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= 028999
         (200 letters)

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

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



>pdb|1AM9|A Chain A, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|B Chain B, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|C Chain C, Human Srebp-1a Bound To Ldl Receptor Promoter
 pdb|1AM9|D Chain D, Human Srebp-1a Bound To Ldl Receptor Promoter
          Length = 82

 Score = 32.0 bits (71), Expect = 0.24,   Method: Compositional matrix adjust.
 Identities = 23/68 (33%), Positives = 39/68 (57%), Gaps = 4/68 (5%)

Query: 54  EKLRRERLNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEE 113
           EK  R  +ND+ ++L  ++  G  A+ +K A+L  AI  +  L+  +Q+LK+ N  L+  
Sbjct: 14  EKRYRSSINDKIIELKDLV-VGTEAKLNKSAVLRKAIDYIRFLQHSNQKLKQENLSLRTA 72

Query: 114 I---KSLK 118
           +   KSLK
Sbjct: 73  VHKSKSLK 80


>pdb|2DFS|A Chain A, 3-D Structure Of Myosin-V Inhibited State
 pdb|2DFS|M Chain M, 3-D Structure Of Myosin-V Inhibited State
          Length = 1080

 Score = 27.7 bits (60), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 16/50 (32%), Positives = 33/50 (66%), Gaps = 3/50 (6%)

Query: 93   LNQLRTESQELKETNEKLQEEIKSLKAEKNELREEKLILKADKEKLEQQL 142
            L+Q +TE + ++E  +K + E + L +E   L+E+  +LK +KE+L +++
Sbjct: 1000 LHQTQTEKKTIEEWADKYKHETEQLVSE---LKEQNTLLKTEKEELNRRI 1046


>pdb|2M1L|A Chain A, Solution Nmr Structure Of Cyclin-Dependent Kinase
          2-Associated Protein 2 (Cdk2ap2, Doc-1r) From Homo
          Sapiens, Northeast Structural Genomics Consortium
          (Nesg) Target Hr8910c
 pdb|2M1L|B Chain B, Solution Nmr Structure Of Cyclin-Dependent Kinase
          2-Associated Protein 2 (Cdk2ap2, Doc-1r) From Homo
          Sapiens, Northeast Structural Genomics Consortium
          (Nesg) Target Hr8910c
          Length = 69

 Score = 26.9 bits (58), Expect = 6.6,   Method: Compositional matrix adjust.
 Identities = 14/33 (42%), Positives = 20/33 (60%)

Query: 48 GSKACREKLRRERLNDRFLDLSCILEPGRPART 80
          GSK+  E+L+R  ++ R L   C+ E  R ART
Sbjct: 37 GSKSAMERLKRGIIHARALVRECLAETERNART 69


>pdb|3VX3|A Chain A, Crystal Structure Of [nife] Hydrogenase Maturation Protein
           Hypb From Thermococcus Kodakarensis Kod1
 pdb|3VX3|B Chain B, Crystal Structure Of [nife] Hydrogenase Maturation Protein
           Hypb From Thermococcus Kodakarensis Kod1
          Length = 248

 Score = 26.9 bits (58), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 10/84 (11%)

Query: 61  LNDRFLDLSCILEPGRPARTDKPAILDDAIRVLNQLRTESQELKETNEKLQEEIKSLKAE 120
           L D+ LD+   L+ G       P+ L      LN +R   + LKE   K+   ++++K  
Sbjct: 137 LGDQLLDVLRFLKRGEFLVVATPSKLS-----LNVVRKLIELLKEEGHKVIGVVENMKLR 191

Query: 121 KNELREEKLILKADKEKLEQQLKV 144
             +L +EK     D EKL ++  V
Sbjct: 192 SEQLDDEK-----DVEKLAEEFGV 210


  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
   0.314    0.131    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,896,530
Number of Sequences: 62578
Number of extensions: 230165
Number of successful extensions: 996
Number of sequences better than 100.0: 64
Number of HSP's better than 100.0 without gapping: 26
Number of HSP's successfully gapped in prelim test: 38
Number of HSP's that attempted gapping in prelim test: 939
Number of HSP's gapped (non-prelim): 92
length of query: 200
length of database: 14,973,337
effective HSP length: 94
effective length of query: 106
effective length of database: 9,091,005
effective search space: 963646530
effective search space used: 963646530
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: 49 (23.5 bits)