BLAST2 result
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= AC138453.6 - phase: 0 /pseudo
(667 letters)
Database: GMGI
63,676 sequences; 37,918,896 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
BM188122 weakly similar to PIR|I46200|I4620 retrovirus-related r... 63 2e-18
TC232593 weakly similar to UP|Q9XG91 (Q9XG91) Tpv2-1c protein (F... 52 1e-06
CO981347 37 0.028
AW185460 34 0.18
TC228845 weakly similar to GB|AAO44030.1|28466843|BT004764 At3g5... 34 0.24
AI855818 weakly similar to GP|21741393|e OSJNBb0051N19.6 {Oryza ... 34 0.24
BI701169 33 0.53
TC204438 homologue to UP|Q84VH6 (Q84VH6) Gag-pol polyprotein, co... 32 0.69
BF596801 weakly similar to GP|29423270|g gag-pol polyprotein {Gl... 31 1.5
BM886329 30 4.5
TC212454 29 5.9
TC222253 similar to UP|Q9ZQE4 (Q9ZQE4) Copia-like retroelement p... 25 8.3
>BM188122 weakly similar to PIR|I46200|I4620 retrovirus-related reverse
transcriptase homolog - pine (Pinus coulteri)
retrotransposon copia-like, partial (53%)
Length = 420
Score = 62.8 bits (151), Expect(2) = 2e-18
Identities = 37/63 (58%), Positives = 47/63 (73%)
Frame = +2
Query: 461 VQVKLLYMSKK*VVIYFLFLYMLVTCL**EVMRS**KS*RLKFSKY*R*QSLV*CLIFLS 520
+QVKL YMSKK VVIY FL++L+TCL* +MRS ++ +LK S Y R*Q+L CL F +
Sbjct: 143 LQVKLSYMSKKNVVIYL*FLFILMTCL*Q*LMRSWWENSKLKCSNYLR*QTLASCLTFWA 322
Query: 521 WR* 523
WR*
Sbjct: 323 WR* 331
Score = 48.1 bits (113), Expect(2) = 2e-18
Identities = 27/45 (60%), Positives = 33/45 (73%)
Frame = +3
Query: 415 SLKVSK*RDKRRRFTC*RRPYIVLNRLQGPSIAELMSIFKDLDLL 459
SL+V+K RD+RRR *RRP +VL +LQ P LMSIF+ LDLL
Sbjct: 3 SLRVAKLRDRRRRSIS*RRP*MVLIKLQRPGTTCLMSIFRGLDLL 137
>TC232593 weakly similar to UP|Q9XG91 (Q9XG91) Tpv2-1c protein (Fragment),
partial (16%)
Length = 562
Score = 51.6 bits (122), Expect = 1e-06
Identities = 45/108 (41%), Positives = 61/108 (55%)
Frame = +2
Query: 479 FLYMLVTCL**EVMRS**KS*RLKFSKY*R*QSLV*CLIFLSWR*TNIVMEISYANRSMQ 538
FL ML+T * E+M+ * +S K K +* LV LIFL R + + + +MQ
Sbjct: 200 FLSMLMTF**LEMMQG*LRSSSKK*CKLLK*LILVS*LIFLELRSSKVRTKC*SVKGNMQ 379
Query: 539 RKYSKSCTWKIAKALQLQ*IKRRNSAKMMELEKLLKAKIEA*LVA*CI 586
+K+ +S W+ A L Q*IKRR+S + L KL+K I A*L *CI
Sbjct: 380 KKF*RSFKWRNANLLAHQ*IKRRSSTR*TVLIKLMKDIIGA*LDV*CI 523
>CO981347
Length = 624
Score = 37.0 bits (84), Expect = 0.028
Identities = 22/79 (27%), Positives = 35/79 (43%), Gaps = 8/79 (10%)
Frame = +2
Query: 101 FDKFCEEYGIEHQ--------QNGVNERKKKEALWRWKDACYMKKIFQKSCGQRLQKCNI 152
F++FC + GI+ QNG+ ER L R + ++ + G+ +
Sbjct: 209 FNEFCRKIGIKRHKIVPHTP*QNGLAERMNMTILERVRCMLLSARLPKTFWGEAANTTSY 388
Query: 153 LLNMLPSRVMHKKTPFETW 171
L+N PS + KTP E W
Sbjct: 389 LINRCPSSTLGFKTPMEAW 445
>AW185460
Length = 411
