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= 008500
         (563 letters)

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

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



>pdb|2ZIU|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
 pdb|2ZIX|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
          Length = 341

 Score = 32.7 bits (73), Expect = 0.51,   Method: Compositional matrix adjust.
 Identities = 62/297 (20%), Positives = 107/297 (36%), Gaps = 47/297 (15%)

Query: 279 GGHLLTRFAEKRFKYRIASNPIERSIVWTMPVPEHISQISPQGMEIPYILLIYEAEEFCN 338
           GG LL        +  I +  +  S+ W        S+     +E P +L++  AE F +
Sbjct: 37  GGQLLGALQTMECRCVIEAQAVPCSVTWRRRAGP--SEDREDWVEEPTVLVLLRAEAFVS 94

Query: 339 LVLN------ESLMDHVSLVRRHYPSHTICYLTNRLMAHISKKEK--------ERYKNPA 384
           ++ N      +S M     ++      T       L   I  +EK         R K  A
Sbjct: 95  MIDNGKQGSLDSTMKGKETLQGFVTDITAKTAGKALSLVIVDQEKCFSAQNPPRRGKQGA 154

Query: 385 N---------------NSGWRRPPVEEVLAKLTTHFFRVHSRQCIDEAEVAEHVVGLTSS 429
           N                S   R   EE L  L  H     ++      E+A+     T +
Sbjct: 155 NKQTKKQQQRQPEASIGSMVSRVDAEEALVDLQLHT-EAQAQIVQSWKELADFTCAFTKA 213

Query: 430 LASCQFRKKLTRLSVN-------ANGSLISKDSVDKNLIKKSPWLKALVSIPKVQPRYAI 482
           +A   F+K     + +       A G  +        L+    W + +  + +V    A 
Sbjct: 214 VAEAPFKKLRDETTFSFCLESDWAGGVKVDLAGRGLALV----WRRQIQQLNRVSLEMAS 269

Query: 483 AIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTV---DGLLGDNRKLGEVCSKRVY 536
           A+   YP+ + L+  Y     S  E++ LL D+ V   +G+   +R++G   S+R+Y
Sbjct: 270 AVVNAYPSPQLLVQAYQQ-CFSDKERQNLLADIQVRRGEGVTSTSRRIGPELSRRIY 325


>pdb|2ZIW|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
          Length = 341

 Score = 32.7 bits (73), Expect = 0.60,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 466 WLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTV---DGLLG 522
           W + +  + +V    A A+   YP+ + L+  Y     S  E++ LL D+ V   +G+  
Sbjct: 253 WRRQIQQLNRVSLEXASAVVNAYPSPQLLVQAYQQ-CFSDKERQNLLADIQVRRGEGVTS 311

Query: 523 DNRKLGEVCSKRVY 536
            +R++G   S+R+Y
Sbjct: 312 TSRRIGPELSRRIY 325


>pdb|2ZIV|B Chain B, Crystal Structure Of The Mus81-Eme1 Complex
          Length = 351

 Score = 32.3 bits (72), Expect = 0.74,   Method: Compositional matrix adjust.
 Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 4/74 (5%)

Query: 466 WLKALVSIPKVQPRYAIAIWKKYPTMKALLSIYMDPSKSVHEKEFLLKDLTV---DGLLG 522
           W + +  + +V    A A+   YP+ + L+  Y     S  E++ LL D+ V   +G+  
Sbjct: 263 WRRQIQQLNRVSLEMASAVVNAYPSPQLLVQAYQQ-CFSDKERQNLLADIQVRRGEGVTS 321

Query: 523 DNRKLGEVCSKRVY 536
            +R++G   S+R+Y
Sbjct: 322 TSRRIGPELSRRIY 335


>pdb|1RLR|A Chain A, Structure Of Ribonucleotide Reductase Protein R1
          Length = 761

