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= 048593
(150 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 31.2 bits (69), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 20 KDQCYFLSVTNLKSIGRERGTVNESGVVFFPVTFLCRTFLPVKGEILHG 68
KD + LS+ ++K IG E V+ G + PV F ++P E++ G
Sbjct: 40 KDVGFVLSIVDVKDIG-EGKVVHGDGSAYHPVVFETLVYIPEMYELIEG 87
>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 = 27.7 bits (60), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 24 YFLSVTNLKSIGRERGTVNES-GVVFFPVTFLCRTFLPVKGEILHGVI 70
+ ++VT + +IG G + G V +PV + F P KGE++ V+
Sbjct: 44 FVIAVTTIDNIGA--GVIQPGRGFVLYPVKYKAIVFRPFKGEVVDAVV 89
>pdb|2R11|A Chain A, Crystal Structure Of Putative Hydrolase (2632844) From
Bacillus Subtilis At 1.96 A Resolution
pdb|2R11|B Chain B, Crystal Structure Of Putative Hydrolase (2632844) From
Bacillus Subtilis At 1.96 A Resolution
pdb|2R11|C Chain C, Crystal Structure Of Putative Hydrolase (2632844) From
Bacillus Subtilis At 1.96 A Resolution
pdb|2R11|D Chain D, Crystal Structure Of Putative Hydrolase (2632844) From
Bacillus Subtilis At 1.96 A Resolution
Length = 306
Score = 27.7 bits (60), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 15/52 (28%), Positives = 28/52 (53%), Gaps = 3/52 (5%)
Query: 43 ESGVVFFPVTFLCR--TFLP-VKGEILHGVIHIAVCEQPFFSNEQQAKIRNG 91
E V++ P + L R +F+P ++ E++ H+ EQP + NE+ + N
Sbjct: 255 EHEVIYDPHSALHRASSFVPDIEAEVIKNAGHVLSXEQPTYVNERVXRFFNA 306
>pdb|2B8K|G Chain G, 12-Subunit Rna Polymerase Ii
Length = 215
Score = 26.9 bits (58), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 7 TRLLKGLINEKACKDQC-YFLSVTNLKSIGRERGTV-NESGVVFFPVTFLCRTFLPVKGE 64
T+LL+ + E +C + Y L V + +I +RG + G F V + F P KGE
Sbjct: 28 TKLLEEV--EGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGE 85
Query: 65 ILHGVI 70
++ G +
Sbjct: 86 VVDGTV 91
>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 = 26.6 bits (57), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 4/66 (6%)
Query: 7 TRLLKGLINEKACKDQ-CYFLSVTNLKSIGRERGTV-NESGVVFFPVTFLCRTFLPVKGE 64
T+LL+ + E +C + Y L V + +I +RG + G F V + F P KGE
Sbjct: 28 TKLLEEV--EGSCTGKFGYILCVLDYDNIDIQRGRILPTDGSAEFNVKYRAVVFKPFKGE 85
Query: 65 ILHGVI 70
++ G +
Sbjct: 86 VVDGTV 91
>pdb|3KDW|A Chain A, Crystal Structure Of Putative Sugar Binding Protein
(Yp_001300177.1) From Bacteroides Vulgatus Atcc 8482 At
1.70 A Resolution
Length = 221
Score = 26.2 bits (56), Expect = 7.0, Method: Compositional matrix adjust.
Identities = 20/77 (25%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 61 VKGEILHGVIHIA----VCEQPFFSNEQQAKIRNGLVVQFLVTAVQWIDEGRNLKKKYLV 116
VK +GV+ + V P E++A+I +LV A ++ + N KK+
Sbjct: 130 VKDGXTYGVVXVTYKATVDXIPTLKEEEKAQI-----XAWLVEAREFAXDAENSNKKHAA 184
Query: 117 FGRVEGESLGPVSLSGW 133
FG+ +G +S G+
Sbjct: 185 FGKYKGRINNYLSKRGY 201
>pdb|2QF2|A Chain A, Rat Cytosolic Pepck In Complex With Oxaloacetic Acid And
Gdp.
pdb|2QF2|B Chain B, Rat Cytosolic Pepck In Complex With Oxaloacetic Acid And
Gdp.
pdb|2QEW|A Chain A, Rat Cytosolic Pepck, In Complex With Manganese Ion.
pdb|2QEY|A Chain A, Rat Cytosolic Pepck In Complex With Gtp
pdb|2QF1|A Chain A, Rat Cytosolic Pepck In Complex With Oxaloacetic Acid.
pdb|2RK7|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Oxalate
pdb|2RK7|B Chain B, The Structure Of Rat Cytosolic Pepck In Complex With
Oxalate
pdb|2RK8|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Phosphonoformate
pdb|2RK8|B Chain B, The Structure Of Rat Cytosolic Pepck In Complex With
Phosphonoformate
pdb|2RKA|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Phosphoglycolate
pdb|2RKA|C Chain C, The Structure Of Rat Cytosolic Pepck In Complex With
Phosphoglycolate
pdb|2RKD|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With 3-
Phosphonopropionate
pdb|2RKE|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Sulfoacetate.
pdb|3DT2|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Oxalate And Gtp
pdb|3DT4|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Oxalate And Gtp
pdb|3DT4|C Chain C, The Structure Of Rat Cytosolic Pepck In Complex With
Oxalate And Gtp
pdb|3DT7|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With Beta-
Sulfopyruvate And Gtp
pdb|3DT7|B Chain B, The Structure Of Rat Cytosolic Pepck In Complex With Beta-
Sulfopyruvate And Gtp
pdb|3DTB|A Chain A, The Structure Of Rat Cytosolic Pepck In Complex With
Phosphoglycolate And Gdp
pdb|3DTB|B Chain B, The Structure Of Rat Cytosolic Pepck In Complex With
Phosphoglycolate And Gdp
Length = 624
Score = 25.8 bits (55), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 103 WIDEGRNLKKKYLVFGRVEGESLGPVSLSGWAGTDD-INLKML 144
W G N + +FGR+EGE ++ G+ +D +NLK L
Sbjct: 529 WPGFGENSRVLEWMFGRIEGEDSAKLTPIGYVPKEDALNLKGL 571
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
0.324 0.141 0.422
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,146,090
Number of Sequences: 62578
Number of extensions: 152770
Number of successful extensions: 309
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 308
Number of HSP's gapped (non-prelim): 8
length of query: 150
length of database: 14,973,337
effective HSP length: 90
effective length of query: 60
effective length of database: 9,341,317
effective search space: 560479020
effective search space used: 560479020
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 47 (22.7 bits)