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= psy17875
         (107 letters)

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

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



>pdb|4B4T|V Chain V, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 306

 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 49/104 (47%), Gaps = 7/104 (6%)

Query: 4   DVAYISEDVYFSMFYLALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLTSKHDRV 63
           +  YIS      M     +   +EV+ +++GE  ++  V  V V+ M  P   T     V
Sbjct: 25  ETVYISSIALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVNVVDVFAM--PQSGTGVS--V 80

Query: 64  EASPEQLFEAVTEAEKLSKLYNRELRVIGWFHSHPHITVWPSDV 107
           EA  + +F+A  +   + K   R+  V+GW+HSHP    W S V
Sbjct: 81  EA-VDDVFQA--KMMDMLKQTGRDQMVVGWYHSHPGFGCWLSSV 121


>pdb|4F7O|A Chain A, Crystal Structure Of Csn5
 pdb|4F7O|B Chain B, Crystal Structure Of Csn5
          Length = 257

 Score = 31.6 bits (70), Expect = 0.11,   Method: Compositional matrix adjust.
 Identities = 23/89 (25%), Positives = 41/89 (46%), Gaps = 8/89 (8%)

Query: 20  ALSNDKLEVLSMLIGETKEEKGVKSVHVYTMVIPLRLT-SKHDRVEASPEQLFEAVTEAE 78
           A S   LEV  + +G+     G   +   +  +P+  T ++ +   A+ E     +  A+
Sbjct: 69  ARSGGNLEVXGLXLGKVD---GETXIIXDSFALPVEGTETRVNAQAAAYEYXAAYIENAK 125

Query: 79  KLSKLYNRELRVIGWFHSHPHITVWPSDV 107
           ++ +L N     IGW+HSHP    W S +
Sbjct: 126 QVGRLEN----AIGWYHSHPGYGCWLSGI 150


>pdb|4GQ2|M Chain M, S. Pombe Nup120-Nup37 Complex
          Length = 950

 Score = 29.3 bits (64), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 13/89 (14%)

Query: 15  SMFYLALSNDKLEVLSML-IGETKEEKGVKSVHVYTM----VIPLRLTSKHDRVEASPEQ 69
           +M  LA  N  L+  S L   E   E  +  +H   +     I +R  +++D V    E+
Sbjct: 760 TMEALASVNTALQFFSALNYSECFSESQISPLHATVISSLSAIFIRDDTENDLVTELVEK 819

Query: 70  LFEAVTEAEKLSKLYNRELRVIGWFHSHP 98
           LF        L K YN  +++IGW +S P
Sbjct: 820 LF--------LFKQYNACMQLIGWLNSDP 840


>pdb|4FHN|B Chain B, Nup37-Nup120 Full-Length Complex From Schizosaccharomyces
           Pombe
 pdb|4FHN|D Chain D, Nup37-Nup120 Full-Length Complex From Schizosaccharomyces
           Pombe
          Length = 1139

 Score = 29.3 bits (64), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 13/89 (14%)

Query: 15  SMFYLALSNDKLEVLSML-IGETKEEKGVKSVHVYTM----VIPLRLTSKHDRVEASPEQ 69
           +M  LA  N  L+  S L   E   E  +  +H   +     I +R  +++D V    E+
Sbjct: 762 TMEALASVNTALQFFSALNYSECFSESQISPLHATVISSLSAIFIRDDTENDLVTELVEK 821

Query: 70  LFEAVTEAEKLSKLYNRELRVIGWFHSHP 98
           LF        L K YN  +++IGW +S P
Sbjct: 822 LF--------LFKQYNACMQLIGWLNSDP 842


>pdb|4FHM|B Chain B, Nup37-Nup120(Aa1-961) Complex From Schizosaccharomyces
           Pombe
          Length = 964

 Score = 29.3 bits (64), Expect = 0.55,   Method: Compositional matrix adjust.
 Identities = 26/89 (29%), Positives = 40/89 (44%), Gaps = 13/89 (14%)

