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= psy4604
         (302 letters)

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

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



>pdb|2YUH|A Chain A, Solution Structure Of The C-Terminal Region In Human
           Tubulin Folding Cofactor C
          Length = 179

 Score = 99.4 bits (246), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 42/107 (39%), Positives = 70/107 (65%)

Query: 178 GFYNRSNETLELPSEDVHKKPVSLSNIDSCVVKVNGNASTIHLNNIKNSQIFLGPVSNSV 237
           GF N  ++ LE  + ++H++ V L+ + +C V++ GN +T+ L    + ++  GPVS SV
Sbjct: 12  GFSNLESQVLEKRASELHQRDVLLTELSNCTVRLYGNPNTLRLTKAHSCKLLCGPVSTSV 71

Query: 238 FIDNCTDSTLYLACHQLRMHTSHKCSVYLHVTSRPIIEHCKNIGFAP 284
           F+++C+D  L +AC QLR+H++    ++L VTSR I+E C  I FAP
Sbjct: 72  FLEDCSDCVLAVACQQLRIHSTKDTRIFLQVTSRAIVEDCSGIQFAP 118


>pdb|3BH6|B Chain B, Crystal Structure Of The Rp2-Arl3 Complex Bound To Gppnhp
 pdb|3BH7|B Chain B, Crystal Structure Of The Rp2-Arl3 Complex Bound To
           Gdp-Alf4
          Length = 352

 Score = 69.3 bits (168), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 54/105 (51%)

Query: 179 FYNRSNETLELPSEDVHKKPVSLSNIDSCVVKVNGNASTIHLNNIKNSQIFLGPVSNSVF 238
           F    +ET+      V  +   + + ++C + +  +++T+ +++  N  IFLGPV  SVF
Sbjct: 44  FSGLKDETVGRLPGTVAGQQFLIQDCENCNIYIFDHSATVTIDDCTNCIIFLGPVKGSVF 103

Query: 239 IDNCTDSTLYLACHQLRMHTSHKCSVYLHVTSRPIIEHCKNIGFA 283
             NC D    LAC Q R+    K  V+L   ++PIIE   NI F 
Sbjct: 104 FRNCRDCKCTLACQQFRVRDCRKLEVFLCCATQPIIESSSNIKFG 148


>pdb|2BX6|A Chain A, Crystal Structure Of The Human Retinitis Pigmentosa
           Protein 2 (Rp2)
          Length = 350

 Score = 68.9 bits (167), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 34/105 (32%), Positives = 54/105 (51%)

Query: 179 FYNRSNETLELPSEDVHKKPVSLSNIDSCVVKVNGNASTIHLNNIKNSQIFLGPVSNSVF 238
           F    +ET+      V  +   + + ++C + +  +++T+ +++  N  IFLGPV  SVF
Sbjct: 42  FSGLKDETVGRLPGTVAGQQFLIQDCENCNIYIFDHSATVTIDDCTNCIIFLGPVKGSVF 101

Query: 239 IDNCTDSTLYLACHQLRMHTSHKCSVYLHVTSRPIIEHCKNIGFA 283
             NC D    LAC Q R+    K  V+L   ++PIIE   NI F 
Sbjct: 102 FRNCRDCKCTLACQQFRVRDCRKLEVFLCCATQPIIESSSNIKFG 146


>pdb|2L3L|A Chain A, The Solution Structure Of The N-Terminal Domain Of Human
           Tubulin Binding Cofactor C Reveals A Platform For The
           Interaction With Ab- Tubulin
          Length = 111

 Score = 40.0 bits (92), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 25/95 (26%), Positives = 52/95 (54%), Gaps = 9/95 (9%)

Query: 14  IPERLLKREQERISAIEKRQEKKGDKEHDGF-SNMFNENYDKIKGMINEIDVDPNSGSVN 72
           +PERL +REQER   +E+R++K+ ++E +   S+ F   + + +  + E+        + 
Sbjct: 1   MPERLQRREQERQLEVERRKQKRQNQEVEKENSHFFVATFARERAAVEEL--------LE 52

Query: 73  KEELKEKFADINKQILLLNHVIVDAKIFLTSYDMK 107
           + E  E+  +   ++  L  +I D+  FL +YD++
Sbjct: 53  RAESVERLEEAASRLQGLQKLINDSVFFLAAYDLR 87


>pdb|4IJB|A Chain A, Crystal Structure Of Engineered Protein, Northeast
           Structural Genomics Consortium Target Or288
          Length = 256

 Score = 30.0 bits (66), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 17/40 (42%), Positives = 24/40 (60%), Gaps = 3/40 (7%)

Query: 176 YIGFYNRSNETLELPSEDVHKKPVSLSNIDSCVVKVNGNA 215
           +IG +++ NETLE+  E+  K    +S I S VVKV G  
Sbjct: 176 FIGIWSQDNETLEINKENQRK---LISXIPSNVVKVAGGG 212


>pdb|2RKK|A Chain A, Crystal Structure Of S.Cerevisiae Vta1 N-Terminal Domain
 pdb|2RKK|B Chain B, Crystal Structure Of S.Cerevisiae Vta1 N-Terminal Domain
          Length = 168

 Score = 27.7 bits (60), Expect = 8.2,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 26/38 (68%), Gaps = 3/38 (7%)

Query: 82  DINKQILLLNHVIVD---AKIFLTSYDMKIYNNKLQEL 116
           D +K + ++N +I D   AKI++ ++ M +YN KL++L
Sbjct: 72  DSDKSLHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQL 109


>pdb|2LUH|A Chain A, Nmr Structure Of The Vta1-Vps60 Complex
          Length = 167

 Score = 27.7 bits (60), Expect = 8.4,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 26/38 (68%), Gaps = 3/38 (7%)

Query: 82  DINKQILLLNHVIVD---AKIFLTSYDMKIYNNKLQEL 116
           D +K + ++N +I D   AKI++ ++ M +YN KL++L
Sbjct: 71  DSDKSLHVMNTLIHDQEKAKIYMLNFTMSLYNEKLKQL 108


  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    0.133    0.375 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,425,844
Number of Sequences: 62578
Number of extensions: 339597
Number of successful extensions: 1134
Number of sequences better than 100.0: 19
Number of HSP's better than 100.0 without gapping: 8
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1124
Number of HSP's gapped (non-prelim): 19
length of query: 302
length of database: 14,973,337
effective HSP length: 98
effective length of query: 204
effective length of database: 8,840,693
effective search space: 1803501372
effective search space used: 1803501372
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)