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= 044301
         (154 letters)

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

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



>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
          Single-Stranded Interacting Protein 1
          Length = 114

 Score = 30.0 bits (66), Expect = 0.58,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 9/51 (17%)

Query: 39 YLSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGF 89
          Y+S +P  MD  +L  +L  +G++          STR+LR      R  GF
Sbjct: 29 YISNLPLSMDEQELENMLKPFGQVI---------STRILRDSSGTSRGVGF 70


>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
          Trypanosoma Cruzi
          Length = 139

 Score = 28.1 bits (61), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/51 (33%), Positives = 28/51 (54%), Gaps = 10/51 (19%)

Query: 40 LSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDG-GF 89
          ++ IP  +D V+LRQ+  +YG I+         S +++  RE R+  G GF
Sbjct: 47 VNYIPTTVDEVQLRQLFERYGPIE---------SVKIVCDRETRQSRGYGF 88


>pdb|2E44|A Chain A, Solution Structure Of Rna Binding Domain In Insulin-Like
          Growth Factor 2 Mrna Binding Protein 3
          Length = 96

 Score = 28.1 bits (61), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 17/64 (26%), Positives = 28/64 (43%), Gaps = 8/64 (12%)

Query: 40 LSRIPPHMDPVKLRQILSQYGEIQRIYLAPEDPSTRVL--------RKRENRKRDGGFQD 91
          +  IPPH+    L  +L QYG ++       D  T V+        + R+   +  GFQ 
Sbjct: 20 IRNIPPHLQWEVLDSLLVQYGVVESCEQVNTDSETAVVNVTYSSKDQARQALDKLNGFQL 79

Query: 92 QGFS 95
          + F+
Sbjct: 80 ENFT 83


>pdb|2E24|A Chain A, Crystal Structure Of A Mutant (R612a) Of Xanthan Lyase
          Length = 752

 Score = 27.3 bits (59), Expect = 3.8,   Method: Composition-based stats.
 Identities = 16/42 (38%), Positives = 20/42 (47%)

Query: 57  SQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGY 98
           ++ G  ++I  AP  PST V R  E    D G    G S GY
Sbjct: 576 ARTGTWKQINNAPATPSTAVTRNYETMWIDHGTNPSGASYGY 617


>pdb|2AEE|A Chain A, Crystal Structure Of Orotate Phosphoribosyltransferase
          From Streptococcus Pyogenes
 pdb|2AEE|B Chain B, Crystal Structure Of Orotate Phosphoribosyltransferase
          From Streptococcus Pyogenes
          Length = 211

 Score = 26.6 bits (57), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 54 QILSQYGEIQRIYLAPEDPST 74
          QI +Q  +I+ +YL PEDP T
Sbjct: 8  QIATQLLDIKAVYLKPEDPFT 28


>pdb|1O1W|A Chain A, Solution Structure Of The Rnase H Domain Of The Hiv-1
           Reverse Transcriptase In The Presence Of Magnesium
          Length = 138

 Score = 26.2 bits (56), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 25/86 (29%), Positives = 38/86 (44%), Gaps = 13/86 (15%)

Query: 50  VKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQ---DQGFSEGYKQKVQQES 106
           V L    +Q  E+Q IYLA +D    V    +++   G  Q   DQ  SE   Q ++Q  
Sbjct: 45  VTLTDTTNQKTELQAIYLALQDSGLEVNIVTDSQYALGIIQAQPDQSESELVNQIIEQLI 104

Query: 107 Q----------THPELPGSEQVTKVI 122
           +           H  + G+EQV K++
Sbjct: 105 KKEKVYLAWVPAHKGIGGNEQVDKLV 130


>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
           Factor
          Length = 103

 Score = 26.2 bits (56), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 19/76 (25%), Positives = 33/76 (43%), Gaps = 10/76 (13%)

Query: 49  PVKLRQILSQYGEIQRIYLAPEDPSTRVLRKRENRKRDGGFQDQGFSEGYKQKVQQESQT 108
           P  LR++  +YG +  +Y+ P +P T+  R         GF    F +    +  + +  
Sbjct: 27  PDSLRRVFEKYGRVGDVYI-PREPHTKAPR---------GFAFVRFHDRRDAQDAEAAMD 76

Query: 109 HPELPGSEQVTKVIRH 124
             EL G E   +V R+
Sbjct: 77  GAELDGRELRVQVARY 92


  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
   0.313    0.133    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,239,996
Number of Sequences: 62578
Number of extensions: 154355
Number of successful extensions: 316
Number of sequences better than 100.0: 37
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 308
Number of HSP's gapped (non-prelim): 37
length of query: 154
length of database: 14,973,337
effective HSP length: 90
effective length of query: 64
effective length of database: 9,341,317
effective search space: 597844288
effective search space used: 597844288
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 47 (22.7 bits)