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= 006343
         (649 letters)

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

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



>pdb|1NA0|A Chain A, Design Of Stable Alpha-Helical Arrays From An Idealized
           Tpr Motif
 pdb|1NA0|B Chain B, Design Of Stable Alpha-Helical Arrays From An Idealized
           Tpr Motif
          Length = 125

 Score = 32.0 bits (71), Expect = 1.2,   Method: Composition-based stats.
 Identities = 23/86 (26%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 77  LISGYLKVGRCEEAARIFEAMVEKD---VVAWGSMVDGYCKKGRVIEAREIFDKMPE--- 130
           L + Y K G  +EA   ++  +E D     AW ++ + Y K+G   EA E + K  E   
Sbjct: 15  LGNAYYKQGDYDEAIEYYQKALELDPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP 74

Query: 131 KNVVAWTAMVDGYMKVDCFEDGFDLF 156
            N  AW  + + Y K   +++  + +
Sbjct: 75  NNAEAWYNLGNAYYKQGDYDEAIEYY 100


>pdb|2WQH|A Chain A, Crystal Structure Of Ctpr3y3
          Length = 125

 Score = 30.8 bits (68), Expect = 2.3,   Method: Composition-based stats.
 Identities = 22/86 (25%), Positives = 40/86 (46%), Gaps = 6/86 (6%)

Query: 77  LISGYLKVGRCEEAARIFEAMVE---KDVVAWGSMVDGYCKKGRVIEAREIFDKMPE--- 130
           L + Y K G  +EA   ++  +E    +  AW ++ + Y K+G   EA E + K  E   
Sbjct: 15  LGNAYYKQGDYDEAIEYYQKALELYPNNAEAWYNLGNAYYKQGDYDEAIEYYQKALELYP 74

Query: 131 KNVVAWTAMVDGYMKVDCFEDGFDLF 156
            N  AW  + + Y K   +++  + +
Sbjct: 75  NNAEAWYNLGNAYYKQGDYDEAIEYY 100



 Score = 29.6 bits (65), Expect = 5.4,   Method: Composition-based stats.
 Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 9/80 (11%)

Query: 54  FYEAEELYVNMPARWRDSVCSNALISGYLKVGRCEEAARIFEAMVE---KDVVAWGSMVD 110
           + +A ELY N    W +      L + Y K G  +EA   ++  +E    +  AW ++ +
Sbjct: 32  YQKALELYPNNAEAWYN------LGNAYYKQGDYDEAIEYYQKALELYPNNAEAWYNLGN 85

Query: 111 GYCKKGRVIEAREIFDKMPE 130
            Y K+G   EA E + K  E
Sbjct: 86  AYYKQGDYDEAIEYYQKALE 105


>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
           (Trigonal Crystal Form)
 pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
           (Orthorombic Crystal Form)
          Length = 136

 Score = 30.8 bits (68), Expect = 2.5,   Method: Composition-based stats.
 Identities = 28/117 (23%), Positives = 53/117 (45%), Gaps = 7/117 (5%)

Query: 47  GFVRRGMFYEAEELYVN-MPARWRDSVCSNALISGYLKVGRCEEAARIFEAMVEKD---V 102
            + ++G + EA E Y   +    R +     L + Y K G  +EA   ++  +E D    
Sbjct: 10  AYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSA 69

Query: 103 VAWGSMVDGYCKKGRVIEAREIFDKMPE---KNVVAWTAMVDGYMKVDCFEDGFDLF 156
            AW ++ + Y K+G   EA E + K  E   ++  AW  + + Y K   +++  + +
Sbjct: 70  EAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYY 126



 Score = 30.4 bits (67), Expect = 3.1,   Method: Composition-based stats.
 Identities = 22/86 (25%), Positives = 41/86 (47%), Gaps = 6/86 (6%)

Query: 77  LISGYLKVGRCEEAARIFEAMVEKD---VVAWGSMVDGYCKKGRVIEAREIFDKMPE--- 130
           L + Y K G  +EA   ++  +E D     AW ++ + Y K+G   EA E + K  E   
Sbjct: 7   LGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKALELDP 66

