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= psy5308
         (137 letters)

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

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



>pdb|2A20|A Chain A, Solution Structure Of Rim2 Zinc Finger Domain
 pdb|2CJS|C Chain C, Structural Basis For A Munc13-1 Dimeric - Munc13-1 - Rim
           Heterodimer Switch: C2-domains As Versatile Protein-
           Protein Interaction Modules
          Length = 62

 Score = 64.7 bits (156), Expect = 2e-11,   Method: Compositional matrix adjust.
 Identities = 29/41 (70%), Positives = 33/41 (80%)

Query: 81  ATCHICLKTKFADGVGHMCNYCNIRCCARCGGKVTLRSNKV 121
            TC IC KTKFADG GH C+YC  + CARCGG+V+LRSNKV
Sbjct: 10  PTCGICHKTKFADGCGHNCSYCQTKFCARCGGRVSLRSNKV 50


>pdb|2VDA|A Chain A, Solution Structure Of The Seca-Signal Peptide Complex
          Length = 828

 Score = 28.1 bits (61), Expect = 1.5,   Method: Composition-based stats.
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 20  PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHL 60
           P+L   TL ER + +S+ + Q++EE    E+MR  +  V L
Sbjct: 720 PELHEETLRERILAQSIEVYQRKEEVVGAEMMRHFEKGVML 760


>pdb|2FSF|A Chain A, Escherichia Coli Seca, The Preprotein Translocase Dimeric
           Atpase
 pdb|2FSF|B Chain B, Escherichia Coli Seca, The Preprotein Translocase Dimeric
           Atpase
 pdb|2FSH|A Chain A, Complex Seca:amp-Pnp From Escherichia Coli
 pdb|2FSH|B Chain B, Complex Seca:amp-Pnp From Escherichia Coli
 pdb|2FSI|A Chain A, Complex Seca:adp From Escherichia Coli
 pdb|2FSI|B Chain B, Complex Seca:adp From Escherichia Coli
          Length = 853

 Score = 28.1 bits (61), Expect = 1.8,   Method: Composition-based stats.
 Identities = 15/41 (36%), Positives = 24/41 (58%)

Query: 20  PDLSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHL 60
           P+L   TL ER + +S+ + Q++EE    E+MR  +  V L
Sbjct: 720 PELHEETLRERILAQSIEVYQRKEEVVGAEMMRHFEKGVML 760


>pdb|4AKR|B Chain B, Crystal Structure Of The Cytoplasmic Actin Capping Protein
           Cap32_34 From Dictyostelium Discoideum
 pdb|4AKR|D Chain D, Crystal Structure Of The Cytoplasmic Actin Capping Protein
           Cap32_34 From Dictyostelium Discoideum
          Length = 290

 Score = 26.9 bits (58), Expect = 3.9,   Method: Compositional matrix adjust.
 Identities = 13/54 (24%), Positives = 32/54 (59%), Gaps = 4/54 (7%)

Query: 36  VMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDATCHICLKT 89
           V+M++ Q++ ++ + MR   D +H++E  + ++     KA  +L +T  + ++T
Sbjct: 150 VLMKKTQDQSKKGQPMRGTWDSIHVVEVKLGKKD----KAVYKLTSTVMLSIET 199


>pdb|1NNE|A Chain A, Crystal Structure Of The Muts-adpbef3-dna Complex
 pdb|1NNE|B Chain B, Crystal Structure Of The Muts-adpbef3-dna Complex
          Length = 765

 Score = 26.2 bits (56), Expect = 5.6,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 35/72 (48%)

Query: 22  LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
           L  +  +ER++     + +++EEE  LE+  R + +   L ++ R  +E    A +   A
Sbjct: 478 LPEMKEKEREVYRLEALIRRREEEVFLEVRERAKRQAEALREAARILAELDVYAALAEVA 537

Query: 82  TCHICLKTKFAD 93
             +  ++ +F D
Sbjct: 538 VRYGYVRPRFGD 549


>pdb|1EWR|A Chain A, Crystal Structure Of Taq Muts
 pdb|1EWR|B Chain B, Crystal Structure Of Taq Muts
          Length = 649

 Score = 26.2 bits (56), Expect = 5.6,   Method: Composition-based stats.
 Identities = 16/72 (22%), Positives = 35/72 (48%)

Query: 22  LSHLTLEERQIIESVMMRQKQEEERELEIMRRKQDEVHLLEQSIRQRSEQQKKAGVELDA 81
           L  +  +ER++     + +++EEE  LE+  R + +   L ++ R  +E    A +   A
Sbjct: 362 LPEMKEKEREVYRLEALIRRREEEVFLEVRERAKRQAEALREAARILAELDVYAALAEVA 421

Query: 82  TCHICLKTKFAD 93
             +  ++ +F D
Sbjct: 422 VRYGYVRPRFGD 433


  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    0.131    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,478,627
Number of Sequences: 62578
Number of extensions: 118056
Number of successful extensions: 389
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 362
Number of HSP's gapped (non-prelim): 31
length of query: 137
length of database: 14,973,337
effective HSP length: 89
effective length of query: 48
effective length of database: 9,403,895
effective search space: 451386960
effective search space used: 451386960
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 46 (22.3 bits)