BLASTP 2.2.26 [Sep-21-2011]
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.
Reference for compositional score matrix adjustment: Altschul, Stephen F.,
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.
Query= 032315
(143 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2C35|B Chain B, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|D Chain D, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|F Chain F, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
pdb|2C35|H Chain H, Subunits Rpb4 And Rpb7 Of Human Rna Polymerase Ii
Length = 172
Score = 107 bits (268), Expect = 2e-24, Method: Compositional matrix adjust.
Identities = 56/125 (44%), Positives = 81/125 (64%), Gaps = 4/125 (3%)
Query: 3 DVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMV 62
+VEGTC+G++GF +A+T ++IG G+I+ G V + V+ + IVFRPFKGE++ A VT V
Sbjct: 33 EVEGTCTGKYGFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQV 92
Query: 63 NKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKIIGTQV 118
NK+G E G + F IP +ME + P Y T D + IQ+D E+ LKI+GT+V
Sbjct: 93 NKVGLFTEIGPMSCFISRHSIPSEMEFDPNSNPPCYKTMDEDIVIQQDDEIRLKIVGTRV 152
Query: 119 DVTEI 123
D +I
Sbjct: 153 DKNDI 157
>pdb|3H0G|G Chain G, Rna Polymerase Ii From Schizosaccharomyces Pombe
pdb|3H0G|S Chain S, Rna Polymerase Ii From Schizosaccharomyces Pombe
Length = 172
Score = 94.4 bits (233), Expect = 2e-20, Method: Compositional matrix adjust.
Identities = 51/129 (39%), Positives = 79/129 (61%), Gaps = 8/129 (6%)
Query: 1 MKDVEGTCSGRHGFAVAITGAESIG--KGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAG 58
+ DVEGTCSG++G+ + + + +I KG + G F V+ + +++RPF+GE++ A
Sbjct: 32 LADVEGTCSGQYGYIICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAI 91
Query: 59 VTMVNKMGFLAEAGAVQIFC---LIPDDMELQ-TGDLPSYTTSDGSVKIQKDCELWLKII 114
VT VNKMGF A G + +F L+P DM+ T + P+Y+ D I+K + LKI+
Sbjct: 92 VTTVNKMGFFANIGPLNVFVSSHLVPPDMKFDPTANPPNYSGEDQV--IEKGSNVRLKIV 149
Query: 115 GTQVDVTEI 123
GT+ D TEI
Sbjct: 150 GTRTDATEI 158
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 63.9 bits (154), Expect = 3e-11, Method: Compositional matrix adjust.
Identities = 39/133 (29%), Positives = 74/133 (55%), Gaps = 14/133 (10%)
Query: 1 MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVT-----FLVRCQCIVFRPFKGEIL 55
+++VEG+C+G+ G+ + + ++I I+ G +L T F V+ + +VF+PFKGE++
Sbjct: 31 LEEVEGSCTGKFGYILCVLDYDNID---IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVV 87
Query: 56 GAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWL 111
V ++ GF + G +++F L+P D+ G + PSY +S+ + I+ + +
Sbjct: 88 DGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIK--SRIRV 145
Query: 112 KIIGTQVDVTEIE 124
KI G V+ I
Sbjct: 146 KIEGCISQVSSIH 158
>pdb|1NT9|G Chain G, Complete 12-Subunit Rna Polymerase Ii
pdb|1PQV|G Chain G, Rna Polymerase Ii-Tfiis Complex
pdb|1WCM|G Chain G, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
pdb|1Y1W|G Chain G, Complete Rna Polymerase Ii Elongation Complex
pdb|1Y77|G Chain G, Complete Rna Polymerase Ii Elongation Complex With
Substrate Analogue Gmpcpp
pdb|1Y1V|G Chain G, Refined Rna Polymerase Ii-tfiis Complex
pdb|1Y1Y|G Chain G, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
pdb|1Y14|B Chain B, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|1Y14|D Chain D, Crystal Structure Of Yeast Subcomplex Of Rpb4 And Rpb7
pdb|2B63|G Chain G, Complete Rna Polymerase Ii-Rna Inhibitor Complex
pdb|2JA5|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
A
pdb|2JA6|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
B
pdb|2JA7|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA7|S Chain S, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
C
pdb|2JA8|G Chain G, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
D
pdb|2R7Z|G Chain G, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
Complex
pdb|2R92|G Chain G, Elongation Complex Of Rna Polymerase Ii With Artificial
Rdrp Scaffold
pdb|2R93|G Chain G, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
Delta Virus-Derived Rna Stem Loop
pdb|2VUM|G Chain G, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
Elongation Complex
pdb|3FKI|G Chain G, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
pdb|3H3V|H Chain H, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
Active Site
pdb|3HOU|G Chain G, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOU|S Chain S, Complete Rna Polymerase Ii Elongation Complex I With A T-U
Mismatch
pdb|3HOV|G Chain G, Complete Rna Polymerase Ii Elongation Complex Ii
pdb|3HOW|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iii With A
T-U Mismatch And A Frayed Rna 3'-Uridine
pdb|3HOX|G Chain G, Complete Rna Polymerase Ii Elongation Complex V
pdb|3HOY|G Chain G, Complete Rna Polymerase Ii Elongation Complex Vi
pdb|3HOZ|G Chain G, Complete Rna Polymerase Ii Elongation Complex Iv With A
T-U Mismatch And A Frayed Rna 3'-Guanine
pdb|3I4M|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex D
pdb|3I4N|G Chain G, 8-oxoguanine Containing Rna Polymerase Ii Elongation
Complex E
pdb|3K1F|G Chain G, Crystal Structure Of Rna Polymerase Ii In Complex With
Tfiib
pdb|3PO2|G Chain G, Arrested Rna Polymerase Ii Elongation Complex
pdb|3PO3|G Chain G, Arrested Rna Polymerase Ii Reactivation Intermediate
pdb|3QT1|G Chain G, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
Subunit
pdb|3J0K|G Chain G, Orientation Of Rna Polymerase Ii Within The Human
Vp16-Mediator-Pol Ii-Tfiif Assembly
pdb|4A3C|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid
pdb|4A3B|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid
pdb|4A3D|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid
pdb|4A3E|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3F|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3J|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid And Soaked With Gmpcpp
pdb|4A3K|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid
pdb|4A3L|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3M|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
Dna-Rna Hybrid And Soaked With Ampcpp
pdb|4A3G|G Chain G, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
Dna-Rna Hybrid
pdb|4A3I|G Chain G, Rna Polymerase Ii Binary Complex With Dna
pdb|4A93|G Chain G, Rna Polymerase Ii Elongation Complex Containing A Cpd
Lesion
pdb|4BBR|G Chain G, Structure Of Rna Polymerase Ii-tfiib Complex
pdb|4BBS|G Chain G, Structure Of An Initially Transcribing Rna Polymerase Ii-
Tfiib Complex
Length = 171
Score = 63.2 bits (152), Expect = 5e-11, Method: Compositional matrix adjust.
