++ Y VIVDD+SRY+WV + K++
Sbjct: 706 HMDTVGPARVQSVERK--WYVLVIVDDFSRYSWVFFMATKDE 745
>gb|AAF69161.1|AC007915_13 (AC007915) F27F5.19 [Arabidopsis thaliana]
Length = 1309
Score = 33.1 bits (74), Expect = 0.77
Identities = 17/43 (39%), Positives = 25/43 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ +GP + LT Y IVDD+SR TW +++ K+DV
Sbjct: 594 HIDTWGP--FYVLTKDGFRYFLTIVDDFSRATWNYLLKNKSDV 634
>gb|AAL31093.1|AC091749_22 (AC091749) putative retrotransposon-related protein [Oryza sativa]
Length = 1229
Score = 33.1 bits (74), Expect = 0.77
Identities = 17/42 (40%), Positives = 26/42 (61%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP++ +L AC Y I+DDYSR W + + +K+D
Sbjct: 486 HADLWGPSRKPSLGG-AC-YMLTIIDDYSRKVWPYFLKHKDD 525
>ref|NP_193935.1| (NM_118325) LTR retrotransposon like protein [Arabidopsis thaliana]
Length = 1120
Score = 32.7 bits (73), Expect = 1.0
Identities = 16/45 (35%), Positives = 25/45 (55%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
H ++GP Y T + Y IVDDYSR WV+++ K++ +
Sbjct: 351 HCDVWGP--YRTPSYSGARYFLTIVDDYSRGVWVYLMTDKSETQK 393
>dbj|BAB10743.1| (AB010695) retroelement pol polyprotein-like [Arabidopsis thaliana]
Length = 1109
Score = 32.7 bits (73), Expect = 1.0
Identities = 16/45 (35%), Positives = 25/45 (55%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
H ++GP Y T + Y IVDDYSR WV+++ K++ +
Sbjct: 351 HCDVWGP--YRTPSYSGARYFLTIVDDYSRGVWVYLMTDKSETQK 393
>pir||T49111 hypothetical retrovirus-related pol polyprotein AT4g22040 -
Arabidopsis thaliana
emb|CAA18107.1| (AL022140) LTR retrotransposon like protein [Arabidopsis thaliana]
emb|CAB79159.1| (AL161556) LTR retrotransposon like protein [Arabidopsis thaliana]
Length = 1109
Score = 32.7 bits (73), Expect = 1.0
Identities = 16/45 (35%), Positives = 25/45 (55%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
H ++GP Y T + Y IVDDYSR WV+++ K++ +
Sbjct: 351 HCDVWGP--YRTPSYSGARYFLTIVDDYSRGVWVYLMTDKSETQK 393
>gb|AAK51235.1|AF287471_1 (AF287471) polyprotein [Arabidopsis thaliana]
Length = 1453
Score = 32.7 bits (73), Expect = 1.0
Identities = 16/42 (38%), Positives = 24/42 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ ++ Y V VDDYSRY+W + + K+D
Sbjct: 519 HCDLWGPSP--VVSKQGFKYYVVFVDDYSRYSWFYPLKAKSD 558
>pir||T02087 gag/pol polyprotein - maize retrotransposon Hopscotch
gb|AAA57005.1| (U12626) copia-like retrotransposon Hopscotch polyprotein [Zea
mays]
Length = 1439
Score = 32.7 bits (73), Expect = 1.0
Identities = 10/24 (41%), Positives = 19/24 (78%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y +DDYS++TW++++ +K+DV
Sbjct: 535 YYVSFIDDYSKFTWIYLLRHKSDV 558
>ref|NP_179258.1| (NM_127219) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD24600.1| (AC005825) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1333
Score = 32.3 bits (72), Expect = 1.3
Identities = 15/41 (36%), Positives = 24/41 (57%)
Frame = -1
Query: 138 LFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVP 16
L+GP Y T + Y I+DDYSR W++++ K++ P
