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= 005902
         (671 letters)

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

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



>pdb|2R55|A Chain A, Human Star-Related Lipid Transfer Protein 5
 pdb|2R55|B Chain B, Human Star-Related Lipid Transfer Protein 5
          Length = 231

 Score = 36.6 bits (83), Expect = 0.047,   Method: Compositional matrix adjust.
 Identities = 35/127 (27%), Positives = 50/127 (39%), Gaps = 3/127 (2%)

Query: 235 WKCVRTLNGVRIFEDVADSKSGRGVLVKAVGVIDASADTVFEVVLNLERHQRYEWDMLTG 294
           WK  R  NGV +      S    G L +  G++  + + V++ V       R +WD    
Sbjct: 45  WKICREGNGVSV--SWRPSVEFPGNLYRGEGIVYGTLEEVWDCVKPAVGGLRVKWDENVT 102

Query: 295 DLELVDSYDGHYDVVYGTYDPKYLTRWQSKRDFVFSRQWFRGQDGTYTILQFPAVHKKRP 354
             E++ S       V  T  P    +  S RDFV      R +DGT +       H   P
Sbjct: 103 GFEIIQSITDTL-CVSRTSTPSAAMKLISPRDFVDLVLVKRYEDGTISSNATHVEHPLCP 161

Query: 355 PKSGYRR 361
           PK G+ R
Sbjct: 162 PKPGFVR 168


>pdb|3IHP|A Chain A, Covalent Ubiquitin-Usp5 Complex
 pdb|3IHP|B Chain B, Covalent Ubiquitin-Usp5 Complex
          Length = 854

 Score = 30.8 bits (68), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 19/26 (73%), Gaps = 1/26 (3%)

Query: 44  GYFEYFGWVYHMGTNSI-GHEYCHLR 68
           G ++ F ++ HMGT+++ GH  CH++
Sbjct: 795 GKYQLFAFISHMGTSTMCGHYVCHIK 820


>pdb|3CGH|A Chain A, Crystal Structure Of A Susd Homolog (Bt_3984) From
           Bacteroides Thetaiotaomicron Vpi-5482 At 1.70 A
           Resolution
          Length = 516

 Score = 29.6 bits (65), Expect = 5.5,   Method: Compositional matrix adjust.
 Identities = 18/72 (25%), Positives = 25/72 (34%)

Query: 70  LFIRGKYVEMYKRDPHENPGIKPIRRGVIGPTLMVEELGRRRFNHGDVYVMRLYNRLDES 129
           L IR  Y    K        + P   GVI              +   +YV   YN++  S
Sbjct: 202 LAIRIAYANPVKAQQXAEEAVNPANGGVIESNADNATWNYFETSQNPIYVATRYNQVQTS 261

Query: 130 KKGEIACATAGE 141
             G + C T G+
Sbjct: 262 DHGGVPCLTGGD 273


>pdb|2VD5|A Chain A, Structure Of Human Myotonic Dystrophy Protein Kinase In
           Complex With The Bisindoylmaleide Inhibitor Bim Viii
 pdb|2VD5|B Chain B, Structure Of Human Myotonic Dystrophy Protein Kinase In
           Complex With The Bisindoylmaleide Inhibitor Bim Viii
          Length = 412

 Score = 28.9 bits (63), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 21/67 (31%), Positives = 34/67 (50%), Gaps = 8/67 (11%)

Query: 70  LFIRGKYVEMYKRDPHENPGIKPIRRGVIGPTLMVEELGRRRFNHGDVYVMRLYNRLDES 129
           + +R K V + +RD  E   +K I RG      +V     +    G VY M++ N+ D  
Sbjct: 49  IVVRLKEVRL-QRDDFEI--LKVIGRGAFSEVAVV-----KMKQTGQVYAMKIMNKWDML 100

Query: 130 KKGEIAC 136
           K+GE++C
Sbjct: 101 KRGEVSC 107


  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
   0.319    0.136    0.416 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,691,877
Number of Sequences: 62578
Number of extensions: 845315
Number of successful extensions: 1579
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 1576
Number of HSP's gapped (non-prelim): 24
length of query: 671
length of database: 14,973,337
effective HSP length: 105
effective length of query: 566
effective length of database: 8,402,647
effective search space: 4755898202
effective search space used: 4755898202
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)