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= TM0065.20
(196 letters)
Database: GMGI
63,676 sequences; 37,918,896 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
TC204439 UP|Q84VI4 (Q84VI4) Gag-pol polyprotein, complete 112 8e-26
TC204438 homologue to UP|Q84VH6 (Q84VH6) Gag-pol polyprotein, co... 112 8e-26
BI784757 74 3e-14
BI424202 70 6e-13
TC235104 weakly similar to UP|Q850H8 (Q850H8) Gag-pol polyprotei... 68 3e-12
TC222253 similar to UP|Q9ZQE4 (Q9ZQE4) Copia-like retroelement p... 62 2e-10
BI425191 weakly similar to GP|14586969|gb| pol polyprotein {Citr... 52 2e-07
TC213393 weakly similar to UP|Q850H8 (Q850H8) Gag-pol polyprotei... 48 3e-06
CO981347 44 4e-05
AI901012 42 2e-04
TC232910 similar to UP|Q6I8N0 (Q6I8N0) Pol polypeptide, partial ... 40 5e-04
TC207859 39 0.001
BF595216 38 0.003
AW831208 36 0.010
AI442763 36 0.013
BI701169 33 0.065
BI321697 33 0.11
TC210859 32 0.14
BI425007 similar to SP|Q9BBS8|RPOC_ DNA-directed RNA polymerase ... 32 0.25
AW704543 32 0.25
>TC204439 UP|Q84VI4 (Q84VI4) Gag-pol polyprotein, complete
Length = 4731
Score = 112 bits (281), Expect = 8e-26
Identities = 67/189 (35%), Positives = 103/189 (54%), Gaps = 9/189 (4%)
Frame = +1
Query: 8 TLHNVRHVPGIKRNLISIGQLDDEGYHTTFGGGAWKVT--KGNLVVARGKKRGSLYMVAE 65
+L+ V V G+ NLISI QL DEG++ F VT K +++ + + + Y+
Sbjct: 1837 SLNKVLLVKGLTANLISISQLCDEGFNVNFTKSECLVTNEKSEVLMKGSRSKDNCYLWTP 2016
Query: 66 EDMIAVTEAVNSSS----IWHQRLGHMSEKGMKIMASKGKMS---NLKHVDLGVCEHCIL 118
++ + ++S IWHQR GH+ +GMK + KG + NLK + +C C +
Sbjct: 2017 QETSYSSTCLSSKEDEVRIWHQRFGHLHLRGMKKIIDKGAVRGIPNLKIEEGRICGECQI 2196
Query: 119 GKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTRKV*VYFLKN 178
GKQ K+S K ++ L+L+H D+ GP V+SLGG RY +DD +R V F++
Sbjct: 2197 GKQVKMSHQKLQHQTTSRVLELLHMDLMGPMQVESLGGKRYAYVVVDDFSRFTWVNFIRE 2376
Query: 179 KSDVFSVFK 187
KS+ F VFK
Sbjct: 2377 KSETFEVFK 2403
>TC204438 homologue to UP|Q84VH6 (Q84VH6) Gag-pol polyprotein, complete
Length = 4734
Score = 112 bits (281), Expect = 8e-26
Identities = 68/189 (35%), Positives = 102/189 (52%), Gaps = 9/189 (4%)
Frame = +1
Query: 8 TLHNVRHVPGIKRNLISIGQLDDEGYHTTFGGGAWKVT--KGNLVVARGKKRGSLYMVAE 65
+L+ V V G+ NLISI QL DEG++ F VT K +++ + + + Y+
Sbjct: 1840 SLNKVLLVKGLTANLISISQLCDEGFNVNFTKSECLVTNEKSEVLMKGSRSKDNCYLWTP 2019
Query: 66 EDMIAVTEAVNSSS----IWHQRLGHMSEKGMKIMASKGKMS---NLKHVDLGVCEHCIL 118
++ + + S IWHQR GH+ +GMK + KG + NLK + +C C +
Sbjct: 2020 QETSYSSTCLFSKEDEVKIWHQRFGHLHLRGMKKIIDKGAVRGIPNLKIEEGRICGECQI 2199
Query: 119 GKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTRKV*VYFLKN 178
GKQ K+S K ++ L+L+H D+ GP V+SLGG RY +DD +R V F++
Sbjct: 2200 GKQVKMSHQKLQHQTTSRVLELLHMDLMGPMQVESLGGKRYAYVVVDDFSRFTWVNFIRE 2379