Sbjct: 454 LWGP--YRTPSHTGARYFLTIIDDYSRGVWLYLLNDKSEAP 492
>gb|AAL31689.1|AC092390_10 (AC092390) putative polyprotein [Oryza sativa]
Length = 282
Score = 32.3 bits (72), Expect = 1.3
Identities = 16/38 (42%), Positives = 22/38 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIIL 34
+M LFGP Y L+ YG IVD++S +TWV +
Sbjct: 185 NMDLFGPIAY--LSNGGNKYGLAIVDNFSCFTWVFFFM 220
>dbj|BAB03384.1| (AP002538) Similar to Zea mays retrotransposon Opie-2 (T04112)
[Oryza sativa (japonica cultivar-group)]
Length = 1410
Score = 32.3 bits (72), Expect = 1.3
Identities = 15/42 (35%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM GP + ++ Y V+VDD+SRY+WV+ + K +
Sbjct: 565 HMNTVGPARVQSVGGK--WYVLVVVDDFSRYSWVYFLESKEE 604
>gb|AAK52561.1|AC079853_14 (AC079853) Putative retroelement pol polyprotein [Oryza sativa]
Length = 1326
Score = 32.0 bits (71), Expect = 1.7
Identities = 15/42 (35%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP++ + L Y I+DDYSR W + + +K+D
Sbjct: 489 HTDLWGPSRKAYLG--GARYMLTIIDDYSRKVWPYFLKHKDD 528
>ref|NP_194451.1| (NM_118855) putative protein [Arabidopsis thaliana]
pir||T05745 hypothetical protein M4I22.20 - Arabidopsis thaliana
emb|CAA19715.1| (AL030978) putative protein [Arabidopsis thaliana]
emb|CAB79576.1| (AL161566) putative protein [Arabidopsis thaliana]
Length = 1318
Score = 31.6 bits (70), Expect = 2.2
Identities = 14/42 (33%), Positives = 25/42 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GPT +++ Y V +D YSR++W++ + K+D
Sbjct: 331 HCDLWGPTTITSVQGFR--YYAVFIDHYSRFSWIYPLKLKSD 370
>dbj|BAB90546.1| (AP003791) putative rice retrotransposon retrofit gag/pol
polyprotein [Oryza sativa (japonica cultivar-group)]
Length = 1448
Score = 31.6 bits (70), Expect = 2.2
Identities = 9/24 (37%), Positives = 19/24 (78%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y +DD+S++TW++++ YK++V
Sbjct: 538 YYVSFIDDFSKFTWIYLLKYKSEV 561
>pir||T10728 probable gag/pol polyprotein - long-staminate rice retrotransposon
retrofit
gb|AAB82754.1| (U72725) retrofit [Oryza longistaminata]
Length = 1445
Score = 31.6 bits (70), Expect = 2.2
Identities = 9/24 (37%), Positives = 19/24 (78%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y +DD+S++TW++++ YK++V
Sbjct: 534 YYVSFIDDFSKFTWIYLLKYKSEV 557
>ref|NP_193182.1| (NM_117525) retrovirus-related like polyprotein [Arabidopsis
thaliana]
pir||G71406 probable retrovirus-related polyprotein - Arabidopsis thaliana
emb|CAB10225.1| (Z97336) retrovirus-related like polyprotein [Arabidopsis thaliana]
emb|CAB78488.1| (AL161539) retrovirus-related like polyprotein [Arabidopsis
thaliana]
Length = 1489
Score = 31.2 bits (69), Expect = 2.9
Identities = 15/43 (34%), Positives = 25/43 (57%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H+ ++GP +S + Y +VDD +R TWV+++ K DV
Sbjct: 637 HLDIWGP--FSIESIEGFRYFLTVVDDCTRTTWVYMLRNKKDV 677
>ref|NP_175784.1| (NM_104258) hypothetical protein [Arabidopsis thaliana]
gb|AAF02855.1|AC009324_4 (AC009324) Similar to retrotransposon proteins [Arabidopsis
