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= 027155
         (227 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 = 32.0 bits (71), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 127 VVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-QIVINEAVD 183
           +VD    H+  ID ++    K     R+  +E + L L ++E+  + ++    V  + VD
Sbjct: 51  LVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVD 110

Query: 184 LAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASK 221
           L K++ D  A + +NG L    +     A I +SK  K
Sbjct: 111 LVKKYADEKAGKFVNGVLSAIYK-----AYITSSKEEK 143



 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 22 RAARELALLVVYAACLEGSDPIRLFEKRL---NSRREPGYEFDK 62
          + AR+ A LV+Y   L G +P  LF++ +   N + +  YE+ K
Sbjct: 6  KGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAK 49


>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 = 32.0 bits (71), Expect = 0.32,   Method: Compositional matrix adjust.
 Identities = 26/98 (26%), Positives = 46/98 (46%), Gaps = 8/98 (8%)

Query: 127 VVDKWDAHVHIIDKVVPPIWKDQPAGRI--LELSILHLAMSEITVVGTRH-QIVINEAVD 183
           +VD    H+  ID ++    K     R+  +E + L L ++E+  + ++    V  + VD
Sbjct: 50  LVDTAVRHIEEIDSIIEKHLKGWSIDRLGYVERNALRLGVAELIFLKSKEPGRVFIDIVD 109

Query: 184 LAKRFCDGAAPRIINGCLRTFVRNLEGTANIEASKASK 221
           L K++ D  A + +NG L    +     A I +SK  K
Sbjct: 110 LVKKYADEKAGKFVNGVLSAIYK-----AYITSSKEEK 142



 Score = 28.1 bits (61), Expect = 4.7,   Method: Compositional matrix adjust.
 Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)

Query: 22 RAARELALLVVYAACLEGSDPIRLFEKRL---NSRREPGYEFDK 62
          + AR+ A LV+Y   L G +P  LF++ +   N + +  YE+ K
Sbjct: 5  KGARDTAFLVLYRWDLRGENPGELFKEVVEEKNIKNKDAYEYAK 48


>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 = 30.4 bits (67), Expect = 0.75,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 155 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 201
           +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 = 30.4 bits (67), Expect = 0.81,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 155 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 201
           +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 = 30.4 bits (67), Expect = 0.84,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 30/48 (62%), Gaps = 1/48 (2%)

Query: 155 LELSILHLAMSEITV-VGTRHQIVINEAVDLAKRFCDGAAPRIINGCL 201
           +E ++L +A+ E++      +++ INEA++LAK F    + + +NG L
Sbjct: 82  VEKAVLRIALYELSKRSDVPYKVAINEAIELAKSFGAEDSHKFVNGVL 129


>pdb|2VSY|A Chain A, Xanthomonas Campestris Putative Ogt (Xcc0866),
           Apostructure
 pdb|2VSY|B Chain B, Xanthomonas Campestris Putative Ogt (Xcc0866),
           Apostructure
 pdb|2JLB|A Chain A, Xanthomonas Campestris Putative Ogt (Xcc0866), Complex
           With Udp-Glcnac Phosphonate Analogue
 pdb|2JLB|B Chain B, Xanthomonas Campestris Putative Ogt (Xcc0866), Complex
           With Udp-Glcnac Phosphonate Analogue
 pdb|2XGM|A Chain A, Substrate And Product Analogues As Human O-Glcnac
           Transferase Inhibitors.
 pdb|2XGM|B Chain B, Substrate And Product Analogues As Human O-Glcnac
           Transferase Inhibitors.
 pdb|2XGO|A Chain A, Xcogt In Complex With Udp-S-Glcnac
 pdb|2XGO|B Chain B, Xcogt In Complex With Udp-S-Glcnac
 pdb|2XGS|A Chain A, Xcogt In Complex With C-Udp
 pdb|2XGS|B Chain B, Xcogt In Complex With C-Udp
          Length = 568

 Score = 28.1 bits (61), Expect = 4.3,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 13/94 (13%)

Query: 85  EADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPP 144
           EAD  LR+      ++A+ L   PKL + + L R+    L      ++AH    D     
Sbjct: 417 EADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDA---- 472

Query: 145 IWKDQP---------AGRILELSILHLAMSEITV 169
           +W   P         A R+      HL + E+ V
Sbjct: 473 LWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNV 506


>pdb|2VSN|A Chain A, Structure And Topological Arrangement Of An O-Glcnac
           Transferase Homolog: Insight Into Molecular Control Of
           Intracellular Glycosylation
 pdb|2VSN|B Chain B, Structure And Topological Arrangement Of An O-Glcnac
           Transferase Homolog: Insight Into Molecular Control Of
           Intracellular Glycosylation
          Length = 568

 Score = 28.1 bits (61), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 24/94 (25%), Positives = 37/94 (39%), Gaps = 13/94 (13%)

Query: 85  EADELLRSDEEESAIEAEVLSAPPKLVYSKLLLRFTRKLLVAVVDKWDAHVHIIDKVVPP 144
           EAD  LR+      ++A+ L   PKL + + L R+    L      ++AH    D     
Sbjct: 417 EADARLRAFAHAQGVDAQRLVFMPKLPHPQYLARYRHADLFLDTHPYNAHTTASDA---- 472

Query: 145 IWKDQP---------AGRILELSILHLAMSEITV 169
           +W   P         A R+      HL + E+ V
Sbjct: 473 LWTGCPVLTTPGETFAARVAGSLNHHLGLDEMNV 506


>pdb|1TZT|A Chain A, T. Maritima Nusb, P21
 pdb|1TZT|B Chain B, T. Maritima Nusb, P21
 pdb|1TZU|A Chain A, T. Maritima Nusb, P212121
 pdb|1TZV|A Chain A, T. Maritima Nusb, P3121, Form 1
 pdb|1TZW|A Chain A, T. Maritima Nusb, P3121, Form 2
 pdb|1TZX|A Chain A, T. Maritima Nusb, P3221
 pdb|1TZX|B Chain B, T. Maritima Nusb, P3221
          Length = 142

 Score = 27.7 bits (60), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 9/27 (33%), Positives = 19/27 (70%)

Query: 175 QIVINEAVDLAKRFCDGAAPRIINGCL 201
           ++ I+EA+++AKR+    + + +NG L
Sbjct: 101 EVTIDEAIEIAKRYGTENSGKFVNGIL 127


>pdb|1EYV|A Chain A, The Crystal Structure Of Nusb From Mycobacterium
           Tuberculosis
 pdb|1EYV|B Chain B, The Crystal Structure Of Nusb From Mycobacterium
           Tuberculosis
          Length = 156

 Score = 26.9 bits (58), Expect = 8.3,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 16/26 (61%)

Query: 176 IVINEAVDLAKRFCDGAAPRIINGCL 201
           +V++EAV LAK      +P  +NG L
Sbjct: 110 VVVDEAVQLAKELSTDDSPGFVNGVL 135


  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
   0.318    0.134    0.383 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,234,967
Number of Sequences: 62578
Number of extensions: 233930
Number of successful extensions: 554
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 548
Number of HSP's gapped (non-prelim): 12
length of query: 227
length of database: 14,973,337
effective HSP length: 95
effective length of query: 132
effective length of database: 9,028,427
effective search space: 1191752364
effective search space used: 1191752364
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: 50 (23.9 bits)