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= 034762
         (84 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|3H0G|K Chain K, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|W Chain W, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 123

 Score = 82.8 bits (203), Expect = 5e-17,   Method: Compositional matrix adjust.
 Identities = 40/76 (52%), Positives = 53/76 (69%), Gaps = 1/76 (1%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MN P+RYE  +   G  KV+YE D+K  NAA  T+E+E+HT+ N+L  QL  DE VLFAG
Sbjct: 1  MNQPERYE-LIELMGLPKVTYELDSKSPNAAVVTLEKEDHTLANMLANQLLSDERVLFAG 59

Query: 61 YKLPHPLQYKIIVRAE 76
          YK+PHPL +  I+R +
Sbjct: 60 YKVPHPLNHNFILRVQ 75


>pdb|1I3Q|K Chain K, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|K Chain K, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|K Chain K, Rna Polymerase Ii Elongation Complex
 pdb|1K83|K Chain K, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
          With The Inhibitor Alpha Amanitin
 pdb|1NIK|K Chain K, Wild Type Rna Polymerase Ii
 pdb|1NT9|K Chain K, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|K Chain K, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|K Chain K, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex,
          Matched Nucleotide
 pdb|1R9T|K Chain K, Rna Polymerase Ii Strand Separated Elongation Complex,
          Mismatched Nucleotide
 pdb|1TWA|K Chain K, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|K Chain K, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|K Chain K, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|K Chain K, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|K Chain K, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|K Chain K, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|K Chain K, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|K Chain K, Complete Rna Polymerase Ii Elongation Complex With
          Substrate Analogue Gmpcpp
 pdb|1Y1V|K Chain K, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|K Chain K, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|K Chain K, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|K Chain K, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|K Chain K, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With
          Gtp
 pdb|2E2I|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dgtp
 pdb|2E2J|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          Gmpcpp
 pdb|2NVQ|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          2'dutp
 pdb|2NVT|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Gmpcpp
 pdb|2NVX|K Chain K, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dutp
 pdb|2NVY|K Chain K, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|K Chain K, Rna Polymerase Ii Elongation Complex With Utp, Updated
          112006
 pdb|2JA5|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex A
 pdb|2JA6|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex B
 pdb|2JA7|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA7|W Chain W, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA8|K Chain K, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|2YU9|K Chain K, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Utp
 pdb|2R7Z|K Chain K, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
          Complex
 pdb|2R92|K Chain K, Elongation Complex Of Rna Polymerase Ii With Artificial
          Rdrp Scaffold
 pdb|2R93|K Chain K, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
          Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|K Chain K, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
          Elongation Complex
 pdb|3CQZ|K Chain K, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
          Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|K Chain K, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|K Chain K, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|K Chain K, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|K Chain K, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|K Chain K, Backtracked Rna Polymerase Ii Complex With 13mer With
          G<>u Mismatch
 pdb|3GTM|K Chain K, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|K Chain K, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|K Chain K, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|K Chain K, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|L Chain L, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
          Active Site
 pdb|3HOU|K Chain K, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOU|W Chain W, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOV|K Chain K, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|K Chain K, Complete Rna Polymerase Ii Elongation Complex Iii With A
          T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|K Chain K, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|K Chain K, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|K Chain K, Complete Rna Polymerase Ii Elongation Complex Iv With A
          T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|K Chain K, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|3I4N|K Chain K, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex E
 pdb|3K1F|K Chain K, Crystal Structure Of Rna Polymerase Ii In Complex With
          Tfiib
 pdb|3K7A|K Chain K, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|K Chain K, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|K Chain K, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|K Chain K, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|K Chain K, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|K Chain K, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
          Subunit
 pdb|3RZD|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|K Chain K, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|K Chain K, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|K Chain K, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|K Chain K, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|K Chain K, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 1)
 pdb|3S1N|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 2)
 pdb|3S1Q|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Atp
 pdb|3S1R|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Gtp
 pdb|3S2D|K Chain K, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          Containing A 5br- U
 pdb|3S2H|K Chain K, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
          Containing A 2[prime]-Iodo Atp
 pdb|3J0K|K Chain K, Orientation Of Rna Polymerase Ii Within The Human
          Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid
 pdb|4A3B|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid
 pdb|4A3D|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid
 pdb|4A3E|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid
 pdb|4A3L|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|K Chain K, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid
 pdb|4A3I|K Chain K, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|K Chain K, Rna Polymerase Ii Elongation Complex Containing A Cpd
          Lesion
 pdb|4BBR|K Chain K, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|K Chain K, Structure Of An Initially Transcribing Rna Polymerase
          Ii- Tfiib Complex
          Length = 120

 Score = 77.8 bits (190), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 35/74 (47%), Positives = 49/74 (66%)

Query: 1  MNAPDRYERFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAG 60
          MNAPDR+E F++ EG  K+  + DTK  NA   T E+E+HT+GN++R +L  D  VLFA 
Sbjct: 1  MNAPDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLNDRKVLFAA 60

Query: 61 YKLPHPLQYKIIVR 74
          YK+ HP   +  +R
Sbjct: 61 YKVEHPFFARFKLR 74


>pdb|2PA8|L Chain L, X-Ray Crystal Structure Of The DL SUBCOMPLEX OF THE
          SULFOLOBUS Solfataricus Rna Polymerase
 pdb|2PMZ|L Chain L, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|2PMZ|X Chain X, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|3HKZ|L Chain L, The X-Ray Crystal Structure Of Rna Polymerase From
          Archaea
 pdb|3HKZ|V Chain V, The X-Ray Crystal Structure Of Rna Polymerase From
          Archaea
          Length = 92