thaliana]
Length = 1522
Score = 31.2 bits (69), Expect = 2.9
Identities = 15/42 (35%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ S++ Y V +D YSR+TW + + K+D
Sbjct: 520 HCDLWGPSPTSSVQGFR--YYVVFIDHYSRFTWFYPLKLKSD 559
>gb|AAK50412.1|AC021891_13 (AC021891) Putative retroelement [Oryza sativa]
Length = 1217
Score = 31.2 bits (69), Expect = 2.9
Identities = 17/41 (41%), Positives = 22/41 (53%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKN 25
HM L GP ST Y +IVDD+S + WV +I K+
Sbjct: 549 HMDLCGPITPSTFAGNR--YFMLIVDDFSNWMWVFVIKLKD 587
>dbj|BAB01972.1| (AP002064) copia-like retrotransposable element [Arabidopsis
thaliana]
Length = 1499
Score = 30.8 bits (68), Expect = 3.8
Identities = 14/43 (32%), Positives = 23/43 (52%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H + GP Q ++ Y +DD+SR TWV+ + K++V
Sbjct: 520 HSDVCGPMQTESIN--GSRYFLTFIDDFSRMTWVYFLKNKSEV 560
>dbj|BAB63714.1| (AP003289) putative gag/pol polyprotein [Oryza sativa (japonica
cultivar-group)]
Length = 1449
Score = 30.8 bits (68), Expect = 3.8
Identities = 9/24 (37%), Positives = 19/24 (78%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y +DD+S++TW+++I +K++V
Sbjct: 534 YYVSFIDDFSKFTWIYLIKFKSEV 557
>dbj|BAA95819.1| (AP002069) Similar to Zea mays chromosome 4 22 kDa zein-associated
intercluster region, copia-type pol polyprotein.
(AF105716) [Oryza sativa (japonica cultivar-group)]
Length = 925
Score = 30.8 bits (68), Expect = 3.8
Identities = 12/23 (52%), Positives = 17/23 (73%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKND 22
Y VIVDD+SRY+WV + K++
Sbjct: 237 YVLVIVDDFSRYSWVFFMATKDE 259
>ref|NP_176077.1| (NM_104561) polyprotein, putative [Arabidopsis thaliana]
gb|AAG50751.1|AC079733_19 (AC079733) polyprotein, putative [Arabidopsis thaliana]
Length = 1468
Score = 30.8 bits (68), Expect = 3.8
Identities = 15/45 (33%), Positives = 24/45 (53%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
H ++GP Y + Y IVDDYSR WV+++ K++ +
Sbjct: 575 HCDVWGP--YRAPSYSGARYFLTIVDDYSRGVWVYLMTDKSETQK 617
>gb|AAM08852.1|AC113337_16 (AC113337) Putative retroelement [Oryza sativa] [Oryza sativa
(japonica cultivar-group)]
Length = 1318
Score = 30.8 bits (68), Expect = 3.8
Identities = 15/42 (35%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
HM GP + ++ Y VIV+D+SRY+WV + K++
Sbjct: 684 HMDTVGPARVQSVGGK--WYVLVIVEDFSRYSWVFFMATKDE 723
>ref|NP_174406.1| (NM_102859) putative reverse transcriptase [Arabidopsis thaliana]
gb|AAD21687.1| (AC004793) Strong similarity to gi|3600044 T12H20.12 protease
homolog from Arabidopsis thaliana BAC gb|AF080119 and is
a member of the reverse transcriptase family PF|00078
Length = 1415
Score = 30.8 bits (68), Expect = 3.8
Identities = 14/42 (33%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ ++ Y + VDDYSRY+W + + K++
Sbjct: 516 HCDLWGPSP--VVSNQGLKYYAIFVDDYSRYSWFYPLHNKSE 555
>ref|NP_194619.1| (NM_119034) putative protein [Arabidopsis thaliana]
pir||T08945 hypothetical protein F25O24.20 - Arabidopsis thaliana