Query: 131 KNVVAWTAMVDGYMKVDCFEDGFDLF 156
           ++  AW  + + Y K   +++  + +
Sbjct: 67  RSAEAWYNLGNAYYKQGDYDEAIEYY 92


>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
          Length = 1134

 Score = 29.6 bits (65), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 18/89 (20%), Positives = 45/89 (50%), Gaps = 11/89 (12%)

Query: 363 ESDVSIQNSLVSLYSKCGNVVDAYRIFTNI--------DERNIVS---YNSMISGFAQNG 411
           ++ +S Q   +  + KC  + D   +  ++         +R +++   YN+++ G+A+ G
Sbjct: 120 QAQLSGQQQRLLAFFKCCLLTDQLPLAHHLLVVHHGQRQKRKLLTLDMYNAVMLGWARQG 179

Query: 412 LGEEALNLFRKMKDEGLVPNQITFLSVLS 440
             +E + +   +KD GL P+ +++ + L 
Sbjct: 180 AFKELVYVLFMVKDAGLTPDLLSYAAALQ 208


>pdb|3TP4|A Chain A, Crystal Structure Of Engineered Protein At The Resolution
           1.98a, Northeast Structural Genomics Consortium Target
           Or128
 pdb|3TP4|B Chain B, Crystal Structure Of Engineered Protein At The Resolution
           1.98a, Northeast Structural Genomics Consortium Target
           Or128
          Length = 475

 Score = 29.6 bits (65), Expect = 5.4,   Method: Compositional matrix adjust.
 Identities = 28/106 (26%), Positives = 44/106 (41%), Gaps = 8/106 (7%)

Query: 390 TNIDERNIVSYNSMISGFAQNGL-GEEALNLFRKMKDE--GLVPNQITFLSVLSACNHVG 446
           T  D +N+      + G++ + + G +   L    +DE   L  + I     +   N VG
Sbjct: 52  TTSDVKNVTGDFPAVFGWSTSIIEGNQRPGLAENTRDENIALFADYIRKADAIGGVNTVG 111

Query: 447 LVEEGFI-----YFKSMKTLYNIEPGPEHYACMVDILGRAGSLAEA 487
              E F+     Y  S  TL  + PG  H+A +V  L     LA+A
Sbjct: 112 AGVENFVTGGSFYDTSGDTLRAVLPGGSHHAELVAYLDDIAELADA 157


>pdb|3MKQ|B Chain B, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
           Of The Copi Vesicular Coat
 pdb|3MKQ|D Chain D, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
           Of The Copi Vesicular Coat
 pdb|3MKQ|F Chain F, Crystal Structure Of Yeast AlphaBETAPRIME-Cop Subcomplex
           Of The Copi Vesicular Coat
          Length = 177

 Score = 29.6 bits (65), Expect = 6.2,   Method: Composition-based stats.
 Identities = 24/104 (23%), Positives = 49/104 (47%), Gaps = 13/104 (12%)

Query: 213 YGRL-GFMDEANKVFSMMSKRDAVSWNSLISGYVHNGEIEEAYRLFERMPGKDFVSWTTM 271
           YG L   +DEA K+       D+++W  LI   +  G    A  +++     D +S+  +
Sbjct: 18  YGNLDAALDEAKKL------NDSITWERLIQEALAQGNASLAEMIYQTQHSFDKLSFLYL 71

Query: 272 ITGFSSKGNLEKSIELFNMMPEKDDVTWTAIISGFVNNEQYEEA 315
           +T     G++ K  ++ N+   ++D   + +++ F NN   E +
Sbjct: 72  VT-----GDVNKLSKMQNIAQTREDFG-SMLLNTFYNNSTKERS 109


  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
   0.322    0.137    0.415 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,053,436
Number of Sequences: 62578
Number of extensions: 793063
Number of successful extensions: 1810
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1803
Number of HSP's gapped (non-prelim): 14
length of query: 649
length of database: 14,973,337
effective HSP length: 105
effective length of query: 544
effective length of database: 8,402,647
effective search space: 4571039968
effective search space used: 4571039968
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)