Query: 179 KSDVFSVFK 187
KSD F VFK
Sbjct: 2380 KSDTFEVFK 2406
>BI784757
Length = 430
Score = 74.3 bits (181), Expect = 3e-14
Identities = 34/76 (44%), Positives = 53/76 (69%)
Frame = +1
Query: 112 VCEHCILGKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTRKV 171
VC+ C+ KQ + +F + EKL+++++DV GP +SLGG+RY+++FID+ TRKV
Sbjct: 64 VCDGCLQCKQSRSTFKQNVPIRAKEKLEVIYSDVCGPMQTESLGGNRYFISFIDELTRKV 243
Query: 172 *VYFLKNKSDVFSVFK 187
VY ++ KSD F VF+
Sbjct: 244 WVYLIRRKSDFFEVFE 291
>BI424202
Length = 421
Score = 70.1 bits (170), Expect = 6e-13
Identities = 37/100 (37%), Positives = 58/100 (58%)
Frame = -3
Query: 77 SSSIWHQRLGHMSEKGMKIMASKGKMSNLKHVDLGVCEHCILGKQRKVSFSKAGRKSKLE 136
SS +WH+RLGH+S + +K + ++G +S L D CI GKQ + SK G K
Sbjct: 386 SSMLWHRRLGHISIERIKRLVNEGVLSTLDFADFETYVDCIKGKQ--TNKSKKGAKRSSN 213
Query: 137 KLKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTRKV*VYFL 176
L+++HTD+ P +Y++TFIDD +R + +YF+
Sbjct: 212 LLEIIHTDIC--CPDMDANSLKYFITFIDDYSRYMYLYFI 99
>TC235104 weakly similar to UP|Q850H8 (Q850H8) Gag-pol polyprotein
(Fragment), partial (28%)
Length = 865
Score = 67.8 bits (164), Expect = 3e-12
Identities = 57/193 (29%), Positives = 96/193 (49%), Gaps = 5/193 (2%)
Frame = +2
Query: 8 TLHNVRHVPGIKRNLISIGQLDD-EGYHTTFGGGAWKVTKGNL--VVARGKKRGSLYMVA 64
+L++V + G N+ S+ QL TF ++ + + + G + LY +
Sbjct: 89 SLNSVVFILGCPFNITSLSQLTRFRNCSVTFDANSFVIQECGTGWTIGVGIESHGLYYL- 265
Query: 65 EEDMIAVTEAVNSSSIWHQRLGHMSEKGMKIMASKGKMSNLKHVDLGVCEHCILGKQRKV 124
+ ++ V AV S + H+RLGH +KIM + +L+ + CE C LGK +
Sbjct: 266 KPNLSWVCSAVTSPKLLHERLGHPHLSKLKIM-----VPSLEKIKDLFCESCQLGKHVRS 430
Query: 125 SFSKAGRKSKLEKLKLV-HTDVWGPAPVKSLGGSRYYVTFIDDSTRKV*VYFLKNKSDVF 183
S +S+++ LV H D+WGP V S+ RY+VTFID+ ++ V+ +K +S++
Sbjct: 431 SXRHV--ESRVDSPFLVIHXDIWGPNRVSSMS-YRYFVTFIDEFSQCTRVFLMKERSEIL 601
Query: 184 SVFKGTTK-KTGF 195
S K KT F
Sbjct: 602 SFLTSVNKIKTQF 640
>TC222253 similar to UP|Q9ZQE4 (Q9ZQE4) Copia-like retroelement pol
polyprotein, partial (4%)
Length = 919
Score = 62.0 bits (149), Expect = 2e-10
Identities = 34/79 (43%), Positives = 51/79 (64%), Gaps = 2/79 (2%)
Frame = +1
Query: 111 GVCEHCILGKQRKVSF--SKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDDST 168
GVC+ C +GK+ + SF K+ R KL LK+VH D+ + + G + Y++TFIDD +
Sbjct: 325 GVCDTCEIGKKHRESFPTGKSWRMKKL--LKIVHLDLC-TVEIPTHGDNNYFITFIDDFS 495
Query: 169 RKV*VYFLKNKSDVFSVFK 187
+K+ VYFLK KS+ + FK
Sbjct: 496 KKMWVYFLKQKSEACNAFK 552
>BI425191 weakly similar to GP|14586969|gb| pol polyprotein {Citrus x
paradisi}, partial (7%)
Length = 423
Score = 52.0 bits (123), Expect = 2e-07
Identities = 30/84 (35%), Positives = 45/84 (52%)
Frame = +3
Query: 104 NLKHVDLGVCEHCILGKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTF 163
