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= psy13564
         (323 letters)

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

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



>pdb|3TJ1|A Chain A, Crystal Structure Of Rna Polymerase I Transcription
           Initiation Factor Rrn3
 pdb|3TJ1|B Chain B, Crystal Structure Of Rna Polymerase I Transcription
           Initiation Factor Rrn3
          Length = 649

 Score = 60.5 bits (145), Expect = 1e-09,   Method: Compositional matrix adjust.
 Identities = 59/270 (21%), Positives = 114/270 (42%), Gaps = 68/270 (25%)

Query: 2   LFNELLAVFESTILPTHGITHVPFLVFYFCSLRLSIGENF------IEFLWKKIANVKIY 55
           +FN L  +F++ +LPT+    + +++F+    +L + ++F      I F   + A  KI 
Sbjct: 382 VFNTLTTLFKTHVLPTYYTRSIQYIMFHVSQQQLELMDSFLVTLIDISFAVNEAAEKKIK 441

Query: 56  NIFRQSCCHYVSSLLIHAHFMPVSIGENFIEFLWKKIANVKIYNIFRQSCCHYVSSLLIH 115
           ++       Y+ S +  A                KK++  +I          +V+S L  
Sbjct: 442 SL------QYLGSYIARA----------------KKLSRTQII---------FVASYL-- 468

Query: 116 AHFMPVRVIKTCLNEMSQWCHSYLDNTDLTDEEACSPVKHPVFYSVCQALFSVITYKHSI 175
                           + W + Y+   +   ++     +   FY+  QAL  +  ++H+I
Sbjct: 469 ----------------TSWLNRYVIEREEEVDQRGGMERFKHFYAAFQALCYIFCFRHNI 512

Query: 176 LVDSKKNM-----KFLQSLNLTRLVMSQLNPLRSCNAEIVSHFASITNTYQIVYCYNVI- 229
             D+  N      KF Q     R+V+S+ NPL+ CN  ++  FA I     + YC+++I 
Sbjct: 513 FRDTDGNWECELDKFFQ-----RMVISKFNPLKFCNENVMLMFARIAQQESVAYCFSIIE 567

Query: 230 -HQNARL-NVLPIVSTDALGNIIKLNTVNA 257
            + N RL  ++    +D   N  + NT ++
Sbjct: 568 NNNNERLRGIIGKADSDKKENSAQANTTSS 597


>pdb|3RIP|A Chain A, Crystal Structure Of Human Gamma-Tubulin Complex Protein 4
           (Gcp4)
          Length = 677

 Score = 29.3 bits (64), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 17/65 (26%), Positives = 37/65 (56%), Gaps = 1/65 (1%)

Query: 74  HFMPVSIGENFIEFLWKKIANVKIYNIFRQSCCHYVSSLLIHAHFMPVRVIKTCLNEMSQ 133
           +++ V + E+    L  +I + + +   R +  H++S+LL  + F+ ++ +  CLNE+  
Sbjct: 529 YYLQVDVLESQFSQLLHQINSTRDFESIRLAHDHFLSNLLAQS-FILLKPVFHCLNEILD 587

Query: 134 WCHSY 138
            CHS+
Sbjct: 588 LCHSF 592


  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
   0.326    0.137    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,813,773
Number of Sequences: 62578
Number of extensions: 334758
Number of successful extensions: 690
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 688
Number of HSP's gapped (non-prelim): 3
length of query: 323
length of database: 14,973,337
effective HSP length: 99
effective length of query: 224
effective length of database: 8,778,115
effective search space: 1966297760
effective search space used: 1966297760
T: 11
A: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)