Identities = 39/133 (29%), Positives = 74/133 (55%), Gaps = 14/133 (10%)
Query: 1 MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVT-----FLVRCQCIVFRPFKGEIL 55
+++VEG+C+G+ G+ + + ++I I+ G +L T F V+ + +VF+PFKGE++
Sbjct: 31 LEEVEGSCTGKFGYILCVLDYDNID---IQRGRILPTDGSAEFNVKYRAVVFKPFKGEVV 87
Query: 56 GAGVTMVNKMGFLAEAGAVQIFC---LIPDDMELQTG-DLPSYTTSDGSVKIQKDCELWL 111
V ++ GF + G +++F L+P D+ G + PSY +S+ + I+ + +
Sbjct: 88 DGTVVSCSQHGFEVQVGPMKVFVTKHLMPQDLTFNAGSNPPSYQSSEDVITIKS--RIRV 145
Query: 112 KIIGTQVDVTEIE 124
KI G V+ I
Sbjct: 146 KIEGCISQVSSIH 158
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE
RNA Polymerase Iii
Length = 203
Score = 33.5 bits (75), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 37/77 (48%), Gaps = 11/77 (14%)
Query: 13 GFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTMVNKMGFLAEAG 72
G A+ + IG+G+I+ G V + I+FRPF+GE+ M+ K+ +E G
Sbjct: 43 GLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEV------MLGKIKSCSEEG 96
Query: 73 ---AVQIF--CLIPDDM 84
+ F IP DM
Sbjct: 97 IRVTISFFDDIFIPKDM 113
>pdb|2VSQ|A Chain A, Structure Of Surfactin A Synthetase C (Srfa-C), A
Nonribosomal Peptide Synthetase Termination Module
Length = 1304
Score = 26.9 bits (58), Expect = 3.9, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 81 PDDMELQTGDLPSYTTSDGSVKIQKDCELWLKIIGTQVDVTEIEKARRE 129
P + +TGDL + DG+++ + +KI G ++++ EIEK +E
Sbjct: 835 PGETLYRTGDLARWL-PDGTIEYAGRIDDQVKIRGHRIELEEIEKQLQE 882
>pdb|1GO3|E Chain E, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
pdb|1GO3|M Chain M, Structure Of An Archeal Homolog Of The Eukaryotic Rna
Polymerase Ii Rpb4RPB7 COMPLEX
Length = 187
Score = 26.9 bits (58), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 32/74 (43%)
Query: 1 MKDVEGTCSGRHGFAVAITGAESIGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVT 60
M+ EG GF ++I + IG+G + +G V + +V+ P E++ V
Sbjct: 31 MEKYEGRLDKDVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEVV 90
Query: 61 MVNKMGFLAEAGAV 74
V + G G +
Sbjct: 91 DVVEFGSFVRLGPL 104
>pdb|3AGJ|B Chain B, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|D Chain D, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|F Chain F, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
pdb|3AGJ|H Chain H, Crystal Structure Of Archaeal Pelota And Gtp-bound Ef1
Alpha Complex
Length = 358
Score = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 24 IGKGLIRNGTVLVTFLVRCQCIVFRPFKGEILGAGVTM 61
+G G R V++T +R I F+PF G++ +G+ +
Sbjct: 48 VGSG--RKERVVMTLRIRLDSIEFQPFTGKLRISGIVV 83
>pdb|1PUJ|A Chain A, Structure Of B. Subtilis Ylqf Gtpase
Length = 282
Score = 25.8 bits (55), Expect = 8.8, Method: Compositional matrix adjust.
Identities = 12/23 (52%), Positives = 15/23 (65%)
Query: 87 QTGDLPSYTTSDGSVKIQKDCEL 109
+TGD P TTS VK+ K+ EL
Sbjct: 147 KTGDRPGITTSQQWVKVGKELEL 169
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.322 0.139 0.412
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,180,096
Number of Sequences: 62578
Number of extensions: 158528
Number of successful extensions: 349
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 334
Number of HSP's gapped (non-prelim): 11
length of query: 143
length of database: 14,973,337
effective HSP length: 89
effective length of query: 54
effective length of database: 9,403,895
effective search space: 507810330
effective search space used: 507810330
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 46 (22.3 bits)