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= 040426
         (120 letters)

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

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



>pdb|3QT1|I Chain I, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
           Subunit
          Length = 133

 Score = 47.8 bits (112), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 35/118 (29%), Positives = 52/118 (44%), Gaps = 14/118 (11%)

Query: 9   FLFCKFCGTML----RMESNHVV--CSSCKFKKNVQDVADREISYAVTAEEIKRELGISL 62
           F FC+ C  ML      E+N ++  C +C +   V++     +        I    G+  
Sbjct: 24  FRFCRDCNNMLYPREDKENNRLLFECRTCSY---VEEAGSPLVYRHELITNIGETAGVV- 79

Query: 63  FEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
               Q    +  L +  R C KC + E  +   Q RSADE  TT+Y C  CGHR +E+
Sbjct: 80  ----QDIGSDPTLPRSDRECPKCHSRENVFFQLQIRSADEPMTTFYKCVNCGHRWKEN 133


>pdb|1QYP|A Chain A, Thermococcus Celer Rpb9, Nmr, 25 Structures
          Length = 57

 Score = 41.2 bits (95), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 18/41 (43%), Positives = 22/41 (53%)

Query: 75  LSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115
           L   K  C KC N   Y+   QTR+ DE  T +Y C +CGH
Sbjct: 11  LPTTKITCPKCGNDTAYWWEMQTRAGDEPSTIFYKCTKCGH 51


>pdb|1TFI|A Chain A, A Novel Zn Finger Motif In The Basal Transcriptional
           Machinery: Three-Dimensional Nmr Studies Of The Nucleic-
           Acid Binding Domain Of Transcriptional Elongation Factor
           Tfiis
          Length = 50

 Score = 38.1 bits (87), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 17/36 (47%), Positives = 22/36 (61%)

Query: 81  ACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHR 116
            C KC+     Y+  QTRSADE  TT+ +C  CG+R
Sbjct: 11  TCGKCKKKNCTYTQVQTRSADEPMTTFVVCNECGNR 46


>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
          Length = 309

 Score = 35.4 bits (80), Expect = 0.008,   Method: Compositional matrix adjust.
 Identities = 17/37 (45%), Positives = 23/37 (62%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQ 118
           C KC+  ++ Y   QTRSADE  TT+  C  CG+R +
Sbjct: 271 CGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWK 307


>pdb|1Y1V|S Chain S, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|S Chain S, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
          Length = 179

 Score = 35.0 bits (79), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 18/39 (46%), Positives = 24/39 (61%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
           C KC+  ++ Y   QTRSADE  TT+  C  CG+R + S
Sbjct: 141 CGKCKEKKVSYYQLQTRSADEPLTTFCTCEACGNRWKFS 179


>pdb|3GTM|S Chain S, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
          Length = 173

 Score = 33.5 bits (75), Expect = 0.033,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 23/39 (58%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
           C KC+  ++ Y   QTRSAD   TT+  C  CG+R + S
Sbjct: 135 CGKCKEKKVSYYQLQTRSADHPLTTFCTCEACGNRWKFS 173