Score = 34.3 bits (77), Expect = 0.18
Identities = 26/71 (36%), Positives = 32/71 (44%)
Frame = +3
Query: 594 *CMF*VCFQGLCIVLVKYLINLSKES*DTSKGHLIMALSIHDVQSFNLLAILIVIGQDQQ 653
*CM V +Q C VKY + KE * K I + N LA VIGQ QQ
Sbjct: 105 *CMLQVFYQDSCKAQVKYTLEQEKEF*GIYKEQKRSVYGILPKPTQNYLATPTVIGQVQQ 284
Query: 654 MI*KAQWVIVS 664
M *+ ++S
Sbjct: 285 MT*RVPLAMLS 317
>TC228845 weakly similar to GB|AAO44030.1|28466843|BT004764 At3g56220
{Arabidopsis thaliana;} , partial (51%)
Length = 594
Score = 33.9 bits (76), Expect = 0.24
Identities = 19/64 (29%), Positives = 31/64 (47%)
Frame = +3
Query: 129 WKDACYMKKIFQKSCGQRLQKCNILLNMLPSRVMHKKTPFETWFVTNQIYKV*RFLFVFA 188
W Y ++ S G + Q CN L ++ +MH F+ +F TNQ + FL VF
Sbjct: 12 W*KRIYATQVATTSIGYKFQCCNSLYTLIIIYMMHINFGFQCFFSTNQEFHY--FLTVFF 185
Query: 189 FILY 192
+++
Sbjct: 186 LLIW 197
>AI855818 weakly similar to GP|21741393|e OSJNBb0051N19.6 {Oryza sativa
(japonica cultivar-group)}, partial (10%)
Length = 463
Score = 33.9 bits (76), Expect = 0.24
Identities = 36/111 (32%), Positives = 52/111 (46%)
Frame = -1
Query: 333 SGFIGPN*MMMVQ*TSTRPS**LRDIAKCLE*TSRKRLLRWHAWIP*GCCLL*LPIMHGR 392
+GF+ N*M M R ** + I K E*T +K +L+ C P
Sbjct: 370 NGFLEIN*MNMA*LLEIRLD**QKGIIKKRE*TMKKHMLQLQD*KSLECF*HMYP**ILN 191
Query: 393 YINWMLNQLF*MSILKKRFTLSSLKVSK*RDKRRRFTC*RRPYIVLNRLQG 443
I WML LF*M KK++ L++ + K R + F +R ++V N+ G
Sbjct: 190 SIKWMLKVLF*MV*FKKKYMLNNPQALKSRINQLMFINCKRLFMV*NKPLG 38
>BI701169
Length = 407
Score = 32.7 bits (73), Expect = 0.53
Identities = 16/38 (42%), Positives = 23/38 (60%), Gaps = 8/38 (21%)
Frame = +2
Query: 97 *NNDFDKFCEEYGIEH--------QQNGVNERKKKEAL 126
*+N+F K+C+++GI QQNGV ERK + L
Sbjct: 272 *SNEFQKYCDDHGIRRPLMVLRSPQQNGVAERKNRTIL 385
>TC204438 homologue to UP|Q84VH6 (Q84VH6) Gag-pol polyprotein, complete
Length = 4734
Score = 32.3 bits (72), Expect = 0.69
Identities = 47/150 (31%), Positives = 66/150 (43%)
Frame = +2
Query: 516 LIFLSWR*TNIVMEISYANRSMQRKYSKSCTWKIAKALQLQ*IKRRNSAKMMELEKLLKA 575
LIF +*+ S SMQR S+S WK+ + + + KM L+K
Sbjct: 3887 LIFWDSK*SRWKTPYSSHKASMQRTLSRSLGWKMPAIKEHLHLLT*SCQKMKLAPVLIKV 4066
Query: 576 KIEA*LVA*CI*KPLDKI*CMF*VCFQGLCIVLVKYLINLSKES*DTSKGHLIMALSIHD 635
EA*L A I*+ D M *V Q + +L +E *+ + M L
Sbjct: 4067 CTEA*LGAYYI*QLADLTSPMQ*VFVQDIKPILR*VT*IK*REF*NM*MAPVTMGLCTVI 4246
Query: 636 VQSFNLLAILIVIGQDQQMI*KAQWVIVSV 665
VQ L I+++IG + QM KA V VS+
Sbjct: 4247 VQIQCWLGIVMLIGLEVQMTEKALLVDVSI 4336
Score = 28.5 bits (62), Expect = 10.0
Identities = 20/82 (24%), Positives = 33/82 (39%), Gaps = 8/82 (9%)
Frame = +1
Query: 98 NNDFDKFCEEYGIEH--------QQNGVNERKKKEALWRWKDACYMKKIFQKSCGQRLQK 149
N+ F +FC GI H QQNG+ ERK + + + K++ + +
