RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy9368
(179 letters)
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 39.3 bits (91), Expect = 5e-04
Identities = 25/222 (11%), Positives = 62/222 (27%), Gaps = 60/222 (27%)
Query: 4 SVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVA-- 61
++A + ++V + I + + + + S + ++ +VA
Sbjct: 103 ALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFR--AVGEGNAQLVAIF 160
Query: 62 ----EPQSIVTELQSIVTEPQSIVAEPQSIVTEP-QSIVAEPQSI-------------VT 103
EL+ + +V + E ++ +
Sbjct: 161 GGQGNTDDYFEELRDLYQTYHVLVGDLIKFSAETLSELIRTTLDAEKVFTQGLNILEWLE 220
Query: 104 EPQSI----------VAEP--------QSIVT------EPQSIVAEPQSIVTEPQSIVVS 139
P + ++ P +VT P + + + Q +V +
Sbjct: 221 NPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTA 280
Query: 140 QA-----------KLPRTVIT--FYMG-QSTQTFSISTLSPR 167
A R IT F++G + + + ++L P
Sbjct: 281 VAIAETDSWESFFVSVRKAITVLFFIGVRCYEAYPNTSLPPS 322
>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1752
Score = 35.8 bits (82), Expect = 0.005
Identities = 37/128 (28%), Positives = 37/128 (28%)
Query: 8 TSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIV 67
TS P S P S P S P S P S P S P S P S
Sbjct: 1616 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1675
Query: 68 TELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQ 127
S P S P S P S P S P S P S P S P
Sbjct: 1676 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1735
Query: 128 SIVTEPQS 135
S P S
Sbjct: 1736 SPSYSPTS 1743
Score = 35.4 bits (81), Expect = 0.007
Identities = 35/122 (28%), Positives = 35/122 (28%)
Query: 14 PQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIVTELQSI 73
P S P S P S P S P S P S P S P S S
Sbjct: 1629 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1688
Query: 74 VTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEP 133
P S P S P S P S P S P S P S P S P
Sbjct: 1689 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSP 1748
Query: 134 QS 135
S
Sbjct: 1749 TS 1750
Score = 35.4 bits (81), Expect = 0.008
Identities = 36/128 (28%), Positives = 36/128 (28%)
Query: 8 TSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIV 67
TS S P S P S P S P S P S P S P S
Sbjct: 1602 TSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1661
Query: 68 TELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQ 127
S P S P S P S P S P S P S P S P
Sbjct: 1662 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1721
Query: 128 SIVTEPQS 135
S P S
Sbjct: 1722 SPSYSPTS 1729
Score = 34.3 bits (78), Expect = 0.021
Identities = 35/121 (28%), Positives = 35/121 (28%)
Query: 8 TSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIV 67
TS P S P S P S P S P S P S P S P S
Sbjct: 1630 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1689
Query: 68 TELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQ 127
S P S P S P S P S P S P S P S P
Sbjct: 1690 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1749
Query: 128 S 128
S
Sbjct: 1750 S 1750
Score = 32.7 bits (74), Expect = 0.067
Identities = 35/120 (29%), Positives = 36/120 (30%)
Query: 2 SESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVA 61
S S + TS P S P S P S P S P S P S P S
Sbjct: 1631 SPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1690
Query: 62 EPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQS 121
P S S P S P S P S P S P S P S P S
Sbjct: 1691 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTS 1750
Score = 32.4 bits (73), Expect = 0.090
Identities = 36/128 (28%), Positives = 36/128 (28%)
Query: 8 TSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIV 67
TS P S P S P S S P S P S P S P S
Sbjct: 1581 TSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1640
Query: 68 TELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQ 127
S P S P S P S P S P S P S P S P
Sbjct: 1641 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1700
Query: 128 SIVTEPQS 135
S P S
Sbjct: 1701 SPSYSPTS 1708
Score = 31.6 bits (71), Expect = 0.14
Identities = 36/135 (26%), Positives = 38/135 (28%)
Query: 1 MSESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIV 60
S + +S P S P S P S P S S P S P S
Sbjct: 1567 TSPAYMPSSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSATSPSYSPTSPSYSPTSPS 1626
Query: 61 AEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQ 120
P S S P S P S P S P S P S P S P
Sbjct: 1627 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1686
Query: 121 SIVAEPQSIVTEPQS 135
S P S P S
Sbjct: 1687 SPSYSPTSPSYSPTS 1701
Score = 30.4 bits (68), Expect = 0.30
Identities = 39/135 (28%), Positives = 40/135 (29%)
Query: 1 MSESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIV 60
S S + TS P S P S P S P S P S P S P S
Sbjct: 1602 TSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1661
Query: 61 AEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQ 120
P S S P S P S P S P S P S P S P
Sbjct: 1662 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1721
Query: 121 SIVAEPQSIVTEPQS 135
S P S P S
Sbjct: 1722 SPSYSPTSPSYSPTS 1736
Score = 27.3 bits (60), Expect = 3.2
Identities = 42/176 (23%), Positives = 51/176 (28%), Gaps = 6/176 (3%)
Query: 4 SVALTSIVTEPQSIVTEPQSIVAEPQSIV------TEPQSIVAEPQSIVTEPQSIVAEPQ 57
S TS + S S P S P S P S P S P
Sbjct: 1536 SPGYTSPFSSAMSPGYGLTSPSYSPSSPGYSTSPAYMPSSPSYSPTSPSYSPTSPSYSPT 1595
Query: 58 SIVAEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVT 117
S P S S P S P S P S P S P S P S
Sbjct: 1596 SPSYSPTSPSYSATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1655
Query: 118 EPQSIVAEPQSIVTEPQSIVVSQAKLPRTVITFYMGQSTQTFSISTLSPRPILLSY 173
