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= 022911
         (290 letters)

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

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



>pdb|3R2D|A Chain A, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Dsrna
 pdb|3R2D|B Chain B, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Dsrna
          Length = 149

 Score = 31.6 bits (70), Expect = 0.49,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 190 VVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-QIVINEAVD 246
           +VD    H+  ID ++    K     R+  +E + L L ++E+  + ++    V  + VD
Sbjct: 51  LVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVD 110

Query: 247 LAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASK 284
           L K++ D  A + +NG L    +     A I +SK  K
Sbjct: 111 LVKKYADEKAGKFVNGVLSAIYK-----AYITSSKEEK 143


>pdb|2JR0|A Chain A, Solution Structure Of Nusb From Aquifex Aeolicus
 pdb|3R2C|A Chain A, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Boxa Rna
 pdb|3R2C|B Chain B, Crystal Structure Of Antitermination Factors Nusb And Nuse
           In Complex With Boxa Rna
 pdb|4EYA|A Chain A, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|B Chain B, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|C Chain C, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|D Chain D, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|E Chain E, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|F Chain F, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|G Chain G, Crystal Structure Of A Plectonemic Rna Supercoil
 pdb|4EYA|H Chain H, Crystal Structure Of A Plectonemic Rna Supercoil
          Length = 148

 Score = 31.6 bits (70), Expect = 0.50,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 190 VVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-QIVINEAVD 246
           +VD    H+  ID ++    K     R+  +E + L L ++E+  + ++    V  + VD
Sbjct: 50  LVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVD 109

Query: 247 LAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASK 284
           L K++ D  A + +NG L    +     A I +SK  K
Sbjct: 110 LVKKYADEKAGKFVNGVLSAIYK-----AYITSSKEEK 142


>pdb|3IMQ|A Chain A, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex
 pdb|3IMQ|B Chain B, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex
 pdb|3IMQ|C Chain C, Crystal Structure Of The Nusb101-S10(Delta Loop) Complex
          Length = 141

 Score = 30.0 bits (66), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 218 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 264
           +E ++L +A+ E++      +++ INEA++LAK F    + + +NG L
Sbjct: 82  VEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAENSHKFVNGVL 129


>pdb|1EY1|A Chain A, Solution Structure Of Escherichia Coli Nusb
          Length = 139

 Score = 30.0 bits (66), Expect = 1.4,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 218 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 264
           +E ++L +A+ E++      +++ INEA++LAK F    + + +NG L
Sbjct: 80  VEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVL 127


>pdb|3D3B|A Chain A, Structural And Functional Analysis Of The E. Coli Nusb-s10
           Transcription Antitermination Complex.
 pdb|3D3C|A Chain A, Structural And Functional Analysis Of The E. Coli Nusb-S10
           Transcription Antitermination Complex.
 pdb|3D3C|B Chain B, Structural And Functional Analysis Of The E. Coli Nusb-S10
           Transcription Antitermination Complex.
 pdb|3D3C|C Chain C, Structural And Functional Analysis Of The E. Coli Nusb-S10
           Transcription Antitermination Complex
          Length = 141

 Score = 30.0 bits (66), Expect = 1.5,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 218 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 264
           +E ++L +A+ E++      +++ INEA++LAK F    + + +NG L
Sbjct: 82  VEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVL 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
   0.316    0.129    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,734,268
Number of Sequences: 62578
Number of extensions: 281512
Number of successful extensions: 701
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 701
Number of HSP's gapped (non-prelim): 6
length of query: 290
length of database: 14,973,337
effective HSP length: 98
effective length of query: 192
effective length of database: 8,840,693
effective search space: 1697413056
effective search space used: 1697413056
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (24.3 bits)