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= 033231
         (124 letters)

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

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



>pdb|1QKL|A Chain A, Hrpabc14.4, Essential Subunit Of Human Rna Polymerases I,
           Ii And Iii
          Length = 127

 Score =  133 bits (334), Expect = 3e-32,   Method: Compositional matrix adjust.
 Identities = 64/77 (83%), Positives = 69/77 (89%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERAR+LGTRALQI+M APVMVELEGETDPL IAMKEL+ RKIP  IRRYL
Sbjct: 51  RITTPYMTKYERARVLGTRALQIAMCAPVMVELEGETDPLLIAMKELKARKIPIIIRRYL 110

Query: 99  PDGSYEDWGVDELIVED 115
           PDGSYEDWGVDELI+ D
Sbjct: 111 PDGSYEDWGVDELIITD 127


>pdb|1I3Q|F Chain F, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|F Chain F, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|F Chain F, Rna Polymerase Ii Elongation Complex
 pdb|1K83|F Chain F, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 pdb|1NIK|F Chain F, Wild Type Rna Polymerase Ii
 pdb|1NT9|F Chain F, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|F Chain F, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|F Chain F, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|F Chain F, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|F Chain F, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 pdb|1R9T|F Chain F, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 pdb|1TWA|F Chain F, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|F Chain F, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|F Chain F, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|F Chain F, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|F Chain F, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|F Chain F, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|F Chain F, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|F Chain F, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|F Chain F, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|F Chain F, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|F Chain F, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|F Chain F, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|F Chain F, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 pdb|2E2I|F Chain F, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 pdb|2E2J|F Chain F, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 pdb|2NVQ|F Chain F, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 pdb|2NVT|F Chain F, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 pdb|2NVX|F Chain F, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 pdb|2NVY|F Chain F, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|F Chain F, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 pdb|2JA5|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|R Chain R, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|F Chain F, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2YU9|F Chain F, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 pdb|2R7Z|F Chain F, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|F Chain F, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|F Chain F, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|F Chain F, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3CQZ|F Chain F, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|F Chain F, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|F Chain F, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|F Chain F, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|F Chain F, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|F Chain F, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 pdb|3GTM|F Chain F, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|F Chain F, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|F Chain F, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|F Chain F, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|G Chain G, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|F Chain F, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|R Chain R, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|F Chain F, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|F Chain F, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|F Chain F, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|F Chain F, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|F Chain F, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|F Chain F, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|F Chain F, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|F Chain F, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3K7A|F Chain F, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|F Chain F, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|F Chain F, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|F Chain F, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|F Chain F, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|F Chain F, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
 pdb|3RZD|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|F Chain F, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|F Chain F, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|F Chain F, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|F Chain F, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|F Chain F, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 1)
 pdb|3S1N|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 2)
 pdb|3S1Q|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Atp
 pdb|3S1R|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Gtp
 pdb|3S2D|F Chain F, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           Containing A 5br- U
 pdb|3S2H|F Chain F, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
           Containing A 2[prime]-Iodo Atp
 pdb|4A3C|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|F Chain F, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|F Chain F, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|F Chain F, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
 pdb|4BBR|F Chain F, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|F Chain F, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 155

 Score =  131 bits (329), Expect = 1e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 79  RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 138

Query: 99  PDGSYEDWGVDELIVE 114
           PDGS+EDW V+ELIV+
Sbjct: 139 PDGSFEDWSVEELIVD 154


>pdb|3J0K|F Chain F, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
          Length = 84

 Score =  130 bits (328), Expect = 2e-31,   Method: Compositional matrix adjust.
 Identities = 62/76 (81%), Positives = 68/76 (89%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV V+LEGETDPL IAMKEL E+KIP  IRRYL
Sbjct: 8   RATTPYMTKYERARILGTRALQISMNAPVFVDLEGETDPLRIAMKELAEKKIPLVIRRYL 67

Query: 99  PDGSYEDWGVDELIVE 114
           PDGS+EDW V+ELIV+
Sbjct: 68  PDGSFEDWSVEELIVD 83


>pdb|3H0G|F Chain F, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|R Chain R, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 142

 Score =  130 bits (326), Expect = 3e-31,   Method: Compositional matrix adjust.
 Identities = 60/74 (81%), Positives = 67/74 (90%)

Query: 39  RKTSKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPFTIRRYL 98
           R T+ YMTKYERARILGTRALQISMNAPV+V+LEGETDPL+IAMKEL ++KIP  +RRYL
Sbjct: 69  RTTTPYMTKYERARILGTRALQISMNAPVLVDLEGETDPLQIAMKELAQKKIPLLVRRYL 128

Query: 99  PDGSYEDWGVDELI 112
           PDGSYEDW V ELI
Sbjct: 129 PDGSYEDWSVAELI 142


>pdb|2WAQ|K Chain K, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|I Chain I, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
 pdb|2WB1|K Chain K, The Complete Structure Of The Archaeal 13-Subunit Dna-
           Directed Rna Polymerase
          Length = 95

 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%), Gaps = 2/59 (3%)

