RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= 045556
(96 letters)
>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
streptolydigin, antibiotic, transcription regulation;
HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3aoh_C* 3aoi_C*
3dxj_C* 3eql_C* 1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C ...
Length = 1119
Score = 58.5 bits (142), Expect = 8e-12
Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 13/67 (19%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL--------RH-----FDERYKQKGSRKLVLSKLYKA 72
+D+I NPL VP RMN+G I E L + FD + + L +
Sbjct: 867 VDVILNPLGVPSRMNLGQILETHLGLAGYFLGQRYISPIFDGAKEPEIKELLAQAFEVYF 926
Query: 73 CKQTANP 79
K+
Sbjct: 927 GKRKGEG 933
>3lu0_C DNA-directed RNA polymerase subunit beta; E. coli RNA polymerase,
nucleotidyltransferase, transcription, transferase;
11.20A {Escherichia coli} PDB: 3iyd_C*
Length = 1342
Score = 33.9 bits (78), Expect = 0.004
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 8/55 (14%)
Query: 26 IDIIFNPLEVPPRMNIGHIFECSL--------RHFDERYKQKGSRKLVLSKLYKA 72
+DI+ NPL VP RMNIG I E L + KQ+ + + +A
Sbjct: 1094 VDIVLNPLGVPSRMNIGQILETHLGMAAKGIGDKINAMLKQQQEVAKLREFIQRA 1148
>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
multi-protein complex, DNA- binding, magnesium; 3.65A
{Schizosaccharomyces pombe}
Length = 1210
Score = 33.7 bits (77), Expect = 0.004
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 27 DIIFNPLEVPPRMNIGHIFECSL 49
DII NP +P RM + H+ EC L
Sbjct: 998 DIIINPHAIPSRMTVAHLVECQL 1020
>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
mRNA, multiprotein complex; HET: UTP; 2.30A
{Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
Length = 1224
Score = 33.7 bits (77), Expect = 0.005
Identities = 11/23 (47%), Positives = 15/23 (65%)
Query: 27 DIIFNPLEVPPRMNIGHIFECSL 49
D+I NP +P RM + H+ EC L
Sbjct: 1009 DLIINPHAIPSRMTVAHLIECLL 1031
>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
Length = 1131
Score = 33.3 bits (76), Expect = 0.007
Identities = 10/21 (47%), Positives = 13/21 (61%)
Query: 27 DIIFNPLEVPPRMNIGHIFEC 47
D+I NP +P RM +G I E
Sbjct: 910 DVILNPHALPSRMTLGQIMEG 930
>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 = 31.2 bits (70), Expect = 0.035
Identities = 17/124 (13%), Positives = 27/124 (21%), Gaps = 50/124 (40%)
Query: 11 VELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECSLRHFDERY-------------- 56
EL+ F + + + P +V + L F+ Y
Sbjct: 58 AELVGKFLGY-----VSSLVEPSKVGQF---DQVLNLCLTEFENCYLEGNDIHALAAKLL 109
Query: 57 ----KQKGSRKLVLSKLYKACKQTANPCKTLD--------------------GQMGNP-- 90
K ++ A P GQ GN
Sbjct: 110 QENDTTLVKTKELIKNYITARIMAKRPFDKKSNSALFRAVGEGNAQLVAIFGGQ-GNTDD 168
Query: 91 -FKE 93
F+E
Sbjct: 169 YFEE 172
>1lb6_A TNF receptor-associated factor 6; TRAF6-CD40 complex, signaling
protein; 1.80A {Homo sapiens} SCOP: b.8.1.1 PDB: 1lb5_A
1lb4_A
Length = 160
Score = 26.0 bits (57), Expect = 2.0
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 4/39 (10%)
Query: 10 DVELLWPFFTHHRFSNIDIIFNPLEVPPRMNIGHIFECS 48
D L WPF R + +D E P R N I +
Sbjct: 73 DSHLPWPFQGTIRLTILD----QSEAPVRQNHEEIMDAK 107
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 24.8 bits (53), Expect = 5.7
Identities = 18/107 (16%), Positives = 33/107 (30%), Gaps = 31/107 (28%)
Query: 3 LEIAHFEDVELLWPF--F--THHRFSNIDIIFNPLEVPPRMNIGHIFE---CSLRHFDER 55
L++ V+ F F ++ + + L+ + + + S
Sbjct: 168 LDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQ-----KLLYQIDPNWTSRSDHSSN 222
Query: 56 YK------QKGSRKLVLSKLYKAC---------KQTANP----CKTL 83
K Q R+L+ SK Y+ C + N CK L
Sbjct: 223 IKLRIHSIQAELRRLLKSKPYENCLLVLLNVQNAKAWNAFNLSCKIL 269
>2r6a_A DNAB helicase, replicative helicase; replication, DNAB; 2.90A
{Geobacillus stearothermophilus} PDB: 2r6c_A 2r6d_A
2r6e_A 2vyf_A 2vye_A
Length = 454
Score = 24.0 bits (53), Expect = 8.8
Identities = 7/29 (24%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 10 DVELLW-PFFTHHRFSNIDIIFNPLEVPP 37
V+L + + +F N++ F+ ++PP
Sbjct: 426 TVQLAFIKEYN--KFVNLERRFDEAQIPP 452
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
0.327 0.142 0.457
Gapped
Lambda K H
0.267 0.0620 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,559,900
Number of extensions: 78661
Number of successful extensions: 197
Number of sequences better than 10.0: 1
Number of HSP's gapped: 197
Number of HSP's successfully gapped: 10
Length of query: 96
Length of database: 6,701,793
Length adjustment: 62
Effective length of query: 34
Effective length of database: 4,970,691
Effective search space: 169003494
Effective search space used: 169003494
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (23.7 bits)