emb|CAB43904.1| (AL078469) putative protein [Arabidopsis thaliana]
emb|CAB81478.1| (AL161573) putative protein [Arabidopsis thaliana]
Length = 1415
Score = 30.8 bits (68), Expect = 3.8
Identities = 13/42 (30%), Positives = 24/42 (56%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP +++ Y + +D+YSR+TW + + K+D
Sbjct: 486 HCDLWGPAP--VVSSQGFRYYVIFIDNYSRFTWFYPLRLKSD 525
>ref|NP_189623.1| (NM_113903) Ty1/Copia-type retroelement polyprotein [Arabidopsis
thaliana]
Length = 1348
Score = 30.8 bits (68), Expect = 3.8
Identities = 14/43 (32%), Positives = 23/43 (52%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H + GP Q ++ Y +DD+SR TWV+ + K++V
Sbjct: 520 HSDVCGPMQTESIN--GSRYFLTFIDDFSRMTWVYFLKNKSEV 560
>ref|NP_189172.1| (NM_113441) hypothetical protein [Arabidopsis thaliana]
Length = 1343
Score = 30.8 bits (68), Expect = 3.8
Identities = 16/42 (38%), Positives = 23/42 (54%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L GP ST Y FV++DD+SRY W ++ K++
Sbjct: 489 HGDLCGPISPSTAAKKR--YVFVLIDDHSRYMWSILLKEKSE 528
>ref|NP_193336.1| (NM_117694) reverse transcriptase like protein [Arabidopsis thaliana]
pir||B71426 hypothetical protein - Arabidopsis thaliana
emb|CAB10380.1| (Z97340) reverse transcriptase like protein [Arabidopsis thaliana]
emb|CAB78643.1| (AL161543) reverse transcriptase like protein [Arabidopsis thaliana]
Length = 1942
Score = 30.4 bits (67), Expect = 5.0
Identities = 13/42 (30%), Positives = 23/42 (53%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ ++ Y + +D+YSRY W + + K+D
Sbjct: 1347 HCDLWGPSP--VMSVQGFRYYVIFIDNYSRYCWFYPLKLKSD 1386
Score = 30.4 bits (67), Expect = 5.0
Identities = 13/42 (30%), Positives = 23/42 (53%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ ++ Y + +D+YSRY W + + K+D
Sbjct: 447 HCDLWGPSP--VMSVQGFRYYVIFIDNYSRYCWFYPLKLKSD 486
>gb|AAL78658.1|AF405555_1 (AF405555) Hopscotch polyprotein [Fagus sylvatica]
Length = 226
Score = 30.4 bits (67), Expect = 5.0
Identities = 10/23 (43%), Positives = 18/23 (77%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKND 22
Y + VDD++RYTW++ + +K+D
Sbjct: 11 YYVIFVDDHTRYTWLYPLKHKSD 33
>dbj|BAB10837.1| (AB016892) retroelement pol polyprotein-like [Arabidopsis thaliana]
Length = 1462
Score = 30.4 bits (67), Expect = 5.0
Identities = 14/44 (31%), Positives = 23/44 (51%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDVP 16
H L+GP Y T + Y +VD+Y+R W++++ K P
Sbjct: 529 HCDLWGP--YRTTSICGSNYFLTLVDNYTRAVWLYLLPSKQTAP 570
>gb|AAF63110.1|AC006423_11 (AC006423) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1150
Score = 30.4 bits (67), Expect = 5.0
Identities = 16/42 (38%), Positives = 23/42 (54%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L GP ST Y FV++DD+SRY W ++ K++
Sbjct: 372 HGDLCGPITPSTAAGNR--YVFVLIDDHSRYMWTILLKEKSE 411
>pir||T01956 hypothetical protein T2L5.9 - Arabidopsis thaliana
gb|AAC62795.1| (AF096371) contains similarity to retroviral aspartyl proteases