 Score = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 22/46 (47%), Positives = 27/46 (58%)

Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          N     IE E+HT+GN++   L R   V FA Y  PHPL  KIIV+
Sbjct: 11 NYLELEIEGEDHTLGNLIAGTLRRISGVSFASYYQPHPLSDKIIVK 56


>pdb|2WAQ|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna-
          Directed Rna Polymerase
 pdb|2WB1|L Chain L, The Complete Structure Of The Archaeal 13-Subunit Dna-
          Directed Rna Polymerase
 pdb|2WB1|M Chain M, The Complete Structure Of The Archaeal 13-Subunit Dna-
          Directed Rna Polymerase
 pdb|2Y0S|L Chain L, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase
          In P21 Space Group
 pdb|2Y0S|M Chain M, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase
          In P21 Space Group
 pdb|4AYB|L Chain L, Rnap At 3.2ang
 pdb|4B1O|L Chain L, Archaeal Rnap-Dna Binary Complex At 4.32ang
 pdb|4B1P|M Chain M, Archaeal Rnap-Dna Binary Complex At 4.32ang
          Length = 92

 Score = 43.5 bits (101), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 21/46 (45%), Positives = 27/46 (58%)

Query: 29 NAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPHPLQYKIIVR 74
          N     IE E+HT+GN++   L +   V FA Y  PHPL  KIIV+
Sbjct: 11 NYLELEIEGEDHTLGNLIAGTLRKISGVSFASYYQPHPLTDKIIVK 56


>pdb|1PVH|B Chain B, Crystal Structure Of Leukemia Inhibitory Factor In Complex
           With Gp130
 pdb|1PVH|D Chain D, Crystal Structure Of Leukemia Inhibitory Factor In Complex
           With Gp130
          Length = 169

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 9   RFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPH 65
           R VV  GT   +  RD KI+N ++ ++  + +   +ILR  L      L + Y + H
Sbjct: 74  RIVVYLGTSLGNITRDQKILNPSALSLHSKLNATADILRGLLSNVLCRLCSKYHVGH 130


>pdb|2Q7N|B Chain B, Crystal Structure Of Leukemia Inhibitory Factor In Complex
           With Lif Receptor (Domains 1-5)
 pdb|2Q7N|D Chain D, Crystal Structure Of Leukemia Inhibitory Factor In Complex
           With Lif Receptor (Domains 1-5)
          Length = 180

 Score = 28.1 bits (61), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 9   RFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPH 65
           R VV  GT   +  RD KI+N ++ ++  + +   +ILR  L      L + Y + H
Sbjct: 85  RIVVYLGTSLGNITRDQKILNPSALSLHSKLNATADILRGLLSNVLCRLCSKYHVGH 141


>pdb|1EMR|A Chain A, Crystal Structure Of Human Leukemia Inhibitory Factor
           (Lif)
          Length = 159

 Score = 28.1 bits (61), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 17/57 (29%), Positives = 28/57 (49%)

Query: 9   RFVVPEGTKKVSYERDTKIINAASFTIEREEHTIGNILRMQLHRDENVLFAGYKLPH 65
           R VV  GT   +  RD KI+N ++ ++  + +   +ILR  L      L + Y + H
Sbjct: 64  RIVVYLGTSLGNITRDQKILNPSALSLHSKLNATADILRGLLSNVLCRLCSKYHVGH 120


>pdb|3AN1|A Chain A, Crystal Structure Of Rat D428a Mutant, Urate Bound Form
 pdb|3AN1|B Chain B, Crystal Structure Of Rat D428a Mutant, Urate Bound Form
          Length = 1331

 Score = 28.1 bits (61), Expect = 1.4,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 40  HTIGNILRMQLHRDENVLFAGYKLPHPLQYKI 71
           H  G  +R  L RDE++L  G + P   +YK+
Sbjct: 817 HKTGRPVRCMLDRDEDMLITGGRHPFLAKYKV 848


>pdb|2E3T|A Chain A, Crystal Structure Of Rat Xanthine Oxidoreductase Mutant
           (W335a And F336l)
 pdb|2E3T|B Chain B, Crystal Structure Of Rat Xanthine Oxidoreductase Mutant
           (W335a And F336l)
          Length = 1331

 Score = 28.1 bits (61), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 40  HTIGNILRMQLHRDENVLFAGYKLPHPLQYKI 71
           H  G  +R  L RDE++L  G + P   +YK+
Sbjct: 817 HKTGRPVRCMLDRDEDMLITGGRHPFLAKYKV 848


>pdb|1WYG|A Chain A, Crystal Structure Of A Rat Xanthine Dehydrogenase Triple
           Mutant (C535a, C992r And C1324s)
          Length = 1331

 Score = 27.7 bits (60), Expect = 1.5,   Method: Composition-based stats.
 Identities = 12/32 (37%), Positives = 18/32 (56%)

Query: 40  HTIGNILRMQLHRDENVLFAGYKLPHPLQYKI 71
           H  G  +R  L RDE++L  G + P   +YK+
Sbjct: 817 HKTGRPVRCMLDRDEDMLITGGRHPFLAKYKV 848


  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
   0.321    0.137    0.392 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,410,835
Number of Sequences: 62578
Number of extensions: 76620
Number of successful extensions: 215
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: 205
Number of HSP's gapped (non-prelim): 11
length of query: 84
length of database: 14,973,337
effective HSP length: 52
effective length of query: 32
effective length of database: 11,719,281
effective search space: 375016992
effective search space used: 375016992
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: 45 (21.9 bits)