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= psy12906
         (303 letters)

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

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



>pdb|2GWF|B Chain B, Structure Of A Usp8-Nrdp1 Complex
 pdb|2GWF|D Chain D, Structure Of A Usp8-Nrdp1 Complex
 pdb|2GWF|F Chain F, Structure Of A Usp8-Nrdp1 Complex
          Length = 134

 Score =  187 bits (475), Expect = 6e-48,   Method: Compositional matrix adjust.
 Identities = 82/125 (65%), Positives = 102/125 (81%)

Query: 179 AENMERDDVARWSNSLSRARVTRWGGMISTPDVMLQAMIKRSLAESGCPGHILDQLMHNS 238
              +E +++  W NSL  ARVTRWGGMISTPD +LQA+IKRSL ESGCP  I+++L+ N+
Sbjct: 8   GSTIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENA 67

Query: 239 HERNWPQGLSSLETRQNNRRQYENYVCKRIPSKQAVVVLLCDNVHLPEDMISAPGLVMIF 298
           HER+WPQGL++LETRQ NRR YENYV KRIP KQAVVV+ C+N H+ +DM+  PGLVMIF
Sbjct: 68  HERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIF 127

Query: 299 AHGIE 303
           AHG+E
Sbjct: 128 AHGVE 132


>pdb|2FZP|A Chain A, Crystal Structure Of The Usp8 Interaction Domain Of Human
           Nrdp1
          Length = 144

 Score =  187 bits (474), Expect = 8e-48,   Method: Compositional matrix adjust.
 Identities = 82/125 (65%), Positives = 102/125 (81%)

Query: 179 AENMERDDVARWSNSLSRARVTRWGGMISTPDVMLQAMIKRSLAESGCPGHILDQLMHNS 238
              +E +++  W NSL  ARVTRWGGMISTPD +LQA+IKRSL ESGCP  I+++L+ N+
Sbjct: 18  GSTIEYNEILEWVNSLQPARVTRWGGMISTPDAVLQAVIKRSLVESGCPASIVNELIENA 77

Query: 239 HERNWPQGLSSLETRQNNRRQYENYVCKRIPSKQAVVVLLCDNVHLPEDMISAPGLVMIF 298
           HER+WPQGL++LETRQ NRR YENYV KRIP KQAVVV+ C+N H+ +DM+  PGLVMIF
Sbjct: 78  HERSWPQGLATLETRQMNRRYYENYVAKRIPGKQAVVVMACENQHMGDDMVQEPGLVMIF 137

Query: 299 AHGIE 303
           AHG+E
Sbjct: 138 AHGVE 142


>pdb|2OGB|A Chain A, Crystal Structure Of The C-Terminal Domain Of Mouse Nrdp1
 pdb|2OGB|B Chain B, Crystal Structure Of The C-Terminal Domain Of Mouse Nrdp1
          Length = 126

 Score =  178 bits (452), Expect = 3e-45,   Method: Compositional matrix adjust.
 Identities = 79/122 (64%), Positives = 97/122 (79%)

Query: 182 MERDDVARWSNSLSRARVTRWGGMISTPDVMLQAMIKRSLAESGCPGHILDQLMHNSHER 241
           +E +++  W NSL  ARVTRWGG ISTPD +LQA+IKRSL ESGCP  I+++L+ N+HER
Sbjct: 3   IEYNEILEWVNSLQPARVTRWGGXISTPDAVLQAVIKRSLVESGCPASIVNELIENAHER 62

Query: 242 NWPQGLSSLETRQNNRRQYENYVCKRIPSKQAVVVLLCDNVHLPEDMISAPGLVMIFAHG 301
           +WPQGL++LETRQ NRR YENYV KRIP KQAVVV  C+N H  +D +  PGLV IFAHG
Sbjct: 63  SWPQGLATLETRQXNRRYYENYVAKRIPGKQAVVVXACENQHXGDDXVQEPGLVXIFAHG 122

Query: 302 IE 303
           +E
Sbjct: 123 VE 124


>pdb|1H4P|A Chain A, Crystal Structure Of Exo-1,3-Beta Glucanse From
          Saccharomyces Cerevisiae
 pdb|1H4P|B Chain B, Crystal Structure Of Exo-1,3-Beta Glucanse From
          Saccharomyces Cerevisiae
          Length = 408

 Score = 29.3 bits (64), Expect = 3.1,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 25/50 (50%), Gaps = 4/50 (8%)

Query: 46 IPMDELKYLSNQCEYHQHDSHGTDLELSFCTPYQSLHTANTAIMGYEIVR 95
          IP+DE  +    C+Y   D   + L+  + T YQ    AN A  G+ +VR
Sbjct: 46 IPVDEYHF----CQYLGKDLAKSRLQSHWSTFYQEQDFANIASQGFNLVR 91


>pdb|2C7M|A Chain A, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|A Chain A, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|C Chain C, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|E Chain E, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|G Chain G, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|I Chain I, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
 pdb|2C7N|K Chain K, Human Rabex-5 Residues 1-74 In Complex With Ubiquitin
          Length = 74

 Score = 28.1 bits (61), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 103 ELICSICSGVFEEPLQDHNCVKELRSIVHKQQQKMVNMETEMSEQRFQMTE 153
           +L+C    G +  P     C K  R   HK +QK +  + E++E R Q  E
Sbjct: 16  DLLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAE-RLQREE 65


>pdb|3HNW|A Chain A, Crystal Structure Of A Basic Coiled-coil Protein Of
           Unknown Function From Eubacterium Eligens Atcc 27750
 pdb|3HNW|B Chain B, Crystal Structure Of A Basic Coiled-coil Protein Of
           Unknown Function From Eubacterium Eligens Atcc 27750
          Length = 138

 Score = 27.7 bits (60), Expect = 7.3,   Method: Compositional matrix adjust.
 Identities = 10/26 (38%), Positives = 21/26 (80%)

Query: 123 VKELRSIVHKQQQKMVNMETEMSEQR 148
           +KEL+S ++K Q+ +V +ETE+++ +
Sbjct: 112 IKELKSEINKYQKNIVKLETELNDSK 137


>pdb|2FID|B Chain B, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
           With Ubiquitin
 pdb|2FIF|B Chain B, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
           With Ubiquitin
 pdb|2FIF|D Chain D, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
           With Ubiquitin
 pdb|2FIF|F Chain F, Crystal Structure Of A Bovine Rabex-5 Fragment Complexed
           With Ubiquitin
          Length = 70

 Score = 27.7 bits (60), Expect = 8.8,   Method: Composition-based stats.
 Identities = 17/51 (33%), Positives = 24/51 (47%), Gaps = 1/51 (1%)

Query: 103 ELICSICSGVFEEPLQDHNCVKELRSIVHKQQQKMVNMETEMSEQRFQMTE 153
           EL+C    G +  P     C K  R   HK +QK +  + E++E R Q  E
Sbjct: 13  ELLCKKGCGYYGNPAWQGFCSKCWREEYHKARQKQIQEDWELAE-RLQREE 62


  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    0.132    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,685,161
Number of Sequences: 62578
Number of extensions: 327845
Number of successful extensions: 726
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 719
Number of HSP's gapped (non-prelim): 12
length of query: 303
length of database: 14,973,337
effective HSP length: 98
effective length of query: 205
effective length of database: 8,840,693
effective search space: 1812342065
effective search space used: 1812342065
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: 51 (24.3 bits)