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= psy8522
         (78 letters)

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

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



>pdb|1DIP|A Chain A, The Solution Structure Of Porcine Delta-Sleep-Inducing
          Peptide Immunoreactive Peptide, Nmr, 10 Structures
 pdb|1DIP|B Chain B, The Solution Structure Of Porcine Delta-Sleep-Inducing
          Peptide Immunoreactive Peptide, Nmr, 10 Structures
          Length = 78

 Score = 61.2 bits (147), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 31/48 (64%), Positives = 41/48 (85%)

Query: 22 DLVKSHLMFAVREEVEVLKEKIAELMERINQLEMENSILKANATQETL 69
          DLVK+HLM+AVREEVE+LKE+I EL+E+ +QLE EN++LK  A+ E L
Sbjct: 3  DLVKNHLMYAVREEVEILKEQIRELVEKNSQLERENTLLKTLASPEQL 50


>pdb|1DZF|A Chain A, Rpb5 From S.Cerevisiae
 pdb|1I3Q|E Chain E, Rna Polymerase Ii Crystal Form I At 3.1 A Resolution
 pdb|1I50|E Chain E, Rna Polymerase Ii Crystal Form Ii At 2.8 A Resolution
 pdb|1I6H|E Chain E, Rna Polymerase Ii Elongation Complex
 pdb|1K83|E Chain E, Crystal Structure Of Yeast Rna Polymerase Ii Complexed
          With The Inhibitor Alpha Amanitin
 pdb|1NIK|E Chain E, Wild Type Rna Polymerase Ii
 pdb|1NT9|E Chain E, Complete 12-Subunit Rna Polymerase Ii
 pdb|1PQV|E Chain E, Rna Polymerase Ii-Tfiis Complex
 pdb|1R5U|E Chain E, Rna Polymerase Ii Tfiib Complex
 pdb|1SFO|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex
 pdb|1R9S|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
          Matched Nucleotide
 pdb|1R9T|E Chain E, Rna Polymerase Ii Strand Separated Elongation Complex,
          Mismatched Nucleotide
 pdb|1TWA|E Chain E, Rna Polymerase Ii Complexed With Atp
 pdb|1TWC|E Chain E, Rna Polymerase Ii Complexed With Gtp
 pdb|1TWF|E Chain E, Rna Polymerase Ii Complexed With Utp At 2.3 A Resolution
 pdb|1TWG|E Chain E, Rna Polymerase Ii Complexed With Ctp
 pdb|1TWH|E Chain E, Rna Polymerase Ii Complexed With 2'datp
 pdb|1WCM|E Chain E, Complete 12-Subunit Rna Polymerase Ii At 3.8 Ang
 pdb|1Y1W|E Chain E, Complete Rna Polymerase Ii Elongation Complex
 pdb|1Y77|E Chain E, Complete Rna Polymerase Ii Elongation Complex With
          Substrate Analogue Gmpcpp
 pdb|1Y1V|E Chain E, Refined Rna Polymerase Ii-tfiis Complex
 pdb|1Y1Y|E Chain E, Rna Polymerase Ii-Tfiis-DnaRNA COMPLEX
 pdb|2B63|E Chain E, Complete Rna Polymerase Ii-Rna Inhibitor Complex
 pdb|2B8K|E Chain E, 12-Subunit Rna Polymerase Ii
 pdb|2E2H|E Chain E, Rna Polymerase Ii Elongation Complex At 5 Mm Mg2+ With
          Gtp
 pdb|2E2I|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dgtp
 pdb|2E2J|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          Gmpcpp
 pdb|2NVQ|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          2'dutp
 pdb|2NVT|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Gmpcpp
 pdb|2NVX|E Chain E, Rna Polymerase Ii Elongation Complex In 5 Mm Mg+2 With
          2'- Dutp
 pdb|2NVY|E Chain E, Rna Polymerase Ii Form Ii In 150 Mm Mn+2
 pdb|2NVZ|E Chain E, Rna Polymerase Ii Elongation Complex With Utp, Updated
          112006
 pdb|2JA5|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex A
 pdb|2JA6|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex B
 pdb|2JA7|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA7|Q Chain Q, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex C
 pdb|2JA8|E Chain E, Cpd Lesion Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|2YU9|E Chain E, Rna Polymerase Ii Elongation Complex In 150 Mm Mg+2 With
          Utp
 pdb|2R7Z|E Chain E, Cisplatin Lesion Containing Rna Polymerase Ii Elongation
          Complex
 pdb|2R92|E Chain E, Elongation Complex Of Rna Polymerase Ii With Artificial
          Rdrp Scaffold
 pdb|2R93|E Chain E, Elongation Complex Of Rna Polymerase Ii With A Hepatitis
          Delta Virus-Derived Rna Stem Loop
 pdb|2VUM|E Chain E, Alpha-Amanitin Inhibited Complete Rna Polymerase Ii
          Elongation Complex
 pdb|3CQZ|E Chain E, Crystal Structure Of 10 Subunit Rna Polymerase Ii In
          Complex With The Inhibitor Alpha-Amanitin
 pdb|3FKI|E Chain E, 12-Subunit Rna Polymerase Ii Refined With Zn-Sad Data
 pdb|3GTG|E Chain E, Backtracked Rna Polymerase Ii Complex With 12mer Rna
 pdb|3GTJ|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer Rna