>pdb|1I3Q|I Chain I, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|I Chain I, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|I Chain I, Rna Polymerase Ii Elongation Complex
 pdb|1K83|I Chain I, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
           With The Inhibitor Alpha Amanitin
 pdb|1NIK|I Chain I, Wild Type Rna Polymerase Ii
 pdb|1NT9|I Chain I, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|I Chain I, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|I Chain I, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
           Matched Nucleotide
 pdb|1R9T|I Chain I, Rna Polymerase Ii Strand Separated Elongation Complex,
           Mismatched Nucleotide
 pdb|1TWA|I Chain I, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|I Chain I, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|I Chain I, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|I Chain I, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|I Chain I, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|I Chain I, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|I Chain I, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|I Chain I, Complete Rna Polymerase Ii Elongation Complex With
           Substrate Analogue Gmpcpp
 pdb|1Y1V|I Chain I, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|I Chain I, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|I Chain I, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|I Chain I, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|I Chain I, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With Gtp
 pdb|2E2I|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dgtp
 pdb|2E2J|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
           Gmpcpp
 pdb|2NVQ|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           2'dutp
 pdb|2NVT|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Gmpcpp
 pdb|2NVX|I Chain I, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With 2'-
           Dutp
 pdb|2NVY|I Chain I, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|I Chain I, Rna Polymerase Ii Elongation Complex With Utp, Updated
           112006
 pdb|2JA5|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           A
 pdb|2JA6|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           B
 pdb|2JA7|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA7|U Chain U, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           C
 pdb|2JA8|I Chain I, Cpd Lesion Containing Rna Polymerase Ii Elongation Complex
           D
 pdb|2YU9|I Chain I, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
           Utp
 pdb|2R7Z|I Chain I, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
           Complex
 pdb|2R92|I Chain I, Elongation Complex Of Rna Polymerase Ii With Artificial
           Rdrp Scaffold
 pdb|2R93|I Chain I, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
           Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|I Chain I, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
           Elongation Complex
 pdb|3CQZ|I Chain I, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
           Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|I Chain I, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|I Chain I, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|I Chain I, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|I Chain I, Backtracked Rna Polymerase Ii Complex With 13mer With G<>u
           Mismatch
 pdb|3GTM|I Chain I, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|I Chain I, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|I Chain I, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|I Chain I, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|J Chain J, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
           Active Site
 pdb|3HOU|I Chain I, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOU|U Chain U, Complete Rna Polymerase Ii Elongation Complex I With A T-U
           Mismatch
 pdb|3HOV|I Chain I, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iii With A
           T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|I Chain I, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|I Chain I, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|I Chain I, Complete Rna Polymerase Ii Elongation Complex Iv With A
           T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex D
 pdb|3I4N|I Chain I, 8-oxoguanine Containing Rna Polymerase Ii Elongation
           Complex E
 pdb|3K1F|I Chain I, Crystal Structure Of Rna Polymerase Ii In Complex With
           Tfiib
 pdb|3K7A|I Chain I, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|I Chain I, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|I Chain I, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|I Chain I, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|I Chain I, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3RZD|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|I Chain I, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|I Chain I, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|I Chain I, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|I Chain I, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 1)
 pdb|3S1N|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           (Variant 2)
 pdb|3S1Q|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Atp
 pdb|3S1R|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt 3'-Deoxy
           Rna Soaked With Gtp
 pdb|3S2D|I Chain I, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
           Containing A 5br- U
 pdb|3S2H|I Chain I, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
           Containing A 2[prime]-Iodo Atp
 pdb|3J0K|I Chain I, Orientation Of Rna Polymerase Ii Within The Human
           Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid
 pdb|4A3B|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid
 pdb|4A3D|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid
 pdb|4A3E|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 5nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 6nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid
 pdb|4A3L|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 7nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 4nt
           Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|I Chain I, Rna Polymerase Ii Initial Transcribing Complex With A 2nt
           Dna-Rna Hybrid
 pdb|4A3I|I Chain I, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|I Chain I, Rna Polymerase Ii Elongation Complex Containing A Cpd
           Lesion
 pdb|4BBR|I Chain I, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|I Chain I, Structure Of An Initially Transcribing Rna Polymerase Ii-
           Tfiib Complex
          Length = 122

 Score = 32.3 bits (72), Expect = 0.069,   Method: Compositional matrix adjust.
 Identities = 26/113 (23%), Positives = 43/113 (38%), Gaps = 14/113 (12%)

Query: 9   FLFCKFCGTML----RMESNHVV--CSSCKFKKNVQDVADREISYAVTAEEIKRELGISL 62
           F FC+ C  ML      E+N ++  C +C +   V++     +        I    G+  
Sbjct: 4   FRFCRDCNNMLYPREDKENNRLLFECRTCSY---VEEAGSPLVYRHELITNIGETAGVV- 59

Query: 63  FEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGH 115
               Q    +  L +  R C KC + E  +   Q R  D     +++C  C H
Sbjct: 60  ----QDIGSDPTLPRSDRECPKCHSRENVFFQSQQRRKDTSMVLFFVCLSCSH 108


>pdb|3RF2|A Chain A, Crystal Structure Of 30s Ribosomal Protein S8 From Aquifex
           Aeolicus
          Length = 168

 Score = 32.0 bits (71), Expect = 0.086,   Method: Compositional matrix adjust.
 Identities = 25/102 (24%), Positives = 45/102 (44%), Gaps = 16/102 (15%)

Query: 2   ADPLGRDFLFCKFCGTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGIS 61
            DP+    +F      ++R + + +   S K K+ + DV             +K+E  I 
Sbjct: 4   VDPIAD--MFSAIKNAIMRRD-DFLYVPSSKLKERILDV-------------LKKEGFIQ 47

Query: 62  LFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEG 103
            +E  +G+K E +  K+K   EK  NP+M    +Q    ++G
Sbjct: 48  DWEALKGEKYEEEYKKMKELAEKSPNPKMKRYLKQLEEYNKG 89