 Score = 28.9 bits (63), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|6R1R|A Chain A, Ribonucleotide Reductase E441d Mutant R1 Protein From
           Escherichia Coli
 pdb|6R1R|B Chain B, Ribonucleotide Reductase E441d Mutant R1 Protein From
           Escherichia Coli
 pdb|6R1R|C Chain C, Ribonucleotide Reductase E441d Mutant R1 Protein From
           Escherichia Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 7.8,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAZ|A Chain A, Ribonucleotide Reductase Y730no2y And C439s Modified R1
           Subunit Of E. Coli
 pdb|2XAZ|B Chain B, Ribonucleotide Reductase Y730no2y And C439s Modified R1
           Subunit Of E. Coli
 pdb|2XAZ|C Chain C, Ribonucleotide Reductase Y730no2y And C439s Modified R1
           Subunit Of E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|5R1R|A Chain A, Ribonucleotide Reductase E441a Mutant R1 Protein From
           Escherichia Coli
 pdb|5R1R|B Chain B, Ribonucleotide Reductase E441a Mutant R1 Protein From
           Escherichia Coli
 pdb|5R1R|C Chain C, Ribonucleotide Reductase E441a Mutant R1 Protein From
           Escherichia Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAP|A Chain A, Ribonucleotide Reductase Y731no2y Modified R1 Subunit Of
           E. Coli To 2.1 A Resolution
 pdb|2XAP|B Chain B, Ribonucleotide Reductase Y731no2y Modified R1 Subunit Of
           E. Coli To 2.1 A Resolution
 pdb|2XAP|C Chain C, Ribonucleotide Reductase Y731no2y Modified R1 Subunit Of
           E. Coli To 2.1 A Resolution
 pdb|2XO5|A Chain A, Ribonucleotide Reductase Y731nh2y Modified R1 Subunit Of
           E. Coli
 pdb|2XO5|B Chain B, Ribonucleotide Reductase Y731nh2y Modified R1 Subunit Of
           E. Coli
 pdb|2XO5|C Chain C, Ribonucleotide Reductase Y731nh2y Modified R1 Subunit Of
           E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAK|A Chain A, Ribonucleotide Reductase Y730no2y Modified R1 Subunit Of
           E. Coli
 pdb|2XAK|B Chain B, Ribonucleotide Reductase Y730no2y Modified R1 Subunit Of
           E. Coli
 pdb|2XAK|C Chain C, Ribonucleotide Reductase Y730no2y Modified R1 Subunit Of
           E. Coli
 pdb|2XO4|A Chain A, Ribonucleotide Reductase Y730nh2y Modified R1 Subunit Of
           E. Coli
 pdb|2XO4|B Chain B, Ribonucleotide Reductase Y730nh2y Modified R1 Subunit Of
           E. Coli
 pdb|2XO4|C Chain C, Ribonucleotide Reductase Y730nh2y Modified R1 Subunit Of
           E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|3R1R|A Chain A, Ribonucleotide Reductase R1 Protein With Amppnp Occupying
           The Activity Site From Escherichia Coli
 pdb|3R1R|B Chain B, Ribonucleotide Reductase R1 Protein With Amppnp Occupying
           The Activity Site From Escherichia Coli
 pdb|3R1R|C Chain C, Ribonucleotide Reductase R1 Protein With Amppnp Occupying
           The Activity Site From Escherichia Coli
 pdb|2R1R|A Chain A, Ribonucleotide Reductase R1 Protein With Dttp Occupying
           The Specificity Site From Escherichia Coli
 pdb|2R1R|B Chain B, Ribonucleotide Reductase R1 Protein With Dttp Occupying
           The Specificity Site From Escherichia Coli
 pdb|2R1R|C Chain C, Ribonucleotide Reductase R1 Protein With Dttp Occupying
           The Specificity Site From Escherichia Coli
 pdb|2X0X|A Chain A, Ribonucleotide Reductase R1 Subunit Of E. Coli To 2.3 A
           Resolution
 pdb|2X0X|B Chain B, Ribonucleotide Reductase R1 Subunit Of E. Coli To 2.3 A
           Resolution
 pdb|2X0X|C Chain C, Ribonucleotide Reductase R1 Subunit Of E. Coli To 2.3 A
           Resolution
 pdb|3UUS|A Chain A, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex
 pdb|3UUS|B Chain B, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex
 pdb|3UUS|C Chain C, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex
 pdb|3UUS|D Chain D, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex
 pdb|4ERM|A Chain A, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex At 4 Angstroms
           Resolution
 pdb|4ERM|B Chain B, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex At 4 Angstroms
           Resolution
 pdb|4ERM|C Chain C, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex At 4 Angstroms
           Resolution
 pdb|4ERM|D Chain D, Crystal Structure Of The Datp Inhibited E. Coli Class Ia
           Ribonucleotide Reductase Complex At 4 Angstroms
           Resolution
 pdb|4ERP|A Chain A, Crystal Structure Of A Gemcitabine-Diphosphate Inhibited
           E. Coli Class Ia Ribonucleotide Reductase Complex
 pdb|4ERP|B Chain B, Crystal Structure Of A Gemcitabine-Diphosphate Inhibited
           E. Coli Class Ia Ribonucleotide Reductase Complex
 pdb|4ERP|C Chain C, Crystal Structure Of A Gemcitabine-Diphosphate Inhibited
           E. Coli Class Ia Ribonucleotide Reductase Complex
 pdb|4ERP|D Chain D, Crystal Structure Of A Gemcitabine-Diphosphate Inhibited
           E. Coli Class Ia Ribonucleotide Reductase Complex
          Length = 761

