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= psy4542
         (273 letters)

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

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



>pdb|4B4T|U Chain U, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 338

 Score = 81.3 bits (199), Expect = 6e-16,   Method: Compositional matrix adjust.
 Identities = 55/233 (23%), Positives = 120/233 (51%), Gaps = 7/233 (3%)

Query: 6   SIKVHPVVLFQIVDAFER-RNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEMVEA- 63
            + + P+VL   +D +ER +  ++ R +G +LG  +   + VTN F +P +E ++  +  
Sbjct: 7   KVTIAPLVLLSALDHYERTQTKENKRCVGVILGDANSSTIRVTNSFALPFEEDEKNSDVW 66

Query: 64  --ELNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDYYIRECK-NPVHMTLDTN 120
             + NY ++M EM +K+N  E ++GW+ +G ++ +    I++ + +  + NP+ + +D  
Sbjct: 67  FLDHNYIENMNEMCKKINAKEKLIGWYHSGPKLRASDLKINELFKKYTQNNPLLLIVDVK 126

Query: 121 LKGPNMGIKGYVHVP-IGVPGGKSGIMFTQIPAEVICYNSEVTGLRLLHKSIKQGAVQPL 179
            +G  +    YV +  +   G  +   F  +P  +    +E  G+  L + ++  A   L
Sbjct: 127 QQGVGLPTDAYVAIEQVKDDGTSTEKTFLHLPCTIEAEEAEEIGVEHLLRDVRDQAAGGL 186

Query: 180 S-ELTLVSEAADKLTVLIDHVLRYVDEVLANRITPDNSIGRQLLDMVNSVPSM 231
           S  LT   ++   L   +  V+ Y+D+V+   +  +++I  +L D+ N +P++
Sbjct: 187 SIRLTNQLKSLKGLQSKLKDVVEYLDKVINKELPINHTILGKLQDVFNLLPNL 239


>pdb|2O95|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34
           Mpn Domain (Residues 1-186)
 pdb|2O95|B Chain B, Crystal Structure Of The Metal-Free Dimeric Human Mov34
           Mpn Domain (Residues 1-186)
          Length = 187

 Score = 79.0 bits (193), Expect = 2e-15,   Method: Compositional matrix adjust.
 Identities = 57/177 (32%), Positives = 91/177 (51%), Gaps = 12/177 (6%)

Query: 9   VHPVVLFQIVDAFER--RNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDE---MVEA 63
           VHP+VL  +VD F R  +  +  RV+G LLG+  K V++V+N F VP  E D+   +   
Sbjct: 12  VHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFL 71

Query: 64  ELNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKG 123
           + +Y ++M+ M +KVN  E IVGW+ TG ++      I++   R C N V + +D   K 
Sbjct: 72  DHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKD 131

Query: 124 PNMGIKGYVHVP----IGVPGGKSGIMFTQIPAEVICYNSEVTGLRLLHKSIKQGAV 176
             +  + Y+ V      G P  K+   F  + +E+    +E  G+  L + IK   V
Sbjct: 132 LGLPTEAYISVEEVHDDGTPTSKT---FEHVTSEIGAEEAEEVGVEHLLRDIKDTTV 185


>pdb|2O96|A Chain A, Crystal Structure Of The Metal-Free Dimeric Human Mov34
           Mpn Domain (Residues 1-177)
 pdb|2O96|B Chain B, Crystal Structure Of The Metal-Free Dimeric Human Mov34
           Mpn Domain (Residues 1-177)
          Length = 178

 Score = 79.0 bits (193), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 51/155 (32%), Positives = 82/155 (52%), Gaps = 12/155 (7%)

Query: 9   VHPVVLFQIVDAFER--RNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDE---MVEA 63
           VHP+VL  +VD F R  +  +  RV+G LLG+  K V++V+N F VP  E D+   +   
Sbjct: 12  VHPLVLLSVVDHFNRIGKVGNQKRVVGVLLGSWQKKVLDVSNSFAVPFDEDDKDDSVWFL 71

Query: 64  ELNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDYYIRECKNPVHMTLDTNLKG 123
           + +Y ++M+ M +KVN  E IVGW+ TG ++      I++   R C N V + +D   K 
Sbjct: 72  DHDYLENMYGMFKKVNARERIVGWYHTGPKLHKNDIAINELMKRYCPNSVLVIIDVKPKD 131

Query: 124 PNMGIKGYVHVP----IGVPGGKSGIMFTQIPAEV 154
             +  + Y+ V      G P  K+   F  + +E+
Sbjct: 132 LGLPTEAYISVEEVHDDGTPTSKT---FEHVTSEI 163


>pdb|4E0Q|A Chain A, Crystal Structure Of Mpn Domain From Cop9 Signalosome
 pdb|4E0Q|B Chain B, Crystal Structure Of Mpn Domain From Cop9 Signalosome
          Length = 141

 Score = 35.0 bits (79), Expect = 0.048,   Method: Compositional matrix adjust.
 Identities = 29/125 (23%), Positives = 55/125 (44%), Gaps = 10/125 (8%)

Query: 4   NVSIKVHPVVLFQIVDAFER---RNLDSHRVIGTLLGTVDKGVVEVTNCFCVPHKEYDEM 60
           +V+I +HP+V+  I + + R   ++ +  +V G L+G      +E+ N F +      + 
Sbjct: 5   SVTISLHPLVIXNISEHWTRFRAQHGEPRQVYGALIGKQKGRNIEIXNSFELKTDVIGDE 64

Query: 61  VEAELNYAQDMFEMNQKVNPSELIVGWWATGDEVTSQSSVIHDY--YIRECK-----NPV 113
                +Y     +  ++V      +GW+ TGD  T+    I      I EC      NP+
Sbjct: 65  TVINKDYYNKKEQQYKQVFSDLDFIGWYTTGDNPTADDIKIQRQIAAINECPIXLQLNPL 124

Query: 114 HMTLD 118
             ++D
Sbjct: 125 SRSVD 129


  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    0.136    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,098,073
Number of Sequences: 62578
Number of extensions: 285769
Number of successful extensions: 782
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 773
Number of HSP's gapped (non-prelim): 14
length of query: 273
length of database: 14,973,337
effective HSP length: 97
effective length of query: 176
effective length of database: 8,903,271
effective search space: 1566975696
effective search space used: 1566975696
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)