(Pfam: rvp.hmm, score: 11.80) [Arabidopsis thaliana]
Length = 1244
Score = 30.4 bits (67), Expect = 5.0
Identities = 12/24 (50%), Positives = 18/24 (75%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y IVDD+SR TWV+++ K++V
Sbjct: 607 YFLTIVDDHSRATWVYLLKTKSEV 630
>ref|NP_178887.1| (NM_126846) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAD15376.1| (AC006136) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 962
Score = 30.4 bits (67), Expect = 5.0
Identities = 18/42 (42%), Positives = 22/42 (51%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L GP ST Y FVI+DD SRY W ++ K+D
Sbjct: 816 HGDLCGPITPSTHAGNK--YIFVIIDDKSRYMWTALLKEKSD 855
>gb|AAK09230.1|AC084320_17 (AC084320) putative copia-like retrotransposon Hopscotch
polyprotein [Oryza sativa (japonica cultivar-group)]
gb|AAK72882.1|AC091123_1 (AC091123) putative gag-pol protein [Oryza sativa]
Length = 1219
Score = 30.0 bits (66), Expect = 6.5
Identities = 13/43 (30%), Positives = 24/43 (55%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKNDV 19
H ++GP S A Y +DDYS++ W++ + +K++V
Sbjct: 507 HSDVWGPASDSV---GAKRYYVSFIDDYSKFVWIYFLKFKSEV 546
>ref|NP_178712.1| (NM_126671) putative retroelement pol polyprotein [Arabidopsis
thaliana]
gb|AAC67200.1| (AC005171) putative retroelement pol polyprotein [Arabidopsis
thaliana]
Length = 1402
Score = 30.0 bits (66), Expect = 6.5
Identities = 13/42 (30%), Positives = 25/42 (58%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ +++ Y V +D YSR++W++ + K+D
Sbjct: 526 HCDLWGPSPITSVQGFR--YYAVFIDHYSRFSWIYPLKLKSD 565
>ref|NP_192807.1| (NM_117137) retrotransposon like protein [Arabidopsis thaliana]
pir||T04204 hypothetical protein T4F9.150 - Arabidopsis thaliana
emb|CAB40035.1| (AL049523) retrotransposon like protein [Arabidopsis thaliana]
emb|CAB81170.1| (AL161518) retrotransposon like protein [Arabidopsis thaliana]
Length = 1515
Score = 30.0 bits (66), Expect = 6.5
Identities = 13/42 (30%), Positives = 23/42 (53%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP ++ Y + +D+YSR+TW + + K+D
Sbjct: 517 HCDLWGPAPVTS--AQGFQYYVIFIDNYSRFTWFYPLKLKSD 556
>dbj|BAB89929.1| (AP003309) putative gag/pol polyprotein [Oryza sativa (japonica
cultivar-group)]
Length = 1090
Score = 30.0 bits (66), Expect = 6.5
Identities = 11/33 (33%), Positives = 20/33 (60%)
Frame = -1
Query: 111 LTTMACLYGFVIVDDYSRYTWVHIILYKNDVPR 13
++T Y V++DD+S + W ++ K+DV R
Sbjct: 193 MSTSGFKYYLVVLDDFSHFCWTFLLRLKSDVHR 225
>gb|AAL75759.1|AC069324_3 (AC069324) Putative pol polyprotein [Oryza sativa]
gb|AAL91607.1|AC099400_13 (AC099400) Putative pol polyprotein [Oryza sativa (japonica
cultivar-group)]
Length = 1005
Score = 30.0 bits (66), Expect = 6.5
Identities = 14/42 (33%), Positives = 23/42 (54%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP+ +L Y I+DD+SR W + + +K+D
Sbjct: 226 HADLWGPSHKPSLG--GARYMLTIIDDHSRKVWPYFLKHKDD 265
>pir||T01908 hypothetical protein T12H20.12 - Arabidopsis thaliana
gb|AAC35532.1| (AF080119) contains similarity to proteases [Arabidopsis thaliana]
