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= psy9817
         (231 letters)

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

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



>pdb|4B4T|S Chain S, Near-Atomic Resolution Structural Model Of The Yeast 26s
           Proteasome
          Length = 523

 Score =  167 bits (423), Expect = 5e-42,   Method: Compositional matrix adjust.
 Identities = 90/232 (38%), Positives = 149/232 (64%), Gaps = 12/232 (5%)

Query: 8   NRRTSDLIAAKCYFYHSRVHEL---------TNNLDKV-RSFLNARLRIATLRNDFEGQA 57
           N R+ +LI AK +FY    HE          ++N + + RS +   L+IA+L++D E +A
Sbjct: 172 NLRSLNLINAKLWFYIYLSHETLARSSEEINSDNQNIILRSTMMKFLKIASLKHDNETKA 231

Query: 58  VLINCLLRNYLHYNLYDQADKLVKKSAFPE-NASNNEWARFHFYLGRIKAVRLEYSTAHK 116
           +LIN +LR++L+    D A   + K  +P  + S++  AR+ FYL +I A++L+YSTA++
Sbjct: 232 MLINLILRDFLNNGEVDSASDFISKLEYPHTDVSSSLEARYFFYLSKINAIQLDYSTANE 291

Query: 117 NLVQALRKAPQTA-AVGFRQTTQKLAVVVELLLGDIPDRQIFRQAVLRRALSPYFQLTQA 175
            ++ A+RKAP  + ++GF Q + KL   ++LL+GDIP+   F Q+ ++++L PY+ LT+A
Sbjct: 292 YIIAAIRKAPHNSKSLGFLQQSNKLHCCIQLLMGDIPELSFFHQSNMQKSLLPYYHLTKA 351

Query: 176 VRMGELQKFNEVLTTYGNQFRTDYTFKLILRLRHNVIKTAIRSIGASYSRIT 227
           V++G+L+KF   +T Y      D T++L +RLR NVIKT IR I  +Y +I+
Sbjct: 352 VKLGDLKKFTSTITKYKQLLLKDDTYQLCVRLRSNVIKTGIRIISLTYKKIS 403


>pdb|3IZS|EE Chain e, Localization Of The Large Subunit Ribosomal Proteins Into
           A 6.1 A Cryo-Em Map Of Saccharomyces Cerevisiae
           Translating 80s Ribosome
 pdb|3O58|G Chain G, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The First 80s In The Asymmetric Unit.
 pdb|3O5H|G Chain G, Yeast 80s Ribosome. This Entry Consists Of The 60s Subunit
           Of The Second 80s In The Asymmetric Unit.
 pdb|3U5E|F Chain F, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome A
 pdb|3U5I|F Chain F, The Structure Of The Eukaryotic Ribosome At 3.0 A
           Resolution. This Entry Contains Proteins Of The 60s
           Subunit, Ribosome B
 pdb|4B6A|F Chain F, Cryo-Em Structure Of The 60s Ribosomal Subunit In Complex
           With Arx1 And Rei1
          Length = 244

 Score = 28.1 bits (61), Expect = 4.2,   Method: Compositional matrix adjust.
 Identities = 32/96 (33%), Positives = 47/96 (48%), Gaps = 7/96 (7%)

Query: 101 LGRIKAVRLEYSTAHKNLVQALRKAPQTAAVGFRQTTQKLAVVVELL-LGDIP--DRQIF 157
           L R  A + EY TA +N++QA R A + A   + +   KL  VV +  +  IP   R++ 
Sbjct: 45  LERNAAYQKEYETAERNIIQAKRDA-KAAGSYYVEAQHKLVFVVRIKGINKIPPKPRKVL 103

Query: 158 RQAVLRRALSPYF-QLTQAVRMGELQKFNEVLTTYG 192
           +   L R  S  F ++T+A    EL K  E    YG
Sbjct: 104 QLLRLTRINSGTFVKVTKATL--ELLKLIEPYVAYG 137


>pdb|1PWU|A Chain A, Crystal Structure Of Anthrax Lethal Factor Complexed With
           (3-(n-hydroxycarboxamido)-2-isobutylpropanoyl-trp-
           Methylamide), A Known Small Molecule Inhibitor Of Matrix
           Metalloproteases.
 pdb|1PWU|B Chain B, Crystal Structure Of Anthrax Lethal Factor Complexed With
           (3-(n-hydroxycarboxamido)-2-isobutylpropanoyl-trp-
           Methylamide), A Known Small Molecule Inhibitor Of Matrix
           Metalloproteases.
 pdb|1PWW|A Chain A, Crystal Structure Of Anthrax Lethal Factor Active Site
           Mutant Protein Complexed With An Optimised Peptide
           Substrate In The Presence Of Zinc.
 pdb|1PWW|B Chain B, Crystal Structure Of Anthrax Lethal Factor Active Site
           Mutant Protein Complexed With An Optimised Peptide
           Substrate In The Presence Of Zinc
          Length = 776

 Score = 27.3 bits (59), Expect = 6.7,   Method: Composition-based stats.
 Identities = 28/89 (31%), Positives = 39/89 (43%), Gaps = 12/89 (13%)

Query: 49  LRNDFEGQAVLINCL---LRNYLHYNLYDQADKLVKKSA-----FPENASN-NEWARFHF 99
           LRND EG    I+C    + +Y  Y L      LV  S      F E  SN   + R + 
Sbjct: 677 LRNDSEG---FIHCFGHAVDDYAGYLLDKNQSDLVTNSKKFIDIFKEEGSNLTSYGRTNE 733

Query: 100 YLGRIKAVRLEYSTAHKNLVQALRKAPQT 128
                +A RL +ST H   ++  + AP+T
Sbjct: 734 AEFFAEAFRLMHSTDHAERLKVQKNAPKT 762


  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
   0.325    0.136    0.387 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,017,517
Number of Sequences: 62578
Number of extensions: 218444
Number of successful extensions: 638
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 633
Number of HSP's gapped (non-prelim): 9
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)