Query: 15  SMFYLALSNDKLEVLSML-IGETKEEKGVKSVHVYTM----VIPLRLTSKHDRVEASPEQ 69
           +M  LA  N  L+  S L   E   E  +  +H   +     I +R  +++D V    E+
Sbjct: 762 TMEALASVNTALQFFSALNYSECFSESQISPLHATVISSLSAIFIRDDTENDLVTELVEK 821

Query: 70  LFEAVTEAEKLSKLYNRELRVIGWFHSHP 98
           LF        L K YN  +++IGW +S P
Sbjct: 822 LF--------LFKQYNACMQLIGWLNSDP 842


>pdb|2ZNR|A Chain A, Crystal Structure Of The Dub Domain Of Human Amsh-Lp
          Length = 178

 Score = 28.5 bits (62), Expect = 0.96,   Method: Compositional matrix adjust.
 Identities = 28/113 (24%), Positives = 46/113 (40%), Gaps = 25/113 (22%)

Query: 2   SLDVAYISEDVYFSMFYLALSND--KLEVLSMLIGE-TKEEKGVKSVHVYTMVIPLRLTS 58
            L    + ED+      LA SN    +E   +L G+ T  E  +  V     ++P     
Sbjct: 7   GLRCVVLPEDLCHKFLQLAESNTVRGIETCGILCGKLTHNEFTITHV-----IVP----- 56

Query: 59  KHDRVEASPEQLFEAVTEAEKLSKLYN----RELRVIGWFHSHPHITVWPSDV 107
              +  A P+       + E + +L+N     +L  +GW H+HP  T + S V
Sbjct: 57  ---KQSAGPD-----YCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSV 101


>pdb|3SNP|A Chain A, Crystal Structure Analysis Of Iron Regulatory Protein 1 In
           Complex With Ferritin H Ire Rna
 pdb|3SNP|B Chain B, Crystal Structure Analysis Of Iron Regulatory Protein 1 In
           Complex With Ferritin H Ire Rna
 pdb|3SN2|A Chain A, Crystal Structure Analysis Of Iron Regulatory Protein 1 In
           Complex With Transferrin Receptor Ire B Rna
          Length = 908

 Score = 27.3 bits (59), Expect = 2.0,   Method: Composition-based stats.
 Identities = 16/47 (34%), Positives = 25/47 (53%), Gaps = 1/47 (2%)

Query: 29  LSMLIGETKEEKGVKSVHVYTMVIPLRLTSK-HDRVEASPEQLFEAV 74
           L  L GE  +  G+     YT++IP  LT + H +V+    + F+AV
Sbjct: 835 LEYLPGENADSLGLTGRERYTIIIPENLTPRMHVQVKLDTGKTFQAV 881


>pdb|2ZNV|A Chain A, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
           With Lys63-Linked Ubiquitin Dimer
 pdb|2ZNV|D Chain D, Crystal Structure Of Human Amsh-Lp Dub Domain In Complex
           With Lys63-Linked Ubiquitin Dimer
          Length = 178

 Score = 26.6 bits (57), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 27/113 (23%), Positives = 45/113 (39%), Gaps = 25/113 (22%)

Query: 2   SLDVAYISEDVYFSMFYLALSND--KLEVLSMLIGE-TKEEKGVKSVHVYTMVIPLRLTS 58
            L    + ED+      LA SN    +    +L G+ T  E  +  V     ++P     
Sbjct: 7   GLRCVVLPEDLCHKFLQLAESNTVRGIATCGILCGKLTHNEFTITHV-----IVP----- 56

Query: 59  KHDRVEASPEQLFEAVTEAEKLSKLYN----RELRVIGWFHSHPHITVWPSDV 107
              +  A P+       + E + +L+N     +L  +GW H+HP  T + S V
Sbjct: 57  ---KQSAGPD-----YCDMENVEELFNVQDQHDLLTLGWIHTHPTQTAFLSSV 101


  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
   0.318    0.133    0.384 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,942,758
Number of Sequences: 62578
Number of extensions: 92734
Number of successful extensions: 258
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 251
Number of HSP's gapped (non-prelim): 13
length of query: 107
length of database: 14,973,337
effective HSP length: 72
effective length of query: 35
effective length of database: 10,467,721
effective search space: 366370235
effective search space used: 366370235
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 45 (21.9 bits)