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= 034085
         (104 letters)

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

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



>pdb|1QGV|A Chain A, Human Spliceosomal Protein U5-15kd
 pdb|1SYX|A Chain A, The Crystal Structure Of A Binary U5 Snrnp Complex
 pdb|1SYX|C Chain C, The Crystal Structure Of A Binary U5 Snrnp Complex
 pdb|1SYX|E Chain E, The Crystal Structure Of A Binary U5 Snrnp Complex
          Length = 142

 Score =  196 bits (497), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 89/104 (85%), Positives = 99/104 (95%)

Query: 1   MQMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYELYDPSTVMFFFRNKHIMIDLGTGN 60
           M+MDEVL S+AE +KNFAVIYLVDI+EVPDFN MYELYDP TVMFFFRNKHIMIDLGTGN
Sbjct: 39  MKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGN 98

Query: 61  NNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYSTKYRY 104
           NNKINWA++DKQE +DI+ETVYRGARKGRGLV++PKDYSTKYRY
Sbjct: 99  NNKINWAMEDKQEMVDIIETVYRGARKGRGLVVSPKDYSTKYRY 142


>pdb|2AV4|A Chain A, Crystal Structure Of Plasmodium Yoelii Thioredoxin-like
           Protein 4a (dim1)
          Length = 160

 Score =  184 bits (467), Expect = 1e-47,   Method: Compositional matrix adjust.
 Identities = 84/104 (80%), Positives = 97/104 (93%)

Query: 1   MQMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYELYDPSTVMFFFRNKHIMIDLGTGN 60
           M+MDE+L  VA+ IKNF VIYLVDI+EVPDFNTMYELYDP +VMFF+RNKH+MIDLGTGN
Sbjct: 57  MKMDELLYKVADDIKNFCVIYLVDITEVPDFNTMYELYDPVSVMFFYRNKHMMIDLGTGN 116

Query: 61  NNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYSTKYRY 104
           NNKINW + +KQEFIDIVET++RGARKGRGLVI+PKDYSTKY+Y
Sbjct: 117 NNKINWPMNNKQEFIDIVETIFRGARKGRGLVISPKDYSTKYKY 160


>pdb|1PQN|A Chain A, Dominant Negative Human Hdim1 (Hdim1 1-128)
          Length = 127

 Score =  169 bits (427), Expect = 4e-43,   Method: Compositional matrix adjust.
 Identities = 77/90 (85%), Positives = 85/90 (94%)

Query: 1   MQMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYELYDPSTVMFFFRNKHIMIDLGTGN 60
           M+MDEVL S+AE +KNFAVIYLVDI+EVPDFN MYELYDP TVMFFFRNKHIMIDLGTGN
Sbjct: 38  MKMDEVLYSIAEKVKNFAVIYLVDITEVPDFNKMYELYDPCTVMFFFRNKHIMIDLGTGN 97

Query: 61  NNKINWALKDKQEFIDIVETVYRGARKGRG 90
           NNKINWA++DKQE +DI+ETVYRGARKGRG
Sbjct: 98  NNKINWAMEDKQEMVDIIETVYRGARKGRG 127


>pdb|1XBS|A Chain A, Crystal Structure Of Human Dim2: A Dim1-Like Protein
          Length = 149

 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/98 (37%), Positives = 64/98 (65%), Gaps = 2/98 (2%)

Query: 1   MQMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYEL-YDPSTVMFFFRNKHIMIDLGTG 59
           +Q+D++LS  +  +   A IYLVD+ +   +   +++ Y PSTV FFF  +H+ +D G+ 
Sbjct: 39  LQLDDILSKTSSDLSKMAAIYLVDVDQTAVYTQYFDISYIPSTV-FFFNGQHMKVDYGSP 97

Query: 60  NNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKD 97
           ++ K   + K KQ+FID++E +YRGA +G+ +V +P D
Sbjct: 98  DHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPID 135


>pdb|3GIX|A Chain A, Crystal Structure Of Human Splicing Factor Dim2
 pdb|3GIX|B Chain B, Crystal Structure Of Human Splicing Factor Dim2
          Length = 149