 pdb|3GTK|E Chain E, Backtracked Rna Polymerase Ii Complex With 18mer Rna
 pdb|3GTL|E Chain E, Backtracked Rna Polymerase Ii Complex With 13mer With
          G<>u Mismatch
 pdb|3GTM|E Chain E, Co-Complex Of Backtracked Rna Polymerase Ii With Tfiis
 pdb|3GTO|E Chain E, Backtracked Rna Polymerase Ii Complex With 15mer Rna
 pdb|3GTP|E Chain E, Backtracked Rna Polymerase Ii Complex With 24mer Rna
 pdb|3GTQ|E Chain E, Backtracked Rna Polymerase Ii Complex Induced By Damage
 pdb|3H3V|F Chain F, Yeast Rnap Ii Containing Poly(A)-Signal Sequence In The
          Active Site
 pdb|3HOU|E Chain E, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOU|Q Chain Q, Complete Rna Polymerase Ii Elongation Complex I With A
          T-U Mismatch
 pdb|3HOV|E Chain E, Complete Rna Polymerase Ii Elongation Complex Ii
 pdb|3HOW|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iii With A
          T-U Mismatch And A Frayed Rna 3'-Uridine
 pdb|3HOX|E Chain E, Complete Rna Polymerase Ii Elongation Complex V
 pdb|3HOY|E Chain E, Complete Rna Polymerase Ii Elongation Complex Vi
 pdb|3HOZ|E Chain E, Complete Rna Polymerase Ii Elongation Complex Iv With A
          T-U Mismatch And A Frayed Rna 3'-Guanine
 pdb|3I4M|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex D
 pdb|3I4N|E Chain E, 8-oxoguanine Containing Rna Polymerase Ii Elongation
          Complex E
 pdb|3K1F|E Chain E, Crystal Structure Of Rna Polymerase Ii In Complex With
          Tfiib
 pdb|3K7A|E Chain E, Crystal Structure Of An Rna Polymerase Ii-Tfiib Complex
 pdb|3M3Y|E Chain E, Rna Polymerase Ii Elongation Complex C
 pdb|3M4O|E Chain E, Rna Polymerase Ii Elongation Complex B
 pdb|3PO2|E Chain E, Arrested Rna Polymerase Ii Elongation Complex
 pdb|3PO3|E Chain E, Arrested Rna Polymerase Ii Reactivation Intermediate
 pdb|3QT1|E Chain E, Rna Polymerase Ii Variant Containing A Chimeric Rpb9-C11
          Subunit
 pdb|3RZD|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
 pdb|3RZO|E Chain E, Rna Polymerase Ii Initiation Complex With A 4-Nt Rna
 pdb|3S14|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
 pdb|3S15|E Chain E, Rna Polymerase Ii Initiation Complex With A 7-Nt Rna
 pdb|3S16|E Chain E, Rna Polymerase Ii Initiation Complex With An 8-Nt Rna
 pdb|3S17|E Chain E, Rna Polymerase Ii Initiation Complex With A 9-Nt Rna
 pdb|3S1M|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 1)
 pdb|3S1N|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          (Variant 2)
 pdb|3S1Q|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Atp
 pdb|3S1R|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt
          3'-Deoxy Rna Soaked With Gtp
 pdb|3S2D|E Chain E, Rna Polymerase Ii Initiation Complex With A 5-Nt Rna
          Containing A 5br- U
 pdb|3S2H|E Chain E, Rna Polymerase Ii Initiation Complex With A 6-Nt Rna
          Containing A 2[prime]-Iodo Atp
 pdb|3J0K|E Chain E, Orientation Of Rna Polymerase Ii Within The Human
          Vp16-Mediator-Pol Ii-Tfiif Assembly
 pdb|4A3C|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid
 pdb|4A3B|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid
 pdb|4A3D|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid
 pdb|4A3E|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          5nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3F|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          6nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3J|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid And Soaked With Gmpcpp
 pdb|4A3K|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid
 pdb|4A3L|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          7nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3M|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          4nt Dna-Rna Hybrid And Soaked With Ampcpp
 pdb|4A3G|E Chain E, Rna Polymerase Ii Initial Transcribing Complex With A
          2nt Dna-Rna Hybrid
 pdb|4A3I|E Chain E, Rna Polymerase Ii Binary Complex With Dna
 pdb|4A93|E Chain E, Rna Polymerase Ii Elongation Complex Containing A Cpd
          Lesion
 pdb|4BBR|E Chain E, Structure Of Rna Polymerase Ii-tfiib Complex
 pdb|4BBS|E Chain E, Structure Of An Initially Transcribing Rna Polymerase
          Ii- Tfiib Complex
          Length = 215

