BLASTP 2.2.23 [Feb-03-2010]
Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Reference for compositional score matrix adjustment:
Altschul, Stephen F., John C. Wootton, E. Michael Gertz, Richa Agarwala,
Aleksandr Morgulis, Alejandro A. Schäffer, and Yi-Kuo Yu (2005) "Protein database
searches using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= Os01g0805800 Os01g0805800|AK103408
(210 letters)
Database: rap3
52,214 sequences; 17,035,801 total letters
Searching..................................................done
Score E
Sequences producing significant alignments: (bits) Value
Os01g0805800 RNA polymerase Rpb5, N-terminal domain contain... 426 e-120
Os11g0143400 RNA polymerase Rpb5, N-terminal domain contain... 143 1e-34
Os12g0139500 RNA polymerase Rpb5, N-terminal domain contain... 141 4e-34
Os04g0487300 Similar to DNA-directed RNA polymerase II 23 k... 83 2e-16
>Os01g0805800 RNA polymerase Rpb5, N-terminal domain containing protein
Length = 210
Score = 426 bits (1096), Expect = e-120, Method: Compositional matrix adjust.
Identities = 210/210 (100%), Positives = 210/210 (100%)
Query: 1 MSAGLVTEEVMVGRLVRIRRTVMQMLRDRGYLVVEHELAMGRRDFLRKYGESFHREDLLI 60
MSAGLVTEEVMVGRLVRIRRTVMQMLRDRGYLVVEHELAMGRRDFLRKYGESFHREDLLI
Sbjct: 1 MSAGLVTEEVMVGRLVRIRRTVMQMLRDRGYLVVEHELAMGRRDFLRKYGESFHREDLLI 60
Query: 61 NKYKKNDPSDQIYVFFPNDDKVGMKHIKKYVEMMKAENVSRAVLVLQQNLTPFARSFLQE 120
NKYKKNDPSDQIYVFFPNDDKVGMKHIKKYVEMMKAENVSRAVLVLQQNLTPFARSFLQE
Sbjct: 61 NKYKKNDPSDQIYVFFPNDDKVGMKHIKKYVEMMKAENVSRAVLVLQQNLTPFARSFLQE 120
Query: 121 LEPKIHLEIFQEAELLINIKEHVLVPEHQVLNNEEKKTLLERYTLKETQLPRIQITDPIA 180
LEPKIHLEIFQEAELLINIKEHVLVPEHQVLNNEEKKTLLERYTLKETQLPRIQITDPIA
Sbjct: 121 LEPKIHLEIFQEAELLINIKEHVLVPEHQVLNNEEKKTLLERYTLKETQLPRIQITDPIA 180
Query: 181 RYYGLRRGQVVKIIRPSETAGRYVTYRYVV 210
RYYGLRRGQVVKIIRPSETAGRYVTYRYVV
Sbjct: 181 RYYGLRRGQVVKIIRPSETAGRYVTYRYVV 210
>Os11g0143400 RNA polymerase Rpb5, N-terminal domain containing protein
Length = 227
Score = 143 bits (360), Expect = 1e-34, Method: Compositional matrix adjust.
Identities = 80/196 (40%), Positives = 118/196 (60%), Gaps = 1/196 (0%)
Query: 14 RLVRIRRTVMQMLRDRGYLVVEHELAMGRRDFLRKYGESFHREDLLINKYKKNDPSDQIY 73
RL RRT M+MLRDRGY V E E+A +F + E E L +DPS ++
Sbjct: 32 RLFLARRTAMEMLRDRGYSVPEAEIARTLPEFRAWWAEKPGIERLAFTTTLVSDPSKKVQ 91
Query: 74 VFFPNDDKVGMKHIKKYVEMMKAENVSRAVLVLQQNLTPFARSFLQELEPKIHLEIFQEA 133
+ F + V + I++ K EN+SR VL+LQ + AR ++E+ K ++IFQ
Sbjct: 92 LVFCPPEPVKIATIREIYLQTKEENLSRLVLILQSKILSRAREAIKEIF-KFKVDIFQAT 150
Query: 134 ELLINIKEHVLVPEHQVLNNEEKKTLLERYTLKETQLPRIQITDPIARYYGLRRGQVVKI 193
+LL+NI +HVL P+H+VL+ ++K LL+ Y ++++QLPR+ TD +ARYYG +G VVK+
Sbjct: 151 DLLVNITKHVLKPKHEVLSADQKAKLLKEYNVEDSQLPRMLETDAVARYYGFDKGTVVKV 210
Query: 194 IRPSETAGRYVTYRYV 209
I E G+ V YR V
Sbjct: 211 IYDGELTGKRVAYRCV 226
>Os12g0139500 RNA polymerase Rpb5, N-terminal domain containing protein
Length = 227
Score = 141 bits (355), Expect = 4e-34, Method: Compositional matrix adjust.
Identities = 79/196 (40%), Positives = 117/196 (59%), Gaps = 1/196 (0%)
Query: 14 RLVRIRRTVMQMLRDRGYLVVEHELAMGRRDFLRKYGESFHREDLLINKYKKNDPSDQIY 73
RL RRT M+MLRDRGY V E E+A +F + E E L +DPS ++
Sbjct: 32 RLFLARRTAMEMLRDRGYSVPEAEIARTLPEFRAWWAEKPGIERLAFTTTLVSDPSKKVQ 91
Query: 74 VFFPNDDKVGMKHIKKYVEMMKAENVSRAVLVLQQNLTPFARSFLQELEPKIHLEIFQEA 133
+ F + V + I++ K EN+SR VL+LQ + AR ++E+ K ++IFQ
Sbjct: 92 LVFCPPEPVKIATIREIYLQTKEENLSRLVLILQSKILSRAREAIKEIF-KFKVDIFQAT 150
Query: 134 ELLINIKEHVLVPEHQVLNNEEKKTLLERYTLKETQLPRIQITDPIARYYGLRRGQVVKI 193
+LL+NI +HVL P+H+VL+ ++K LL+ Y ++++QLPR+ TD +ARYYG +G VVK+
Sbjct: 151 DLLVNITKHVLKPKHEVLSADQKAKLLKEYNVEDSQLPRMLETDAVARYYGFDKGTVVKV 210
Query: 194 IRPSETAGRYVTYRYV 209
E G+ V YR V
Sbjct: 211 TYDGELTGKRVAYRCV 226
>Os04g0487300 Similar to DNA-directed RNA polymerase II 23 kDa polypeptide (EC
2.7.7.6) (RPB25) (RPB5) (RPABC1) (XAP4)
Length = 43
Score = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 39/42 (92%), Positives = 41/42 (97%)
Query: 169 QLPRIQITDPIARYYGLRRGQVVKIIRPSETAGRYVTYRYVV 210
QLPRIQITDPIARYYG++RGQVVKIIR SETAGRYVTYRYVV
Sbjct: 2 QLPRIQITDPIARYYGMKRGQVVKIIRASETAGRYVTYRYVV 43
Database: rap3
Posted date: Nov 19, 2010 6:03 PM
Number of letters in database: 17,035,801
Number of sequences in database: 52,214
Lambda K H
0.323 0.139 0.389
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 52214
Number of Hits to DB: 6,183,670
Number of extensions: 234757
Number of successful extensions: 520
Number of sequences better than 1.0e-10: 4
Number of HSP's gapped: 518
Number of HSP's successfully gapped: 4
Length of query: 210
Length of database: 17,035,801
Length adjustment: 96
Effective length of query: 114
Effective length of database: 12,023,257
Effective search space: 1370651298
Effective search space used: 1370651298
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 154 (63.9 bits)