Sbjct: 2485 NSKFTEFCTSEGITHEFSAAITPQQNGIVERKNRTLQEAARVMLHAKELPYNLWAEAMNT 2664
Query: 150 CNILLNMLPSRVMHKKTPFETW 171
+ N + R T +E W
Sbjct: 2665 ACYIHNRVTLRRGTPTTLYEIW 2730
>BF596801 weakly similar to GP|29423270|g gag-pol polyprotein {Glycine max},
partial (7%)
Length = 336
Score = 31.2 bits (69), Expect = 1.5
Identities = 32/87 (36%), Positives = 40/87 (45%)
Frame = +1
Query: 312 LKKMTLDNWWIKLKIGR*LVLSGFIGPN*MMMVQ*TSTRPS**LRDIAKCLE*TSRKRLL 371
LK+ N LKI L +GF+ N*M MV +P ** +DI K E*T +K +L
Sbjct: 76 LKETMYGN**KNLKIILLLEQNGFLEIN*MNMV*LLEIKPG**RKDIIKKRE*TMKKHML 255
Query: 372 RWHAWIP*GCCLL*LPIMHGRYINWML 398
P C P +I WML
Sbjct: 256 LLQD*KPLECFWHMHP**TLNFIKWML 336
>BM886329
Length = 422
Score = 29.6 bits (65), Expect = 4.5
Identities = 12/35 (34%), Positives = 21/35 (59%)
Frame = -2
Query: 161 VMHKKTPFETWFVTNQIYKV*RFLFVFAFILYNRL 195
++HK+ F WF+ Q + V L++ F+L+N L
Sbjct: 196 IIHKEDDFHFWFIKEQYFYV-SLLYMLLFLLFNLL 95
>TC212454
Length = 309
Score = 29.3 bits (64), Expect = 5.9
Identities = 28/69 (40%), Positives = 41/69 (58%), Gaps = 1/69 (1%)
Frame = +1
Query: 425 RRRFTC*RRPYIVLNRLQGPSIAELMSIFKDLDLLKVQVKLLYMSKK*VVIYFLFL-YML 483
R +FT R ++ + QGPSIA L +LD V++K L + K +V+ L +ML
Sbjct: 46 RTQFTDYTRISMI*S*YQGPSIA*LTLT*SNLDS-GVRMKQLCI*NKMIVVCNL*RHFML 222
Query: 484 VTCL**EVM 492
+TCL**EV+
Sbjct: 223 MTCL**EVI 249
>TC222253 similar to UP|Q9ZQE4 (Q9ZQE4) Copia-like retroelement pol
polyprotein, partial (4%)
Length = 919
Score = 25.4 bits (54), Expect(2) = 8.3
Identities = 13/28 (46%), Positives = 16/28 (56%), Gaps = 8/28 (28%)
Frame = +1
Query: 104 FCEEYGIEHQ--------QNGVNERKKK 123
F E++GI+HQ NGV ERK K
Sbjct: 643 FFEKHGIQHQLTTKYTPQHNGVTERKNK 726
Score = 21.6 bits (44), Expect(2) = 8.3
Identities = 6/14 (42%), Positives = 10/14 (70%)
Frame = +2
Query: 120 RKKKEALWRWKDAC 133
+++ + LW W DAC
Sbjct: 713 KERTKQLWTW*DAC 754
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
0.367 0.164 0.589
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 27,871,420
Number of Sequences: 63676
Number of extensions: 371425
Number of successful extensions: 5365
Number of sequences better than 10.0: 24
Number of HSP's better than 10.0 without gapping: 2127
Number of HSP's successfully gapped in prelim test: 237
Number of HSP's that attempted gapping in prelim test: 3189
Number of HSP's gapped (non-prelim): 2464
length of query: 667
length of database: 12,639,632
effective HSP length: 104
effective length of query: 563
effective length of database: 6,017,328
effective search space: 3387755664
effective search space used: 3387755664
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 (21.7 bits)
S2: 62 (28.5 bits)
Medicago: description of AC138453.6