+L DL +C CI + K + +A R ++L L+++HTD+ P V S G RY++TF
Sbjct: 15 DLAFSDLNICVDCI---KEKHTMKRATRSTQL--LEIMHTDICRPFDVNSFGKERYFITF 179
Query: 164 IDDSTRKV*VYFLKNKSDVFSVFK 187
IDD + VY L K V +
Sbjct: 180 IDDYSHYGYVYLLHEKFQAVDVLE 251
>TC213393 weakly similar to UP|Q850H8 (Q850H8) Gag-pol polyprotein
(Fragment), partial (23%)
Length = 678
Score = 48.1 bits (113), Expect = 3e-06
Identities = 29/88 (32%), Positives = 45/88 (50%)
Frame = -2
Query: 99 KGKMSNLKHVDLGVCEHCILGKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSR 158
K +S+L + CE C GK + SF LVH+DVWG SR
Sbjct: 389 KQMVSSLSKLPTLSCESCQFGKHVQSSFPYCVICRDRFPFVLVHSDVWGLCHGMPTLESR 210
Query: 159 YYVTFIDDSTRKV*VYFLKNKSDVFSVF 186
Y+VTFI+D + + ++ + N+S++F +F
Sbjct: 209 YFVTFIEDYS*QTWLFLMVNRSELF*IF 126
>CO981347
Length = 624
Score = 44.3 bits (103), Expect = 4e-05
Identities = 20/36 (55%), Positives = 28/36 (77%)
Frame = +3
Query: 148 PAPVKSLGGSRYYVTFIDDSTRKV*VYFLKNKSDVF 183
P+ VK+ GGS Y++T IDD +R+V +Y LKNKS+ F
Sbjct: 3 PSRVKTHGGSSYFLTIIDDFSRRVWLYVLKNKSESF 110
>AI901012
Length = 410
Score = 41.6 bits (96), Expect = 2e-04
Identities = 17/37 (45%), Positives = 26/37 (69%)
Frame = +1
Query: 133 SKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTR 169
S + +VH+++WG + + S+ G RYYVTFIDD +R
Sbjct: 58 SHVSSANIVHSNIWGHSCILSILGFRYYVTFIDDFSR 168
>TC232910 similar to UP|Q6I8N0 (Q6I8N0) Pol polypeptide, partial (3%)
Length = 690
Score = 40.4 bits (93), Expect = 5e-04
Identities = 33/120 (27%), Positives = 58/120 (47%), Gaps = 10/120 (8%)
Frame = +2
Query: 11 NVRHVPGIKRNLISIGQLDDEGYHTTFGGGAWKVTKGNLVVARGKKRGSLY-------MV 63
+V VPGI++NL+S L++ G+ + +++ V G + ++ V
Sbjct: 329 DVLFVPGIRKNLLSGMILNNCGFKQVLESDKYILSRHGSFVGFGYRCNEMFKLNIDVPFV 508
Query: 64 AEEDMIAVTEAVNS---SSIWHQRLGHMSEKGMKIMASKGKMSNLKHVDLGVCEHCILGK 120
E +A ++ + S IWH RLGH+ K +K M SK M +++ C+ C+L K
Sbjct: 509 HESVCMASCSSITNMTKSEIWHARLGHVHYKRLKDM-SKTCMIPPFDMNIEKCKTCMLTK 685
>TC207859
Length = 751
Score = 39.3 bits (90), Expect = 0.001
Identities = 22/54 (40%), Positives = 28/54 (51%)
Frame = +1
Query: 113 CEHCILGKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDD 166
CE +LGK + S K LVH+D+WG + V G Y+VTFIDD
Sbjct: 559 CESYLLGKHVCHTCSPHVNKHVASPFALVHSDIWGLSCVYLTLGYFYFVTFIDD 720
>BF595216
Length = 421
Score = 37.7 bits (86), Expect = 0.003
Identities = 17/39 (43%), Positives = 25/39 (63%)
Frame = +2
Query: 143 TDVWGPAPVKSLGGSRYYVTFIDDSTRKV*VYFLKNKSD 181
+D+ PAP S G YYVTF+D TR ++ L++KS+
Sbjct: 8 SDLCSPAPFVSSTGYSYYVTFVDAFTRYTWIFLLRHKSE 124
>AW831208
Length = 327
Score = 36.2 bits (82), Expect = 0.010
Identities = 15/41 (36%), Positives = 25/41 (60%)
Frame = -1
Query: 14 HVPGIKRNLISIGQLDDEGYHTTFGGGAWKVTKGNLVVARG 54