 Score = 29.3 bits (64), Expect = 0.63,   Method: Compositional matrix adjust.
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 7/58 (12%)

Query: 20 IKDLVKSHLMFAVREEVEV----LKEKIAELMERINQLEMENSILKANATQETLGQLP 73
          +K++VK    F  +EEVE+     K K  + M R  +  M     +AN T+E++ + P
Sbjct: 19 VKEMVKDRGYFITQEEVELPLEDFKAKYCDSMGRPQRKMMS---FQANPTEESISKFP 73


>pdb|4ETP|A Chain A, C-Terminal Motor And Motor Homology Domain Of Kar3vik1
          Fused To A Synthetic Heterodimeric Coiled Coil
          Length = 403

 Score = 27.7 bits (60), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 12/25 (48%), Positives = 18/25 (72%)

Query: 31 AVREEVEVLKEKIAELMERINQLEM 55
          A++E++  LKEKIA L E+I   E+
Sbjct: 7  ALKEKIAALKEKIAALKEKIKDTEL 31


>pdb|2YY0|A Chain A, Crystal Structure Of Ms0802, C-Myc-1 Binding Protein
          Domain From Homo Sapiens
 pdb|2YY0|B Chain B, Crystal Structure Of Ms0802, C-Myc-1 Binding Protein
          Domain From Homo Sapiens
 pdb|2YY0|C Chain C, Crystal Structure Of Ms0802, C-Myc-1 Binding Protein
          Domain From Homo Sapiens
 pdb|2YY0|D Chain D, Crystal Structure Of Ms0802, C-Myc-1 Binding Protein
          Domain From Homo Sapiens
          Length = 53

 Score = 27.3 bits (59), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 18/47 (38%), Positives = 27/47 (57%), Gaps = 2/47 (4%)

Query: 22 DLVKSHLMFAVRE--EVEVLKEKIAELMERINQLEMENSILKANATQ 66
          D +K HL  A  E  E+E+L+ ++AE+ E+   +  EN  LKA   Q
Sbjct: 5  DFLKHHLGAATPENPEIELLRLELAEMKEKYEAIVEENKKLKAKLAQ 51


>pdb|1DEQ|A Chain A, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
           Angstrom Resolution)
 pdb|1DEQ|D Chain D, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
           Angstrom Resolution)
 pdb|1DEQ|N Chain N, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
           Angstrom Resolution)
 pdb|1DEQ|Q Chain Q, The Crystal Structure Of Modified Bovine Fibrinogen (At ~4
           Angstrom Resolution)
          Length = 390

 Score = 26.2 bits (56), Expect = 4.6,   Method: Composition-based stats.
 Identities = 9/23 (39%), Positives = 17/23 (73%)

Query: 32  VREEVEVLKEKIAELMERINQLE 54
           +R  +E+L+ K+ E ++RIN L+
Sbjct: 118 LRSRIEILRRKVIEQVQRINLLQ 140


  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
   0.317    0.132    0.356 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 1,990,231
Number of Sequences: 62578
Number of extensions: 57473
Number of successful extensions: 236
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 227
Number of HSP's gapped (non-prelim): 15
length of query: 78
length of database: 14,973,337
effective HSP length: 47
effective length of query: 31
effective length of database: 12,032,171
effective search space: 372997301
effective search space used: 372997301
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 45 (21.9 bits)