>pdb|3H0G|I Chain I, Rna Polymerase Ii From Schizosaccharomyces Pombe
 pdb|3H0G|U Chain U, Rna Polymerase Ii From Schizosaccharomyces Pombe
          Length = 113

 Score = 30.0 bits (66), Expect = 0.36,   Method: Compositional matrix adjust.
 Identities = 25/116 (21%), Positives = 41/116 (35%), Gaps = 20/116 (17%)

Query: 8   DFLFCKFCGTMLRMESNHV------VCSSCKFKKNVQDVADREISYAVTAEEIKRELGIS 61
           +F +C  C  ML    + V       C +C + +            A T++  + EL  S
Sbjct: 3   NFQYCIECNNMLYPREDKVDRVLRLACRNCDYSE-----------IAATSKVYRHELQSS 51

Query: 62  LFEQ---PQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRCG 114
             E          +  L +  + C +C   E  +    +R  D   T  Y+C  CG
Sbjct: 52  NVENTTVSHDASTDPTLPRSDKECPRCHQHEAVFYQTHSRRGDTMMTLIYVCVHCG 107


>pdb|3PO3|S Chain S, Arrested Rna Polymerase Ii Reactivation Intermediate
          Length = 178

 Score = 30.0 bits (66), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 16/39 (41%), Positives = 22/39 (56%)

Query: 82  CEKCQNPEMYYSTRQTRSADEGQTTYYICPRCGHRCQES 120
           C KC+  ++ Y   QTRSA    TT+  C  CG+R + S
Sbjct: 140 CGKCKEKKVSYYQLQTRSAAAPLTTFCTCEACGNRWKFS 178


>pdb|2BX2|L Chain L, Catalytic Domain Of E. Coli Rnase E
 pdb|2C0B|L Chain L, Catalytic Domain Of E. Coli Rnase E In Complex With 13-Mer
           Rna
 pdb|2C4R|L Chain L, Catalytic Domain Of E. Coli Rnase E
          Length = 517

 Score = 28.9 bits (63), Expect = 0.70,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 7/59 (11%)

Query: 55  KRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           +R +   L E  + D+   Q+S + R         +   +RQ  S   G++++++CPRC
Sbjct: 363 QRAVENRLREAVRQDRARIQISHISRF-------GLLEMSRQRLSPSLGESSHHVCPRC 414


>pdb|1T06|A Chain A, 1.9 A Crystal Structure Of A Protein Of Unknown Function
           From Bacillus Cereus Atcc 14579
 pdb|1T06|B Chain B, 1.9 A Crystal Structure Of A Protein Of Unknown Function
           From Bacillus Cereus Atcc 14579
          Length = 235

 Score = 28.9 bits (63), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 23/87 (26%), Positives = 43/87 (49%), Gaps = 6/87 (6%)

Query: 16  GTMLRMESNHVVCSSCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQGDKGETQL 75
           G    M S++VV  +       QDVAD+ I+   + +E+K   G S +    G++ +   
Sbjct: 88  GAYFYMLSDYVVAVTLSESNIAQDVADKWIA---SGDELKMSAGWSCYCWLLGNRKDNAF 144

Query: 76  --SKVKRACEKCQNPEMYYSTRQTRSA 100
             SK+    E  ++  +++S  +T+SA
Sbjct: 145 SESKISDMLEMVKDT-IHHSPERTKSA 170


>pdb|2VMK|A Chain A, Crystal Structure Of E. Coli Rnase E Apoprotein -
           Catalytic Domain
 pdb|2VMK|B Chain B, Crystal Structure Of E. Coli Rnase E Apoprotein -
           Catalytic Domain
 pdb|2VMK|C Chain C, Crystal Structure Of E. Coli Rnase E Apoprotein -
           Catalytic Domain
 pdb|2VMK|D Chain D, Crystal Structure Of E. Coli Rnase E Apoprotein -
           Catalytic Domain
          Length = 515

 Score = 28.9 bits (63), Expect = 0.73,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 7/59 (11%)

Query: 55  KRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           +R +   L E  + D+   Q+S + R         +   +RQ  S   G++++++CPRC
Sbjct: 356 QRAVENRLREAVRQDRARIQISHISRF-------GLLEMSRQRLSPSLGESSHHVCPRC 407