 Score = 80.1 bits (196), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 37/98 (37%), Positives = 64/98 (65%), Gaps = 2/98 (2%)

Query: 1   MQMDEVLSSVAETIKNFAVIYLVDISEVPDFNTMYEL-YDPSTVMFFFRNKHIMIDLGTG 59
           +Q+D++LS  +  +   A IYLVD+ +   +   +++ Y PSTV FFF  +H+ +D G+ 
Sbjct: 39  LQLDDILSKTSSDLSKMAAIYLVDVDQTAVYTQYFDISYIPSTV-FFFNGQHMKVDYGSP 97

Query: 60  NNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKD 97
           ++ K   + K KQ+FID++E +YRGA +G+ +V +P D
Sbjct: 98  DHTKFVGSFKTKQDFIDLIEVIYRGAMRGKLIVQSPID 135


>pdb|1ECR|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Dna
 pdb|2EWJ|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Dna- Locked Form
 pdb|2I05|A Chain A, Escherichia Coli Replication Terminator Protein (Tus)
           Complexed With Tera Dna
 pdb|2I06|A Chain A, Escherichia Coli Replication Terminator Protein (tus)
           Complexed With Dna- Locked Form
          Length = 309

 Score = 28.9 bits (63), Expect = 0.71,   Method: Compositional matrix adjust.
 Identities = 11/26 (42%), Positives = 19/26 (73%)

Query: 31  FNTMYELYDPSTVMFFFRNKHIMIDL 56
           + T+  L+DP+T+ F + NKHI+ +L
Sbjct: 156 YRTLTVLHDPATLRFGWANKHIIKNL 181


>pdb|3DPT|A Chain A, Cor Domain Of Rab Family Protein (Roco)
 pdb|3DPT|B Chain B, Cor Domain Of Rab Family Protein (Roco)
          Length = 332

 Score = 26.9 bits (58), Expect = 2.9,   Method: Compositional matrix adjust.
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 41  STVMFFFRNKHIMID-LGTGNNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYS 99
           S + +    + I  D      NNK  + L +++  +DI++       +G+GL I P +  
Sbjct: 108 SALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLP 167

Query: 100 TK 101
           T+
Sbjct: 168 TQ 169


>pdb|3DPU|A Chain A, Roccor Domain Tandem Of Rab Family Protein (Roco)
 pdb|3DPU|B Chain B, Roccor Domain Tandem Of Rab Family Protein (Roco)
          Length = 535

 Score = 26.2 bits (56), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 15/62 (24%), Positives = 29/62 (46%), Gaps = 1/62 (1%)

Query: 41  STVMFFFRNKHIMID-LGTGNNNKINWALKDKQEFIDIVETVYRGARKGRGLVIAPKDYS 99
           S + +    + I  D      NNK  + L +++  +DI++       +G+GL I P +  
Sbjct: 311 SALGYILNEEQIRCDEYDPAKNNKFTYTLLEQRYLLDIMKQFELCYDEGKGLFIIPSNLP 370

Query: 100 TK 101
           T+
Sbjct: 371 TQ 372


>pdb|1JBA|A Chain A, Unmyristoylated Gcap-2 With Three Calcium Ions Bound
          Length = 204

 Score = 25.4 bits (54), Expect = 7.7,   Method: Compositional matrix adjust.
 Identities = 11/32 (34%), Positives = 18/32 (56%), Gaps = 10/32 (31%)

Query: 62  NKINWALK----------DKQEFIDIVETVYR 83
           +K+ W  K          D+QE +DIVE++Y+
Sbjct: 95  HKLKWTFKIYDKDRNGCIDRQELLDIVESIYK 126


  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
   0.322    0.138    0.402 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,186,928
Number of Sequences: 62578
Number of extensions: 128888
Number of successful extensions: 312
Number of sequences better than 100.0: 22
Number of HSP's better than 100.0 without gapping: 14
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 298
Number of HSP's gapped (non-prelim): 22
length of query: 104
length of database: 14,973,337
effective HSP length: 69
effective length of query: 35
effective length of database: 10,655,455
effective search space: 372940925
effective search space used: 372940925
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)