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= psy11392
(169 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CKZ|B Chain B, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25.
pdb|2CKZ|D Chain D, X-Ray Structure Of Rna Polymerase Iii Subcomplex C17-C25
Length = 218
Score = 78.2 bits (191), Expect = 2e-15, Method: Compositional matrix adjust.
Identities = 39/100 (39%), Positives = 58/100 (58%), Gaps = 15/100 (15%)
Query: 2 LYDITKIEDSVIIPGD--------GASH-------TKVFPNVGLCMMLYDITKIEDSVII 46
++ ++KI D V IP D +H K+ PNVGLC+ +YD+ +E+ +
Sbjct: 1 MFILSKIADLVRIPPDQFHRDTISAITHQLNNKFANKIIPNVGLCITIYDLLTVEEGQLK 60
Query: 47 PGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGVHDS 86
PGDG+S+ V FR VVF+PF+ EI+ G I C+ EG+ S
Sbjct: 61 PGDGSSYINVTFRAVVFKPFLGEIVTGWISKCTAEGIKVS 100
>pdb|3AYH|B Chain B, Crystal Structure Of The C1725 SUBCOMPLEX FROM S. POMBE
RNA Polymerase Iii
Length = 203
Score = 71.6 bits (174), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 30/63 (47%), Positives = 45/63 (71%)
Query: 22 TKVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKE 81
KV N+GL + +YD KI + +I GDG+S+ V FR ++FRPF E+++GKI+SCS+E
Sbjct: 36 NKVIQNIGLAICVYDFLKIGEGIIKYGDGSSYMNVVFRLIIFRPFRGEVMLGKIKSCSEE 95
Query: 82 GVH 84
G+
Sbjct: 96 GIR 98
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 52.0 bits (123), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 35/53 (66%)
Query: 30 LCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
LC++ YD I+ I+P DG++ V++R VVF+PF E++ G + SCS+ G
Sbjct: 46 LCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHG 98
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 22/53 (41%), Positives = 35/53 (66%)
Query: 30 LCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
LC++ YD I+ I+P DG++ V++R VVF+PF E++ G + SCS+ G
Sbjct: 46 LCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGEVVDGTVVSCSQHG 98
>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 = 37.0 bits (84), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 32/53 (60%)
Query: 30 LCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
+C++ + I+ ++PG G + +V++R V++RPF E++ + + +K G
Sbjct: 47 ICVLDSNTIDIDKGRVVPGQGFAEFEVKYRAVLWRPFRGEVVDAIVTTVNKMG 99
>pdb|2WAQ|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|E Chain E, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
pdb|2WB1|T Chain T, The Complete Structure Of The Archaeal 13-Subunit Dna-
Directed Rna Polymerase
Length = 180
Score = 33.1 bits (74), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVF 63
K+ ++GL + + ++ E+ +++ GDGA++ +VEF + +
Sbjct: 37 KILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMITY 77
>pdb|2PMZ|E Chain E, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|2PMZ|T Chain T, Archaeal Rna Polymerase From Sulfolobus Solfataricus
pdb|3HKZ|E Chain E, The X-Ray Crystal Structure Of Rna Polymerase From
Archaea
pdb|3HKZ|Q Chain Q, The X-Ray Crystal Structure Of Rna Polymerase From
Archaea
Length = 180
Score = 33.1 bits (74), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 11/41 (26%), Positives = 27/41 (65%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVF 63
K+ ++GL + + ++ E+ +++ GDGA++ +VEF + +
Sbjct: 37 KILKDLGLVLAILNVKTSEEGILVFGDGATYHEVEFDMITY 77
>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 = 32.7 bits (73), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%)
Query: 29 GLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGV 83
G + + I I VI PG G V+++ +VFRPF E++ + +K G+
Sbjct: 43 GFVIAVTTIDNIGAGVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVVTQVNKVGL 97
>pdb|2Y0S|E Chain E, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|2Y0S|T Chain T, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
P21 Space Group
pdb|4AYB|E Chain E, Rnap At 3.2ang
pdb|4B1O|E Chain E, Archaeal Rnap-Dna Binary Complex At 4.32ang
pdb|4B1P|T Chain T, Archaeal Rnap-Dna Binary Complex At 4.32ang
Length = 180
Score = 32.7 bits (73), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 34/124 (27%), Positives = 58/124 (46%), Gaps = 13/124 (10%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
K+ ++GL + + ++ E+ +++ GDGA++ +VEF + + P V E++ G++ G
Sbjct: 37 KILKDLGLVLAILNVKTSEEGMLVFGDGATYHEVEFDMITYVPVVQEVVEGEVLQVDNYG 96
Query: 83 VHDSQSSNQPEQPISDSTVKDILKY-------FAEKDKP-----DPVRDFLMGAIAPALR 130
V + IS T D LKY F EK K D VR ++ +
Sbjct: 97 VFVNLGPMDGLVHISQIT-DDTLKYDNVRGIIFGEKSKKVIQKGDKVRARVISVASTVTG 155
Query: 131 SLPR 134
LPR
Sbjct: 156 RLPR 159
>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 = 31.6 bits (70), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 14/49 (28%), Positives = 30/49 (61%)
Query: 27 NVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKI 75
+VG + + D+ I + ++ GDG+++ V F +V+ P + E+I G++
Sbjct: 41 DVGFVLSIVDVKDIGEGKVVHGDGSAYHPVVFETLVYIPEMYELIEGEV 89
>pdb|1VP4|A Chain A, Crystal Structure Of A Putative Aminotransferase (Tm1131)