>pdb|2VRT|A Chain A, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
           Fragments - Catalytic Domain
 pdb|2VRT|B Chain B, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
           Fragments - Catalytic Domain
 pdb|2VRT|C Chain C, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
           Fragments - Catalytic Domain
 pdb|2VRT|D Chain D, Crystal Structure Of E. Coli Rnase E Possessing M1 Rna
           Fragments - Catalytic Domain
          Length = 509

 Score = 28.9 bits (63), Expect = 0.74,   Method: Composition-based stats.
 Identities = 15/59 (25%), Positives = 29/59 (49%), Gaps = 7/59 (11%)

Query: 55  KRELGISLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           +R +   L E  + D+   Q+S + R         +   +RQ  S   G++++++CPRC
Sbjct: 356 QRAVENRLREAVRQDRARIQISHISRF-------GLLEMSRQRLSPSLGESSHHVCPRC 407


>pdb|4EGQ|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
           Burkholderia Pseudomallei
 pdb|4EGQ|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
           Burkholderia Pseudomallei
 pdb|4EGQ|C Chain C, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
           Burkholderia Pseudomallei
 pdb|4EGQ|D Chain D, Crystal Structure Of D-Alanine-D-Alanine Ligase B From
           Burkholderia Pseudomallei
          Length = 316

 Score = 28.9 bits (63), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 21/39 (53%)

Query: 43  REISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRA 81
           R   YA  A++I  +LG+ LF +P  +     + KVK A
Sbjct: 130 RGDDYAARAQDIVAKLGVPLFVKPASEGSSVAVEKVKSA 168


>pdb|4EG0|A Chain A, Crystal Structure Of D-Alanine--D-Alanine Ligase From
           Burkholderia Ambifaria
 pdb|4EG0|B Chain B, Crystal Structure Of D-Alanine--D-Alanine Ligase From
           Burkholderia Ambifaria
          Length = 317

 Score = 26.9 bits (58), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 14/39 (35%), Positives = 20/39 (51%)

Query: 43  REISYAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRA 81
           R   YA  A +I  +LG+ LF +P  +     + KVK A
Sbjct: 130 RGDDYAARATDIVAKLGLPLFVKPASEGSSVAVLKVKTA 168


>pdb|2EGQ|A Chain A, Solution Structure Of The Fourth Lim Domain From Human
           Four And A Half Lim Domains 1
          Length = 77

 Score = 26.6 bits (57), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 13/46 (28%), Positives = 21/46 (45%)

Query: 68  GDKGETQLSKVKRACEKCQNPEMYYSTRQTRSADEGQTTYYICPRC 113
           G  G+   + V + C  C+NP   +    +  A EGQ+ +  C  C
Sbjct: 4   GSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHC 49


>pdb|4EGJ|A Chain A, Crystal Structure Of D-Alanine-D-Alanine Ligase From
           Burkholderia Xenovorans
 pdb|4EGJ|B Chain B, Crystal Structure Of D-Alanine-D-Alanine Ligase From
           Burkholderia Xenovorans
 pdb|4EGJ|C Chain C, Crystal Structure Of D-Alanine-D-Alanine Ligase From
           Burkholderia Xenovorans
 pdb|4EGJ|D Chain D, Crystal Structure Of D-Alanine-D-Alanine Ligase From
           Burkholderia Xenovorans
          Length = 334

 Score = 26.2 bits (56), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 13/35 (37%), Positives = 19/35 (54%)

Query: 47  YAVTAEEIKRELGISLFEQPQGDKGETQLSKVKRA 81
           Y   A+EI  +LG+ LF +P  +     + KVK A
Sbjct: 151 YEARAKEIVAKLGLPLFVKPASEGSSVAVIKVKSA 185


>pdb|2PH1|A Chain A, Crystal Structure Of Nucleotide-Binding Protein Af2382
           From Archaeoglobus Fulgidus, Northeast Structural
           Genomics Target Gr165
          Length = 262

 Score = 26.2 bits (56), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 6/12 (50%), Positives = 10/12 (83%)

Query: 106 TYYICPRCGHRC 117
           +Y++CP CGH+ 
Sbjct: 192 SYFVCPNCGHKS 203


>pdb|2YV9|A Chain A, Crystal Structure Of The Clic Homologue Exc-4 From C.
           Elegans
 pdb|2YV9|B Chain B, Crystal Structure Of The Clic Homologue Exc-4 From C.
           Elegans
          Length = 291

 Score = 26.2 bits (56), Expect = 5.0,   Method: Compositional matrix adjust.
 Identities = 21/78 (26%), Positives = 33/78 (42%), Gaps = 14/78 (17%)

