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= 032397
         (141 letters)

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

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



>pdb|2NN6|I Chain I, Structure Of The Human Rna Exosome Composed Of Rrp41,
           Rrp45, Rrp46, Rrp43, Mtr3, Rrp42, Csl4, Rrp4, And Rrp40
          Length = 209

 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 30/101 (29%), Positives = 46/101 (45%), Gaps = 6/101 (5%)

Query: 13  PGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTVEVTGHKAHGP 72
           PGE L    E   G G Y    +G +++SL G L   S         P V V        
Sbjct: 24  PGERLCNLEEGSPGSGTYT--RHGYIFSSLAGCLMKSS----ENGALPVVSVVRETESQL 77

Query: 73  VPEPGSVVIARVTKVMTRMASADIMCVGAKSVREKFSGIIR 113
           +P+ G++V  +V+ + +R A   I+ VG+  ++  F G IR
Sbjct: 78  LPDVGAIVTCKVSSINSRFAKVHILYVGSMPLKNSFRGTIR 118


>pdb|2VE7|C Chain C, Crystal Structure Of A Bonsai Version Of The Human Ndc80
           Complex
 pdb|2VE7|D Chain D, Crystal Structure Of A Bonsai Version Of The Human Ndc80
           Complex
 pdb|3IZ0|D Chain D, Human Ndc80 Bonsai Decorated Microtubule
 pdb|3IZ0|F Chain F, Human Ndc80 Bonsai Decorated Microtubule
          Length = 250

 Score = 30.8 bits (68), Expect = 0.29,   Method: Compositional matrix adjust.
 Identities = 24/60 (40%), Positives = 26/60 (43%), Gaps = 8/60 (13%)

Query: 81  IARVTKVMTRMASADIMCVGAKSVREKFSGIIRFFIFY---IELLMHLLYGYLGSC-KMQ 136
           I RV    T    ADI+C  AK      SGII F  F     E  M  L+ Y  S  KMQ
Sbjct: 103 ICRVNDFET----ADILCPKAKRTSRFLSGIINFIHFREACRETYMEFLWQYKSSADKMQ 158


>pdb|3V1V|A Chain A, Crystal Structure Of 2-Methylisoborneol Synthase From
           Streptomyces Coelicolor A3(2) In Complex With Mg2+ And
           Geranyl-S-Thiolodiphosphate
          Length = 433

 Score = 26.2 bits (56), Expect = 7.1,   Method: Composition-based stats.
 Identities = 10/27 (37%), Positives = 16/27 (59%)

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADI 96
           H PVPEP  V +  V++ + R A  ++
Sbjct: 117 HHPVPEPDPVRVEEVSRRIKRWAEDEV 143


>pdb|3V1X|A Chain A, Crystal Structure Of 2-Methylisoborneol Synthase From
           Streptomyces Coelicolor A3(2) In Complex With Mg2+ And
           2-Fluorogeranyl Diphosphate
          Length = 461

 Score = 25.8 bits (55), Expect = 7.7,   Method: Composition-based stats.
 Identities = 10/27 (37%), Positives = 16/27 (59%)

Query: 70  HGPVPEPGSVVIARVTKVMTRMASADI 96
           H PVPEP  V +  V++ + R A  ++
Sbjct: 145 HHPVPEPDPVRVEEVSRRIKRWAEDEV 171


>pdb|1B9B|A Chain A, Triosephosphate Isomerase Of Thermotoga Maritima
 pdb|1B9B|B Chain B, Triosephosphate Isomerase Of Thermotoga Maritima
          Length = 255

 Score = 25.8 bits (55), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 31/126 (24%), Positives = 46/126 (36%), Gaps = 21/126 (16%)

Query: 3   VKEEEMVLVTPGEVLGKATEVKAGKGAYVAKHNGLVYASLTGLLRTLSPPPDSPDQRPTV 62
           VKE E+V+  P   L +  E+ +G+   +   N + Y         +SP      Q   V
Sbjct: 34  VKEFEIVVCPPFTALSEVGEILSGRNIKLGAQN-VFYEDQGAFTGEISPLML---QEIGV 89

Query: 63  E--VTGHKAHGPVPEPGSVVIARVTKVMTRMASADIMCVGA---------------KSVR 105
           E  + GH     + +     I R  K +       I+CVG                K VR
Sbjct: 90  EYVIVGHSERRRIFKEDDEFINRKVKAVLEKGMTPILCVGETLEEREKGLTFCVVEKQVR 149

Query: 106 EKFSGI 111
           E F G+
Sbjct: 150 EGFYGL 155


  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
   0.320    0.137    0.397 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,142,164
Number of Sequences: 62578
Number of extensions: 150613
Number of successful extensions: 396
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 393
Number of HSP's gapped (non-prelim): 14
length of query: 141
length of database: 14,973,337
effective HSP length: 89
effective length of query: 52
effective length of database: 9,403,895
effective search space: 489002540
effective search space used: 489002540
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: 46 (22.3 bits)