RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy12338
(106 letters)
>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
Length = 1733
Score = 53.2 bits (127), Expect = 8e-10
Identities = 17/102 (16%), Positives = 47/102 (46%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1617 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYS 1676
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWN 104
P ++ P ++ P+++ P ++ P ++ P ++
Sbjct: 1677 PTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYS 1718
Score = 51.2 bits (122), Expect = 4e-09
Identities = 17/103 (16%), Positives = 46/103 (44%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1582 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1641
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWNE 105
P ++ P ++ P ++ P ++ P ++ P ++
Sbjct: 1642 PTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSP 1684
Score = 51.2 bits (122), Expect = 5e-09
Identities = 17/102 (16%), Positives = 47/102 (46%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1610 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYS 1669
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWN 104
P ++ P ++ P ++ P+++ P ++ P ++
Sbjct: 1670 PTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYS 1711
Score = 49.7 bits (118), Expect = 1e-08
Identities = 16/103 (15%), Positives = 45/103 (43%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1624 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYS 1683
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWNE 105
P ++ P+++ P ++ P ++ P ++ +
Sbjct: 1684 PTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDEQKH 1726
Score = 46.2 bits (109), Expect = 3e-07
Identities = 17/102 (16%), Positives = 47/102 (46%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1603 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYS 1662
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWN 104
P ++ P ++ P ++ P ++ P+++ P ++
Sbjct: 1663 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYS 1704
Score = 45.5 bits (107), Expect = 4e-07
Identities = 17/102 (16%), Positives = 47/102 (46%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1596 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1655
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWN 104
P ++ P ++ P ++ P ++ P ++ P+++
Sbjct: 1656 PTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS 1697
Score = 45.5 bits (107), Expect = 5e-07
Identities = 17/102 (16%), Positives = 46/102 (45%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1568 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1627
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWN 104
P ++ P ++ P ++ P ++ P ++ P ++
Sbjct: 1628 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYS 1669
Score = 45.1 bits (106), Expect = 7e-07
Identities = 17/103 (16%), Positives = 45/103 (43%)
Query: 1 MEPHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPH 60
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P
Sbjct: 1587 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1646
Query: 61 WNGMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHW 103
++ P ++ P ++ P ++ P ++ P ++ P +
Sbjct: 1647 YSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1689
Score = 45.1 bits (106), Expect = 7e-07
Identities = 14/92 (15%), Positives = 40/92 (43%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P+++
Sbjct: 1638 PSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYS 1697
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKP 94
P ++ P ++ P ++ + +
Sbjct: 1698 PTSPSYSPTSPGYSPGSPAYSPKQDEQKHNEN 1729
Score = 43.2 bits (101), Expect = 3e-06
Identities = 17/101 (16%), Positives = 45/101 (44%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1575 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1634
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHW 103
P ++ P ++ P ++ P ++ P ++ P +
Sbjct: 1635 PTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSY 1675
Score = 40.5 bits (94), Expect = 3e-05
Identities = 17/102 (16%), Positives = 46/102 (45%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1561 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1620
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHWN 104
P ++ P ++ P ++ P ++ P ++ P ++
Sbjct: 1621 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYS 1662
Score = 32.4 bits (73), Expect = 0.021
Identities = 11/66 (16%), Positives = 28/66 (42%)
Query: 1 MEPHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPH 60
P ++ P ++ P ++ P ++ T P+ + T P ++ P ++ P ++ +
Sbjct: 1664 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPTSPGYSPGSPAYSPKQDE 1723
Query: 61 WNGMEP 66
E
Sbjct: 1724 QKHNEN 1729
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 48.1 bits (114), Expect = 5e-08
Identities = 17/101 (16%), Positives = 45/101 (44%)
Query: 3 PHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHWN 62
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P ++
Sbjct: 1646 PSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYS 1705
Query: 63 GMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEPHW 103
P ++ P ++ P ++ P ++ P ++ P +
Sbjct: 1706 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1746
Score = 47.8 bits (113), Expect = 7e-08
Identities = 17/100 (17%), Positives = 44/100 (44%)
Query: 2 EPHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPHW 61
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P +
Sbjct: 1652 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711
Query: 62 NGMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKPHWNGIEP 101
+ P ++ P ++ P ++ P ++ P ++ P
Sbjct: 1712 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1751
Score = 47.4 bits (112), Expect = 1e-07
Identities = 16/94 (17%), Positives = 41/94 (43%)
Query: 1 MEPHWNGMEPHWNGMQPHWNGMEPHWNGTEPHRNGTKPHWNGMQPHWNGMEPHWNGMEPH 60
P ++ P ++ P ++ P ++ T P + T P ++ P ++ P ++ P
Sbjct: 1658 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1717
Query: 61 WNGMEPHWNGMQPHWNGMQPHWNGMEPHWNGMKP 94
++ P ++ P ++ P ++ P ++ P
Sbjct: 1718 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1751
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.316 0.138 0.586
Gapped
Lambda K H
0.267 0.0603 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,001,540
Number of extensions: 106263
Number of successful extensions: 356
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 87
Length of query: 106
Length of database: 6,701,793
Length adjustment: 71
Effective length of query: 35
Effective length of database: 4,719,402
Effective search space: 165179070
Effective search space used: 165179070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (23.7 bits)