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= 032941
         (130 letters)

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

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



>pdb|2F3I|A Chain A, Solution Structure Of A Subunit Of Rna Polymerase Ii
          Length = 150

 Score =  107 bits (267), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 56/112 (50%), Positives = 81/112 (72%), Gaps = 5/112 (4%)

Query: 5   VLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHT 64
           +LFEDIF V+ IDP+GKKFD+VSR+   S++  M ++LDVN ++YP+ +GDKF + +A T
Sbjct: 4   ILFEDIFDVKDIDPEGKKFDRVSRLHCESESFKMDLILDVNIQIYPVDLGDKFRLVIAST 63

Query: 65  LNLDGTPDTGYYTP-GARKTLADKYEYIMHGKLFKI-GDEGSGKS---LKAY 111
           L  DGT D G Y P   R + AD++EY+M+GK+++I GDE S ++   L AY
Sbjct: 64  LYEDGTLDDGEYNPTDDRPSRADQFEYVMYGKVYRIEGDETSTEAATRLSAY 115


>pdb|1I3Q|H Chain H, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|H Chain H, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|H Chain H, Rna Polymerase Ii Elongation Complex
 pdb|1K83|H Chain H, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 pdb|1NIK|H Chain H, Wild Type Rna Polymerase Ii
 pdb|1NT9|H Chain H, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|H Chain H, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|H Chain H, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|H Chain H, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|H Chain H, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 pdb|1R9T|H Chain H, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 pdb|1TWA|H Chain H, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|H Chain H, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|H Chain H, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|H Chain H, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|H Chain H, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|H Chain H, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|H Chain H, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|H Chain H, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|H Chain H, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|H Chain H, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|H Chain H, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|H Chain H, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|H Chain H, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 pdb|2E2I|H Chain H, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 pdb|2E2J|H Chain H, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 pdb|2NVQ|H Chain H, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 pdb|2NVT|H Chain H, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 pdb|2NVX|H Chain H, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 pdb|2NVY|H Chain H, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|H Chain H, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 pdb|2JA5|H Chain H, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|H Chain H, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|H Chain H, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|T Chain T, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|H Chain H, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2YU9|H Chain H, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 pdb|1A1D|A Chain A, Yeast Rna Polymerase Subunit Rpb8, Nmr, Minimized Average
           Structure, Alpha Carbons Only
 pdb|2R7Z|H Chain H, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|H Chain H, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|H Chain H, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|H Chain H, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3CQZ|H Chain H, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|H Chain H, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|H Chain H, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|H Chain H, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|H Chain H, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|H Chain H, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 pdb|3GTM|H Chain H, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|H Chain H, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|H Chain H, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|H Chain H, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|I Chain I, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|H Chain H, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|T Chain T, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|H Chain H, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|H Chain H, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|H Chain H, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|H Chain H, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|H Chain H, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|H Chain H, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|H Chain H, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|H Chain H, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3K7A|H Chain H, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|H Chain H, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|H Chain H, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|H Chain H, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|H Chain H, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|H Chain H, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
 pdb|3RZD|H Chain H, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|H Chain H, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|H Chain H, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|H Chain H, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|H Chain H, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|H Chain H, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|H Chain H, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 1)
 pdb|3S1N|H Chain H, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 2)
 pdb|3S1Q|H Chain H, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Atp
 pdb|3S1R|H Chain H, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Gtp
 pdb|3S2D|H Chain H, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           Containing A 5br- U
 pdb|3S2H|H Chain H, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
           Containing A 2[prime]-Iodo Atp
 pdb|3J0K|H Chain H, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|H Chain H, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|H Chain H, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|H Chain H, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
 pdb|4BBR|H Chain H, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|H Chain H, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 146

 Score = 73.9 bits (180), Expect = 3e-14,   Method: Compositional matrix adjust.
 Identities = 44/106 (41%), Positives = 64/106 (60%), Gaps = 11/106 (10%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYML-LDVNSELYPMRVGDKFTM 59
           MSN  LF+DIF V ++DP   +++KV RIEA S   D   L LD+N EL+P+   D  T+
Sbjct: 1   MSN-TLFDDIFQVSEVDP--GRYNKVCRIEAASTTQDQCKLTLDINVELFPVAAQDSLTV 57

Query: 60  ALAHTLNLDGTP-----DTGYYTP--GARKTLADKYEYIMHGKLFK 98
            +A +LNL+ TP      T  + P     ++LAD Y+Y+M+G  +K
Sbjct: 58  TIASSLNLEDTPANDSSATRSWRPPQAGDRSLADDYDYVMYGTAYK 103


>pdb|3H0G|H Chain H, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|T Chain T, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 125

 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 36/111 (32%), Positives = 61/111 (54%), Gaps = 17/111 (15%)

Query: 1   MSNIVLFEDIFVVEKIDPDGKKFDKVSRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMA 60
           MS  VL ++IF V  +D   +K+ +VSRI A S   DM + LD+NS++YP+     F++ 
Sbjct: 1   MSESVLLDEIFTVTSVDK--QKYQRVSRITAVSGQNDMNLTLDINSQIYPLEKDATFSLQ 58