Query: 52  EEIKRELGISLFEQPQGDKGETQLSKVK-----------RACEKCQNPEMYYSTRQTRSA 100
           E + R   + L  + + DKG+ + S+V+           R CE+  N +   S R++R  
Sbjct: 124 ENLYRNFKLFLRAKVEFDKGKKEPSRVEDLPAQIKVHYNRVCEQLSNIDQLLSERKSRYL 183

Query: 101 DEGQTTYYIC---PRCGH 115
                T Y C   PR  H
Sbjct: 184 LGNSMTEYDCELMPRLHH 201


>pdb|2VL7|A Chain A, Structure Of S. Tokodaii Xpd4
          Length = 540

 Score = 25.8 bits (55), Expect = 6.9,   Method: Composition-based stats.
 Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 2/34 (5%)

Query: 22  ESNHVVCSSCKFKKNVQDVADREISYAVTAEEIK 55
           E + + CS C+ K  ++ + D+E S  +  EE K
Sbjct: 96  EPDEINCSKCRLKDKIKTIEDKEPSKLI--EEFK 127


>pdb|3LFU|A Chain A, Crystal Structure Of E. Coli Uvrd
          Length = 647

 Score = 25.4 bits (54), Expect = 7.5,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 37/68 (54%), Gaps = 12/68 (17%)

Query: 38  QDVADREISYAVTAEEIKRELGI-SLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQ 96
           Q+ AD  +   V  + + ++ G+ +++EQ +G+KG+T++  ++         E+  +TRQ
Sbjct: 470 QETADMPLH--VQTDRVIKDSGLRTMYEQEKGEKGQTRIENLE---------ELVTATRQ 518

Query: 97  TRSADEGQ 104
               +E +
Sbjct: 519 FSYNEEDE 526


>pdb|1HG3|A Chain A, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|B Chain B, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|C Chain C, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|D Chain D, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|E Chain E, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|F Chain F, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|G Chain G, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei.
 pdb|1HG3|H Chain H, Crystal Structure Of Tetrameric Tim From Pyrococcus
          Woesei
          Length = 225

 Score = 25.4 bits (54), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 10/38 (26%), Positives = 20/38 (52%)

Query: 30 SCKFKKNVQDVADREISYAVTAEEIKRELGISLFEQPQ 67
          +  FK  ++    R +  A  AE++ +E G+++   PQ
Sbjct: 10 AINFKTYIEATGKRALEIAKAAEKVYKETGVTIVVAPQ 47


>pdb|2IS1|A Chain A, Crystal Structure Of Uvrd-Dna-So4 Complex
 pdb|2IS1|B Chain B, Crystal Structure Of Uvrd-Dna-So4 Complex
 pdb|2IS2|A Chain A, Crystal Structure Of Uvrd-Dna Binary Complex
 pdb|2IS2|B Chain B, Crystal Structure Of Uvrd-Dna Binary Complex
 pdb|2IS4|A Chain A, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
 pdb|2IS4|B Chain B, Crystal Structure Of Uvrd-Dna-Adpnp Ternary Complex
 pdb|2IS6|A Chain A, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
 pdb|2IS6|B Chain B, Crystal Structure Of Uvrd-Dna-Adpmgf3 Ternary Complex
          Length = 680

 Score = 25.4 bits (54), Expect = 8.1,   Method: Composition-based stats.
 Identities = 16/68 (23%), Positives = 37/68 (54%), Gaps = 12/68 (17%)

Query: 38  QDVADREISYAVTAEEIKRELGI-SLFEQPQGDKGETQLSKVKRACEKCQNPEMYYSTRQ 96
           Q+ AD  +   V  + + ++ G+ +++EQ +G+KG+T++  ++         E+  +TRQ
Sbjct: 470 QETADMPLH--VQTDRVIKDSGLRTMYEQEKGEKGQTRIENLE---------ELVTATRQ 518

Query: 97  TRSADEGQ 104
               +E +
Sbjct: 519 FSYNEEDE 526


  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
   0.320    0.133    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,385,875
Number of Sequences: 62578
Number of extensions: 110348
Number of successful extensions: 276
Number of sequences better than 100.0: 28
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 254
Number of HSP's gapped (non-prelim): 31
length of query: 120
length of database: 14,973,337
effective HSP length: 82
effective length of query: 38
effective length of database: 9,841,941
effective search space: 373993758
effective search space used: 373993758
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)