P S P S P S S + + ++ ++S ++ S P SY
Sbjct: 1656 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSY 1711
>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 = 35.5 bits (81), Expect = 0.008
Identities = 39/135 (28%), Positives = 40/135 (29%)
Query: 1 MSESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIV 60
S S + TS P S P S P S P S P S P S P S
Sbjct: 1573 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1632
Query: 61 AEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQ 120
P S S P S P S P S P S P S P S P
Sbjct: 1633 YSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1692
Query: 121 SIVAEPQSIVTEPQS 135
S P S P S
Sbjct: 1693 SPNYSPTSPSYSPTS 1707
Score = 34.3 bits (78), Expect = 0.016
Identities = 38/135 (28%), Positives = 40/135 (29%)
Query: 1 MSESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIV 60
S S + TS P S P S P S P S P S P S P S
Sbjct: 1587 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1646
Query: 61 AEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQ 120
P S S P S P S P S P S P S P S P
Sbjct: 1647 YSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPNYSPTSPSYSPT 1706
Query: 121 SIVAEPQSIVTEPQS 135
S P S P+
Sbjct: 1707 SPGYSPGSPAYSPKQ 1721
Score = 33.1 bits (75), Expect = 0.042
Identities = 38/135 (28%), Positives = 40/135 (29%)
Query: 1 MSESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIV 60
S + + TS P S P S P S P S P S P S P S
Sbjct: 1552 TSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1611
Query: 61 AEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQ 120
P S S P S P S P S P S P S P S P
Sbjct: 1612 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPT 1671
Query: 121 SIVAEPQSIVTEPQS 135
S P S P S
Sbjct: 1672 SPSYSPTSPSYSPTS 1686
Score = 32.8 bits (74), Expect = 0.062
Identities = 36/126 (28%), Positives = 36/126 (28%)
Query: 14 PQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIVTELQSI 73
P S P S P S P S P S P S P S P S S
Sbjct: 1558 PTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1617
Query: 74 VTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEP 133
P S P S P S P S P S P S P S P S P
Sbjct: 1618 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSP 1677
Query: 134 QSIVVS 139
S S
Sbjct: 1678 TSPSYS 1683
Score = 32.8 bits (74), Expect = 0.065
Identities = 37/128 (28%), Positives = 37/128 (28%)
Query: 8 TSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIV 67
TS P S P S P S P S P S P S P S P S
Sbjct: 1545 TSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1604
Query: 68 TELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQ 127
S P S P S P S P S P S P S P S P
Sbjct: 1605 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPT 1664
Query: 128 SIVTEPQS 135
S P S
Sbjct: 1665 SPSYSPTS 1672
Score = 32.0 bits (72), Expect = 0.11
Identities = 37/135 (27%), Positives = 39/135 (28%)
Query: 1 MSESVALTSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIV 60
S ++S P S P S P S P S P S P S P S
Sbjct: 1531 TSPGFGVSSPGFSPTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1590
Query: 61 AEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQ 120
P S S P S P S P S P S P S P S P
Sbjct: 1591 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPT 1650
Query: 121 SIVAEPQSIVTEPQS 135
S P S P S
Sbjct: 1651 SPSYSPTSPAYSPTS 1665
Score = 31.2 bits (70), Expect = 0.18
Identities = 37/128 (28%), Positives = 37/128 (28%)
Query: 8 TSIVTEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIV 67
TS P S P S P S P S P S P S P S P S
Sbjct: 1566 TSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS 1625
Query: 68 TELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQ 127
S P S P S P S P S P S P S P S P
Sbjct: 1626 YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPT 1685
Query: 128 SIVTEPQS 135
S P S
Sbjct: 1686 SPSYSPTS 1693
Score = 29.7 bits (66), Expect = 0.66
Identities = 34/121 (28%), Positives = 34/121 (28%)
Query: 21 PQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVAEPQSIVTELQSIVTEPQSI 80
P S P S P S P S P S P S P S S P S
Sbjct: 1544 PTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1603
Query: 81 VAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVVSQ 140
P S P S P S P S P S P S P S P S S
Sbjct: 1604 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSP 1663
Query: 141 A 141
Sbjct: 1664 T 1664
Score = 26.6 bits (58), Expect = 5.3
Identities = 33/132 (25%), Positives = 40/132 (30%)
Query: 42 PQSIVTEPQSIVAEPQSIVAEPQSIVTELQSIVTEPQSIVAEPQSIVTEPQSIVAEPQSI 101
P S P S P S P S S P S P S P S P S
Sbjct: 1544 PTSPTYSPTSPAYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP 1603
Query: 102 VTEPQSIVAEPQSIVTEPQSIVAEPQSIVTEPQSIVVSQAKLPRTVITFYMGQSTQTFSI 161
P S P S P S P S P S S + + ++ +S
Sbjct: 1604 SYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPAYSP 1663
Query: 162 STLSPRPILLSY 173
++ S P SY
Sbjct: 1664 TSPSYSPTSPSY 1675
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
0.307 0.122 0.310
Gapped
Lambda K H
0.267 0.0531 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,014,840
Number of extensions: 102889
Number of successful extensions: 168
Number of sequences better than 10.0: 1
Number of HSP's gapped: 126
Number of HSP's successfully gapped: 23
Length of query: 179
Length of database: 6,701,793
Length adjustment: 87
Effective length of query: 92
Effective length of database: 4,272,666
Effective search space: 393085272
Effective search space used: 393085272
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 54 (25.0 bits)