+VP + RNL+S+ +LD Y+ FG G + + K N ++ G
Sbjct: 132 YVPSLSRNLVSLSKLDVTAYYFNFGNG*FNLFKHNHLIGTG 10
>AI442763
Length = 426
Score = 35.8 bits (81), Expect = 0.013
Identities = 26/74 (35%), Positives = 34/74 (45%)
Frame = -2
Query: 113 CEHCILGKQRKVSFSKAGRKSKLEKLKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTRKV* 172
CE +LGK + S K LV +++WG + V G Y+V IDD K
Sbjct: 224 CESDLLGKHVCQTCSPHVNKHVGSPFALVPSEIWGFSWVYLTLGYFYFVPLIDDFFLKRT 45
Query: 173 VYFLKNKSDVFSVF 186
FL K DVF +F
Sbjct: 44 WVFLMKKCDVFFLF 3
>BI701169
Length = 407
Score = 33.5 bits (75), Expect = 0.065
Identities = 18/40 (45%), Positives = 24/40 (60%), Gaps = 4/40 (10%)
Frame = +2
Query: 160 YVTFIDDSTRKV*VYFLKNKSDVFSVFKG----TTKKTGF 195
+ FIDD +RK VYF K+K +VF FK K++GF
Sbjct: 113 FFLFIDDFSRKTWVYFFKHKLEVFENFKKFKAIVEKESGF 232
>BI321697
Length = 368
Score = 32.7 bits (73), Expect = 0.11
Identities = 16/53 (30%), Positives = 25/53 (46%)
Frame = -3
Query: 2 SNGTLWTLHNVRHVPGIKRNLISIGQLDDEGYHTTFGGGAWKVTKGNLVVARG 54
S+G L V H+ I++NLIS L +GY F +T+ + +G
Sbjct: 180 SSGNFIVLDGVYHISDIRKNLISTSLLVQQGYKVVFESNRVVITRHGNFIGKG 22
>TC210859
Length = 1210
Score = 32.3 bits (72), Expect = 0.14
Identities = 17/33 (51%), Positives = 25/33 (75%)
Frame = -2
Query: 138 LKLVHTDVWGPAPVKSLGGSRYYVTFIDDSTRK 170
L LVH++V+ + +SLGG++ +VTFIDD RK
Sbjct: 96 LDLVHSNVFSMSQ-QSLGGAQ*FVTFIDDHFRK 1
>BI425007 similar to SP|Q9BBS8|RPOC_ DNA-directed RNA polymerase beta' chain
(EC 2.7.7.6). {Lotus japonicus}, partial (9%)
Length = 428
Score = 31.6 bits (70), Expect = 0.25
Identities = 14/35 (40%), Positives = 19/35 (54%)
Frame = +3
Query: 152 KSLGGSRYYVTFIDDSTRKV*VYFLKNKSDVFSVF 186
K G +Y + +DDST VYFLK K++ F
Sbjct: 264 KGASGCKYVMVLVDDST*YTWVYFLKEKNEAIKKF 368
>AW704543
Length = 409
Score = 31.6 bits (70), Expect = 0.25
Identities = 13/31 (41%), Positives = 18/31 (57%)
Frame = +3
Query: 3 NGTLWTLHNVRHVPGIKRNLISIGQLDDEGY 33
N + T NVR VP N+IS+G++ GY
Sbjct: 18 NNIIQTFQNVRFVPSATTNVISLGEMTSPGY 110
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
0.320 0.136 0.407
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,667,127
Number of Sequences: 63676
Number of extensions: 110314
Number of successful extensions: 491
Number of sequences better than 10.0: 51
Number of HSP's better than 10.0 without gapping: 480
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): 481
length of query: 196
length of database: 12,639,632
effective HSP length: 92
effective length of query: 104
effective length of database: 6,781,440
effective search space: 705269760
effective search space used: 705269760
frameshift window, decay const: 50, 0.1
T: 13
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (26.2 bits)
Lotus: description of TM0065.20