From Thermotoga Maritima Msb8 At 1.82 A Resolution
pdb|1VP4|B Chain B, Crystal Structure Of A Putative Aminotransferase (Tm1131)
From Thermotoga Maritima Msb8 At 1.82 A Resolution
Length = 425
Score = 27.7 bits (60), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 6/68 (8%)
Query: 94 QPISDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKYEM 153
Q S +++ILK+ A+KD G P + PR + KEI E + Y +
Sbjct: 26 QNXKSSIIREILKFAADKDA------ISFGGGVPDPETFPRKELAEIAKEIIEKEYHYTL 79
Query: 154 IAEEQSGD 161
GD
Sbjct: 80 QYSTTEGD 87
>pdb|1GZ3|A Chain A, Molecular Mechanism For The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
pdb|1GZ3|B Chain B, Molecular Mechanism For The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
pdb|1GZ3|C Chain C, Molecular Mechanism For The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
pdb|1GZ3|D Chain D, Molecular Mechanism For The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
Length = 554
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 12 VIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVII 46
V PG G ++ +FP V L ++L + I DSV +
Sbjct: 440 VFTPGQG-NNVYIFPGVALAVILCNTRHISDSVFL 473
>pdb|3STX|A Chain A, Crystal Structure Of Tomato Methylketone Synthase I H243a
Variant Complexed With Beta-Ketoheptanoate
pdb|3STX|B Chain B, Crystal Structure Of Tomato Methylketone Synthase I H243a
Variant Complexed With Beta-Ketoheptanoate
Length = 267
Score = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 25/41 (60%), Gaps = 1/41 (2%)
Query: 97 SDSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLF 137
+D+ K+ LK EK+ PD V++ + G+ A + S P+ LF
Sbjct: 217 NDALKKEFLKLMIEKNPPDEVKE-IEGSDAVTMMSKPQQLF 256
>pdb|1GZ4|A Chain A, Molecular Mechanism Of The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
pdb|1GZ4|B Chain B, Molecular Mechanism Of The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
pdb|1GZ4|C Chain C, Molecular Mechanism Of The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
pdb|1GZ4|D Chain D, Molecular Mechanism Of The Regulation Of Human
Mitochondrial Nad(P)+-Dependent Malic Enzyme By Atp And
Fumarate
Length = 551
Score = 26.2 bits (56), Expect = 9.8, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 12 VIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVII 46
V PG G ++ +FP V L ++L + I DSV +
Sbjct: 437 VFTPGQG-NNVYIFPGVALAVILCNTRHISDSVFL 470
>pdb|1QR6|A Chain A, Human Mitochondrial Nad(P)-Dependent Malic Enzyme
pdb|1QR6|B Chain B, Human Mitochondrial Nad(P)-Dependent Malic Enzyme
Length = 584
Score = 26.2 bits (56), Expect = 9.8, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 12 VIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVII 46
V PG G ++ +FP V L ++L + I DSV +
Sbjct: 459 VFTPGQG-NNVYIFPGVALAVILCNTRHISDSVFL 492
>pdb|1EFK|A Chain A, Structure Of Human Malic Enzyme In Complex With
Ketomalonate
pdb|1EFK|B Chain B, Structure Of Human Malic Enzyme In Complex With
Ketomalonate
pdb|1EFK|C Chain C, Structure Of Human Malic Enzyme In Complex With
Ketomalonate
pdb|1EFK|D Chain D, Structure Of Human Malic Enzyme In Complex With
Ketomalonate
pdb|1EFL|A Chain A, Human Malic Enzyme In A Quaternary Complex With Nad, Mg,
And Tartronate
pdb|1EFL|B Chain B, Human Malic Enzyme In A Quaternary Complex With Nad, Mg,
And Tartronate
pdb|1EFL|C Chain C, Human Malic Enzyme In A Quaternary Complex With Nad, Mg,
And Tartronate
pdb|1EFL|D Chain D, Human Malic Enzyme In A Quaternary Complex With Nad, Mg,
And Tartronate
pdb|1PJL|A Chain A, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|B Chain B, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|C Chain C, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|D Chain D, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|E Chain E, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|F Chain F, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|G Chain G, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
pdb|1PJL|H Chain H, Crystal Structure Of Human M-Nad-Me In Ternary Complex
With Nad And Lu3+
Length = 584
Score = 26.2 bits (56), Expect = 9.8, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 1/35 (2%)
Query: 12 VIIPGDGASHTKVFPNVGLCMMLYDITKIEDSVII 46
V PG G ++ +FP V L ++L + I DSV +
Sbjct: 459 VFTPGQG-NNVYIFPGVALAVILCNTRHISDSVFL 492
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
0.319 0.137 0.395
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,136,514
Number of Sequences: 62578
Number of extensions: 201702
Number of successful extensions: 360
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 344
Number of HSP's gapped (non-prelim): 26
length of query: 169
length of database: 14,973,337
effective HSP length: 92
effective length of query: 77
effective length of database: 9,216,161
effective search space: 709644397
effective search space used: 709644397
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 48 (23.1 bits)