Length = 1392
Score = 30.0 bits (66), Expect = 6.5
Identities = 13/42 (30%), Positives = 23/42 (53%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H L+GP ++ Y + +D+YSR+TW + + K+D
Sbjct: 520 HCDLWGPAPVTS--AQGFQYYVIFIDNYSRFTWFYPLKLKSD 559
>pir||T31353 polyprotein - Arabidopsis arenosa Evelknievel retrotransposon
(fragment)
gb|AAC02672.1| (AF039376) polyprotein [Arabidopsis arenosa]
Length = 1390
Score = 30.0 bits (66), Expect = 6.5
Identities = 12/24 (50%), Positives = 17/24 (70%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y VIVD Y+RYTW++ + K+ V
Sbjct: 546 YYLVIVDHYTRYTWLYPLRQKSQV 569
>dbj|BAB02990.1| (AP000736) retroelement pol polyprotein-like [Arabidopsis thaliana]
Length = 1250
Score = 30.0 bits (66), Expect = 6.5
Identities = 11/23 (47%), Positives = 17/23 (73%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKND 22
Y FV++DD+SRY W ++ KN+
Sbjct: 451 YIFVLIDDHSRYMWSILLKEKNE 473
>gb|AAC02666.1| (AF039372) polyprotein [Arabidopsis thaliana]
Length = 1451
Score = 29.6 bits (65), Expect = 8.5
Identities = 12/24 (50%), Positives = 17/24 (70%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y VIVD Y+RYTW++ + K+ V
Sbjct: 546 YYLVIVDHYTRYTWLYPLRKKSQV 569
>gb|AAC02664.1| (AF039371) polyprotein [Arabidopsis thaliana]
Length = 1451
Score = 29.6 bits (65), Expect = 8.5
Identities = 12/24 (50%), Positives = 17/24 (70%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y VIVD Y+RYTW++ + K+ V
Sbjct: 546 YYLVIVDHYTRYTWLYPLRKKSQV 569
>gb|AAC02669.1| (AF039373) polyprotein [Arabidopsis thaliana]
Length = 1451
Score = 29.6 bits (65), Expect = 8.5
Identities = 12/24 (50%), Positives = 17/24 (70%)
Frame = -1
Query: 90 YGFVIVDDYSRYTWVHIILYKNDV 19
Y VIVD Y+RYTW++ + K+ V
Sbjct: 546 YYLVIVDHYTRYTWLYPLRKKSQV 569
>dbj|BAB10876.1| (AB010693) polyprotein [Arabidopsis thaliana]
Length = 1429
Score = 29.6 bits (65), Expect = 8.5
Identities = 14/40 (35%), Positives = 23/40 (57%), Gaps = 6/40 (15%)
Frame = -1
Query: 120 YSTLTTMACL------YGFVIVDDYSRYTWVHIILYKNDV 19
Y+ + T C+ Y VIVD ++RYTW++ + K+ V
Sbjct: 511 YTDVWTSPCISVDNYKYYLVIVDHFTRYTWMYPLKQKSQV 550
>gb|AAL56548.1|AF387862_2 (AF387862) pol polyprotein [Anopheles gambiae]
Length = 942
Score = 29.6 bits (65), Expect = 8.5
Identities = 14/42 (33%), Positives = 25/42 (59%)
Frame = -1
Query: 147 HMALFGPTQYSTLTTMACLYGFVIVDDYSRYTWVHIILYKND 22
H + GP +T+T+ Y ++DD+SRYT V+ + K++
Sbjct: 78 HTDICGPM--NTVTSGGSRYFLTMIDDFSRYTTVYFLKRKSE 117
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: 84,318,521
Number of Sequences: 922381
Number of extensions: 1167906
Number of successful extensions: 2730
Number of sequences better than 10.0: 186
Number of HSP's better than 10.0 without gapping: 2721
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): 2730
length of database: 289,601,141
effective HSP length: 24
effective length of database: 267,463,997
effective search space used: 6419135928
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)