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= 007659
         (594 letters)

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

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



>pdb|2YQR|A Chain A, Solution Structure Of The Kh Domain In Kiaa0907 Protein
          Length = 119

 Score = 67.4 bits (163), Expect = 2e-11,   Method: Composition-based stats.
 Identities = 37/82 (45%), Positives = 51/82 (62%), Gaps = 3/82 (3%)

Query: 259 YINHIMNETGATVLLRGRGSGNSEGLQGEEVHQPLHLFLSSNNPKSLEEAKRLAENLLDT 318
           Y+ HI  ETGA V LRG+GSG  E   G E  +P+++++S   P+ L  AK+L ENLL T
Sbjct: 40  YLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAAKKLCENLLQT 99

Query: 319 ISAECGASRVSSCKVYNAVPPP 340
           + AE   SR  + ++  AVP P
Sbjct: 100 VHAE--YSRFVN-QINTAVPLP 118


>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
           Rna
 pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
           Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
           Target
          Length = 175

 Score = 31.2 bits (69), Expect = 1.9,   Method: Composition-based stats.
 Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 8/84 (9%)

Query: 281 SEGLQGEEVHQPLHLFLSSNNP-KSLEEAK-----RLAENLLDTISAECGASRVSSCKVY 334
           S  ++G E   P +LF+ + NP KS+ E K       A+N L  +    G +R      +
Sbjct: 2   SHMVEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDF 61

Query: 335 NAVPPPQQLL--TGIQGFGNEQKL 356
            +    ++ L  TG++ FGNE KL
Sbjct: 62  ESAEDLEKALELTGLKVFGNEIKL 85


>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
          Length = 101

 Score = 30.4 bits (67), Expect = 2.7,   Method: Composition-based stats.
 Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 8/81 (9%)

Query: 284 LQGEEVHQPLHLFLSSNNP-KSLEEAK-----RLAENLLDTISAECGASRVSSCKVYNAV 337
           ++G E   P +LF+ + NP KS+ E K       A+N L  +    G +R      + + 
Sbjct: 9   VEGSESTTPFNLFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTNRKFGYVDFESA 68

Query: 338 PPPQQLL--TGIQGFGNEQKL 356
              ++ L  TG++ FGNE KL
Sbjct: 69  EDLEKALELTGLKVFGNEIKL 89


>pdb|3HRS|A Chain A, Crystal Structure Of The Manganese-Activated Repressor
           Scar: Apo Form
 pdb|3HRS|B Chain B, Crystal Structure Of The Manganese-Activated Repressor
           Scar: Apo Form
 pdb|3HRT|A Chain A, Crystal Structure Of Scar With Bound Cd2+
 pdb|3HRT|B Chain B, Crystal Structure Of Scar With Bound Cd2+
 pdb|3HRU|A Chain A, Crystal Structure Of Scar With Bound Zn2+
 pdb|3HRU|B Chain B, Crystal Structure Of Scar With Bound Zn2+
          Length = 214

 Score = 30.0 bits (66), Expect = 3.4,   Method: Compositional matrix adjust.
 Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 1/65 (1%)

Query: 175 LAVDHAAAMVEEMLKQGHAGFPTLQTVMGNGVQAMSTSVFLGFDADASLNIAARIRGPNL 234
           L ++ A    + +L + H  F  L  +  NG+Q   T  FLG+D D S   +  + G  +
Sbjct: 141 LTLEEAKEKGDYILARVHDNFDLLTYLERNGLQVGKTIRFLGYD-DFSHLYSLEVDGQEI 199

Query: 235 SLTSP 239
            L  P
Sbjct: 200 QLAQP 204


>pdb|1K1G|A Chain A, Structural Basis For Recognition Of The Intron Branch Site
           Rna By Splicing Factor 1
          Length = 131

 Score = 29.3 bits (64), Expect = 7.0,   Method: Composition-based stats.
 Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 10/65 (15%)

Query: 260 INHIMNETGATVLLRGRGS------GNSEG--LQGEEVHQPLHLFLSSNNPKSLEEAKRL 311
           + +I  E  A +++RG+GS      G  +G  L GE+  +PLH  +++N  +++++A   
Sbjct: 35  LKNIEKECNAKIMIRGKGSVKEGKVGRKDGQMLPGED--EPLHALVTANTMENVKKAVEQ 92

Query: 312 AENLL 316
             N+L
Sbjct: 93  IRNIL 97


  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    0.130    0.371 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,576,765
Number of Sequences: 62578
Number of extensions: 522687
Number of successful extensions: 992
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 990
Number of HSP's gapped (non-prelim): 5
length of query: 594
length of database: 14,973,337
effective HSP length: 104
effective length of query: 490
effective length of database: 8,465,225
effective search space: 4147960250
effective search space used: 4147960250
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: 54 (25.4 bits)