Query: 45  MTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDG 101
           +T+YE AR++  RALQ++M AP ++++     TD + IA +E R   +P TIRR LP+G
Sbjct: 27  LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPNG 85


>pdb|2PMZ|K Chain K, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|2PMZ|W Chain W, Archaeal Rna Polymerase From Sulfolobus Solfataricus
 pdb|3HKZ|K Chain K, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
 pdb|3HKZ|U Chain U, The X-Ray Crystal Structure Of Rna Polymerase From Archaea
          Length = 95

 Score = 56.2 bits (134), Expect = 5e-09,   Method: Compositional matrix adjust.
 Identities = 26/59 (44%), Positives = 40/59 (67%), Gaps = 2/59 (3%)

Query: 45  MTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDG 101
           +T+YE AR++  RALQ++M AP ++++     TD + IA +E R   +P TIRR LP+G
Sbjct: 27  LTRYEIARVISARALQLAMGAPALIDINNLSSTDVISIAEEEFRRGVLPITIRRRLPNG 85


>pdb|2Y0S|I Chain I, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|2Y0S|K Chain K, Crystal Structure Of Sulfolobus Shibatae Rna Polymerase In
           P21 Space Group
 pdb|4AYB|K Chain K, Rnap At 3.2ang
 pdb|4B1O|K Chain K, Archaeal Rnap-Dna Binary Complex At 4.32ang
 pdb|4B1P|I Chain I, Archaeal Rnap-Dna Binary Complex At 4.32ang
          Length = 95

 Score = 55.1 bits (131), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 40/59 (67%), Gaps = 2/59 (3%)

Query: 45  MTKYERARILGTRALQISMNAPVMVELEG--ETDPLEIAMKELRERKIPFTIRRYLPDG 101
           +T+YE AR++  RALQ++M AP ++++     TD + IA +E +   +P TIRR LP+G
Sbjct: 27  LTRYEIARVISARALQLAMGAPALIDINNISSTDVISIAEEEFKRGVLPITIRRRLPNG 85


>pdb|3SGZ|A Chain A, High Resolution Crystal Structure Of Rat Long Chain
           Hydroxy Acid Oxidase In Complex With The Inhibitor
           4-Carboxy-5-[(4-Chiorophenyl) Sulfanyl]-1, 2,
           3-Thiadiazole.
 pdb|3SGZ|B Chain B, High Resolution Crystal Structure Of Rat Long Chain
           Hydroxy Acid Oxidase In Complex With The Inhibitor
           4-Carboxy-5-[(4-Chiorophenyl) Sulfanyl]-1, 2,
           3-Thiadiazole.
 pdb|3SGZ|C Chain C, High Resolution Crystal Structure Of Rat Long Chain
           Hydroxy Acid Oxidase In Complex With The Inhibitor
           4-Carboxy-5-[(4-Chiorophenyl) Sulfanyl]-1, 2,
           3-Thiadiazole
          Length = 352

 Score = 30.4 bits (67), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 8/63 (12%)

Query: 49  ERARILGTRALQISMNAPVM--------VELEGETDPLEIAMKELRERKIPFTIRRYLPD 100
           +RA  LG +AL I+++ PV+         +L  E + L+ A++ L+E K   ++    P 
Sbjct: 142 QRAEALGFKALVITIDTPVLGNRRRDKRNQLNLEANILKAALRALKEEKPTQSVPVLFPK 201

Query: 101 GSY 103
            S+
Sbjct: 202 ASF 204


>pdb|1G6Q|1 Chain 1, Crystal Structure Of Yeast Arginine Methyltransferase,
           Hmt1
 pdb|1G6Q|2 Chain 2, Crystal Structure Of Yeast Arginine Methyltransferase,
           Hmt1
 pdb|1G6Q|3 Chain 3, Crystal Structure Of Yeast Arginine Methyltransferase,
           Hmt1
 pdb|1G6Q|4 Chain 4, Crystal Structure Of Yeast Arginine Methyltransferase,
           Hmt1
 pdb|1G6Q|5 Chain 5, Crystal Structure Of Yeast Arginine Methyltransferase,
           Hmt1
 pdb|1G6Q|6 Chain 6, Crystal Structure Of Yeast Arginine Methyltransferase,
           Hmt1
          Length = 328

 Score = 25.4 bits (54), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 13/51 (25%), Positives = 24/51 (47%)

Query: 42  SKYMTKYERARILGTRALQISMNAPVMVELEGETDPLEIAMKELRERKIPF 92
           S +  K+    ++G     I   A  +VEL G +D + +   +L +  +PF
Sbjct: 53  SMFAAKHGAKHVIGVDMSSIIEMAKELVELNGFSDKITLLRGKLEDVHLPF 103


  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
   0.317    0.135    0.393 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,718,385
Number of Sequences: 62578
Number of extensions: 92846
Number of successful extensions: 202
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 191
Number of HSP's gapped (non-prelim): 9
length of query: 124
length of database: 14,973,337
effective HSP length: 85
effective length of query: 39
effective length of database: 9,654,207
effective search space: 376514073
effective search space used: 376514073
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)