Nr search
BLASTX 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= KMC004610A_C01 KMC004610A_c01
(460 letters)
Database: nr
1,393,205 sequences; 448,689,247 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
pir||T02087 gag/pol polyprotein - maize retrotransposon Hopscotc... 69 3e-11
dbj|BAC55626.1| OJ1081_B12.7 [Oryza sativa (japonica cultivar-gr... 66 1e-10
gb|AAN04167.1| Putative copia-like retrotransposon polyprotein [... 64 6e-10
pir||T10728 probable gag/pol polyprotein - long-staminate rice r... 62 4e-09
pir||T52436 RF28 protein - Arabidopsis thaliana retrotransposon ... 57 9e-08
>pir||T02087 gag/pol polyprotein - maize retrotransposon Hopscotch
gi|531389|gb|AAA57005.1| copia-like retrotransposon
Hopscotch polyprotein
Length = 1439
Score = 68.6 bits (166), Expect = 3e-11
Identities = 50/148 (33%), Positives = 69/148 (45%), Gaps = 1/148 (0%)
Frame = -3
Query: 443 STSFPLVLNNLLHVPGVCKNLSSVSXFCKQNNVFFEFHSDSCLVKSQETEETLLQGTLRN 264
++S L L ++LHVP KNL SV N+VF EFHS L+K ++T+ LL G R+
Sbjct: 372 TSSRSLHLRSVLHVPSTHKNLISVHRLTNDNDVFIEFHSSHFLIKDRQTKAVLLHGKCRD 431
Query: 263 GLCAFDNLLHKVNLHSASTLSNSALLSSSSPASALSVSVFSSNKCAQADIDSRLWHSRLG 84
GL + + H L ++ FSS + + WH RLG
Sbjct: 432 GL-------YPLPPHPDLRLKHN----------------FSSTR-----VPLEHWHKRLG 463
Query: 83 HASQKIVSHVLKQCN-PSLSLNKISVVC 3
H S+ IV V+ N P LS N + VC
Sbjct: 464 HPSRDIVHRVISNNNLPCLSNNSTTSVC 491
>dbj|BAC55626.1| OJ1081_B12.7 [Oryza sativa (japonica cultivar-group)]
Length = 1441
Score = 66.2 bits (160), Expect = 1e-10
Identities = 45/130 (34%), Positives = 57/130 (43%)
Frame = -3
Query: 428 LVLNNLLHVPGVCKNLSSVSXFCKQNNVFFEFHSDSCLVKSQETEETLLQGTLRNGLCAF 249
L L N+LHVP CK+L S F + N F E H LVK Q T LL+G R+G
Sbjct: 336 LTLKNVLHVPDACKSLVSAHRFTRDNKTFVELHPFFFLVKDQVTRMPLLRGRCRSG---- 391
Query: 248 DNLLHKVNLHSASTLSNSALLSSSSPASALSVSVFSSNKCAQADIDSRLWHSRLGHASQK 69
L+ + T+SN P S+F WHSRLGH S
Sbjct: 392 ---LYPLPTDKLQTISNKQAFGVVKP------SLFR-------------WHSRLGHPSFS 429
Query: 68 IVSHVLKQCN 39
+V+ V+ Q N
Sbjct: 430 VVNRVISQNN 439
>gb|AAN04167.1| Putative copia-like retrotransposon polyprotein [Oryza sativa
(japonica cultivar-group)]
Length = 1042
Score = 64.3 bits (155), Expect = 6e-10
Identities = 45/127 (35%), Positives = 57/127 (44%)
Frame = -3
Query: 431 PLVLNNLLHVPGVCKNLSSVSXFCKQNNVFFEFHSDSCLVKSQETEETLLQGTLRNGLCA 252
PL LNN+LHVP KNL S + N+VF E HS L+K + T T+L+G R+GL
Sbjct: 272 PLHLNNVLHVPQAAKNLISATKLASDNSVFVEIHSKYFLIKDRTTRSTVLKGPRRHGL-- 329
Query: 251 FDNLLHKVNLHSASTLSNSALLSSSSPASALSVSVFSSNKCAQADIDSRLWHSRLGHASQ 72
L S+SS A +V+ WHSRLGH S
Sbjct: 330 ------------------YPLPSTSSTKQAFAVAP-----------SLERWHSRLGHPSI 360
Query: 71 KIVSHVL 51
IV V+
Sbjct: 361 PIVMKVI 367
>pir||T10728 probable gag/pol polyprotein - long-staminate rice retrotransposon
retrofit gi|2586082|gb|AAB82754.1| retrofit [Oryza
longistaminata]
Length = 1445
Score = 61.6 bits (148), Expect = 4e-09
Identities = 42/137 (30%), Positives = 59/137 (42%)
Frame = -3
Query: 422 LNNLLHVPGVCKNLSSVSXFCKQNNVFFEFHSDSCLVKSQETEETLLQGTLRNGLCAFDN 243
LNN+L+VP KNL S S N+ F E HS +K Q T + LL+G R+GL
Sbjct: 377 LNNVLYVPQAKKNLISASQLAADNSAFLELHSKFFSIKDQVTRDVLLEGKCRHGLYPIPK 436
Query: 242 LLHKVNLHSASTLSNSALLSSSSPASALSVSVFSSNKCAQADIDSRLWHSRLGHASQKIV 63
+ S+ AL + S ++ WHSRLGH S IV
Sbjct: 437 FFGR-----------------STNKQALGAAKLSLSR----------WHSRLGHPSLPIV 469
Query: 62 SHVLKQCNPSLSLNKIS 12
V+ + N S+ ++
Sbjct: 470 KQVISRNNLPCSVESVN 486
>pir||T52436 RF28 protein - Arabidopsis thaliana retrotransposon (fragment)
gi|6520206|dbj|BAA87949.1| retrotransposon homolog
[Arabidopsis thaliana]
Length = 847
Score = 57.0 bits (136), Expect = 9e-08
Identities = 47/141 (33%), Positives = 66/141 (46%)
Frame = -3
Query: 446 SSTSFPLVLNNLLHVPGVCKNLSSVSXFCKQNNVFFEFHSDSCLVKSQETEETLLQGTLR 267
S+ S PL L+N+L+VP + KNL SV C N V EF S VK T LLQG +
Sbjct: 344 STKSRPLNLHNILYVPNIHKNLISVYRLCNANGVSVEFFPASFQVKDLNTGVPLLQGKTK 403
Query: 266 NGLCAFDNLLHKVNLHSASTLSNSALLSSSSPASALSVSVFSSNKCAQADIDSRLWHSRL 87
+ L + ++SS P VS+F+S + WH+RL
Sbjct: 404 DELYEWP-------------------IASSQP-----VSLFAS---PSSKATHSSWHARL 436
Query: 86 GHASQKIVSHVLKQCNPSLSL 24
GH + I++ V+ N SLS+
Sbjct: 437 GHPAPSILNSVIS--NYSLSV 455
Database: nr
Posted date: Apr 1, 2003 2:05 AM
Number of letters in database: 448,689,247
Number of sequences in database: 1,393,205
Lambda K H
0.318 0.135 0.401
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 359,185,608
Number of Sequences: 1393205
Number of extensions: 6884933
Number of successful extensions: 25723
Number of sequences better than 10.0: 167
Number of HSP's better than 10.0 without gapping: 24470
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): 25580
length of database: 448,689,247
effective HSP length: 112
effective length of database: 292,650,287
effective search space used: 11706011480
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)