 Score = 28.9 bits (63), Expect = 8.0,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|7R1R|A Chain A, Ribonucleotide Reductase E441q Mutant R1 Protein From
           Escherichia Coli
 pdb|7R1R|B Chain B, Ribonucleotide Reductase E441q Mutant R1 Protein From
           Escherichia Coli
 pdb|7R1R|C Chain C, Ribonucleotide Reductase E441q Mutant R1 Protein From
           Escherichia Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|4R1R|A Chain A, Ribonucleotide Reductase R1 Protein With Substrate, Gdp
           And Effector Dttp From Escherichia Coli
 pdb|4R1R|B Chain B, Ribonucleotide Reductase R1 Protein With Substrate, Gdp
           And Effector Dttp From Escherichia Coli
 pdb|4R1R|C Chain C, Ribonucleotide Reductase R1 Protein With Substrate, Gdp
           And Effector Dttp From Escherichia Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAW|A Chain A, Ribonucleotide Reductase Y730no2y And Y731f Modified R1
           Subunit Of E. Coli
 pdb|2XAW|B Chain B, Ribonucleotide Reductase Y730no2y And Y731f Modified R1
           Subunit Of E. Coli
 pdb|2XAW|C Chain C, Ribonucleotide Reductase Y730no2y And Y731f Modified R1
           Subunit Of E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAY|A Chain A, Ribonucleotide Reductase Y730no2y And C439a Modified R1
           Subunit Of E. Coli
 pdb|2XAY|B Chain B, Ribonucleotide Reductase Y730no2y And C439a Modified R1
           Subunit Of E. Coli
 pdb|2XAY|C Chain C, Ribonucleotide Reductase Y730no2y And C439a Modified R1
           Subunit Of E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAV|A Chain A, Ribonucleotide Reductase Y731no2y And Y730f Modified R1
           Subunit Of E. Coli
 pdb|2XAV|B Chain B, Ribonucleotide Reductase Y731no2y And Y730f Modified R1
           Subunit Of E. Coli
 pdb|2XAV|C Chain C, Ribonucleotide Reductase Y731no2y And Y730f Modified R1
           Subunit Of E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|1R1R|A Chain A, Ribonucleotide Reductase R1 Protein Mutant Y730f With A
           Reduced Active Site From Escherichia Coli
 pdb|1R1R|B Chain B, Ribonucleotide Reductase R1 Protein Mutant Y730f With A
           Reduced Active Site From Escherichia Coli
 pdb|1R1R|C Chain C, Ribonucleotide Reductase R1 Protein Mutant Y730f With A
           Reduced Active Site From Escherichia Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


>pdb|2XAX|A Chain A, Ribonucleotide Reductase Y730no2y And Y731a Modified R1
           Subunit Of E. Coli
 pdb|2XAX|B Chain B, Ribonucleotide Reductase Y730no2y And Y731a Modified R1
           Subunit Of E. Coli
 pdb|2XAX|C Chain C, Ribonucleotide Reductase Y730no2y And Y731a Modified R1
           Subunit Of E. Coli
          Length = 761

 Score = 28.9 bits (63), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 1/42 (2%)

Query: 251 MQKWAKGKFAQDSIVTEIDAKVVELGSVGGHLLTRFAEKRFK 292
           ++K A G+F   ++   +  K+VE+G    HLL  + E+ FK
Sbjct: 89  LRKKAYGQFEPPALYDHV-VKMVEMGKYDNHLLEDYTEEEFK 129


  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    0.132    0.389 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,904,534
Number of Sequences: 62578
Number of extensions: 547812
Number of successful extensions: 1081
Number of sequences better than 100.0: 17
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 17
Number of HSP's that attempted gapping in prelim test: 1081
Number of HSP's gapped (non-prelim): 17
length of query: 563
length of database: 14,973,337
effective HSP length: 104
effective length of query: 459
effective length of database: 8,465,225
effective search space: 3885538275
effective search space used: 3885538275
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: 54 (25.4 bits)