Query: 61  LAHTLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKAY 111
           +   LN   +PD           L +  +YIM+GK++++ +E   + +  Y
Sbjct: 59  ITSNLN---SPD-----------LKEAADYIMYGKVYRV-EEAKDEKVSVY 94


>pdb|2X7M|A Chain A, Crystal Structure Of Archaemetzincin (Amza) From
           Methanopyrus Kandleri At 1.5 A Resolution
          Length = 195

 Score = 28.9 bits (63), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 16/46 (34%), Positives = 20/46 (43%)

Query: 27  SRIEAHSQNCDMYMLLDVNSELYPMRVGDKFTMALAHTLNLDGTPD 72
           +R         +  LLD + ELY  RV  + T  L HT  L   PD
Sbjct: 113 ARCPGREAVVSVARLLDPDPELYLERVVKELTHELGHTFGLGHCPD 158


>pdb|3L4N|A Chain A, Crystal Structure Of Yeast Monothiol Glutaredoxin Grx6
          Length = 127

 Score = 26.6 bits (57), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 15/61 (24%), Positives = 32/61 (52%), Gaps = 6/61 (9%)

Query: 57  FTMALAHTLNLDGTP------DTGYYTPGARKTLADKYEYIMHGKLFKIGDEGSGKSLKA 110
           F +   ++L LD +P       T  Y+ G ++ L ++Y++I +  + ++   G G+ L+ 
Sbjct: 1   FNVQKEYSLILDLSPIIIFSKSTCSYSKGXKELLENEYQFIPNYYIIELDKHGHGEELQE 60

Query: 111 Y 111
           Y
Sbjct: 61  Y 61


>pdb|1TKL|A Chain A, Yeast Oxygen-Dependent Coproporphyrinogen Oxidase
 pdb|1TKL|B Chain B, Yeast Oxygen-Dependent Coproporphyrinogen Oxidase
 pdb|1TLB|A Chain A, Yeast Coproporphyrinogen Oxidase
 pdb|1TLB|D Chain D, Yeast Coproporphyrinogen Oxidase
 pdb|1TLB|Q Chain Q, Yeast Coproporphyrinogen Oxidase
 pdb|1TLB|S Chain S, Yeast Coproporphyrinogen Oxidase
 pdb|1TLB|U Chain U, Yeast Coproporphyrinogen Oxidase
 pdb|1TLB|W Chain W, Yeast Coproporphyrinogen Oxidase
          Length = 326

 Score = 26.2 bits (56), Expect = 5.3,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 64  TLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLF 97
           T N DGTP T ++  GA   L   Y Y   G+LF
Sbjct: 137 TWNQDGTPQTWWFGGGA--DLTPSYLYEEDGQLF 168


>pdb|1TK1|A Chain A, Yeast Oxygen-Dependent Coproporphyrinogen Oxidase
          Length = 260

 Score = 26.2 bits (56), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 64  TLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLF 97
           T N DGTP T ++  GA   L   Y Y   G+LF
Sbjct: 134 TWNQDGTPQTWWFGGGA--DLTPSYLYEEDGQLF 165


>pdb|1TXN|A Chain A, Crystal Structure Of Coproporphyrinogen Iii Oxidase
 pdb|1TXN|B Chain B, Crystal Structure Of Coproporphyrinogen Iii Oxidase
          Length = 328

 Score = 26.2 bits (56), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 15/34 (44%), Positives = 18/34 (52%), Gaps = 2/34 (5%)

Query: 64  TLNLDGTPDTGYYTPGARKTLADKYEYIMHGKLF 97
           T N DGTP T ++  GA   L   Y Y   G+LF
Sbjct: 139 TWNQDGTPQTWWFGGGA--DLTPSYLYEEDGQLF 170


>pdb|1DLC|A Chain A, Crystal Structure Of Insecticidal Delta-Endotoxin From
           Bacillus Thuringiensis At 2.5 Angstroms Resolution
          Length = 584

 Score = 25.4 bits (54), Expect = 8.9,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 1/40 (2%)

Query: 38  MYMLLDVN-SELYPMRVGDKFTMALAHTLNLDGTPDTGYY 76
           +Y+  DV+ S+ Y  R+    T  +  TL+LDG P   YY
Sbjct: 489 IYVTPDVSYSQKYRARIHYASTSQITFTLSLDGAPFNQYY 528


  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    0.138    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,337,966
Number of Sequences: 62578
Number of extensions: 172692
Number of successful extensions: 360
Number of sequences better than 100.0: 20
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 14
Number of HSP's that attempted gapping in prelim test: 350
Number of HSP's gapped (non-prelim): 20
length of query: 130
length of database: 14,973,337
effective HSP length: 88
effective length of query: 42
effective length of database: 9,466,473
effective search space: 397591866
effective search space used: 397591866
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 45 (21.9 bits)