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= 000335
         (1646 letters)

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

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



>pdb|1PQV|S Chain S, Rna Polymerase Ii-Tfiis Complex
          Length = 309

 Score = 37.0 bits (84), Expect = 0.093,   Method: Compositional matrix adjust.
 Identities = 32/112 (28%), Positives = 54/112 (48%), Gaps = 8/112 (7%)

Query: 372 DGDKSVEEFLLILLRALDKLPV-NLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWK 430
           + +KS +  +L +L  LDK  V     L+   +G  VN  +   NVEI K  + ++ +WK
Sbjct: 14  EKNKSNDAAVLEILHVLDKEFVPTEKLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWK 73

Query: 431 KRVEAEMDARPRLPEVPHS----GNRQTGASTEVAIKSLVTQPASSKTGAVK 478
             +    + R R  +  H     GN +   +   ++   V QPASS++ A+K
Sbjct: 74  DAINK--NKRSRQAQQHHQDHAPGNAEDKTTVGESVNG-VQQPASSQSDAMK 122


>pdb|1W4S|A Chain A, Crystal Structure Of The Proximal Bah Domain Of Polybromo
          Length = 174

 Score = 32.7 bits (73), Expect = 1.7,   Method: Composition-based stats.
 Identities = 31/112 (27%), Positives = 46/112 (41%), Gaps = 9/112 (8%)

Query: 73  VGDCALFKPPQDS-PPFIGIIRSLTAGKENKLTLSVNWLYRPAEV-KLGKGFLLEAAPNE 130
           VGD    +P + +  P I  I  L      +  L   W YRP E   L     LE    E
Sbjct: 29  VGDYVYVEPAEANLQPHIVCIERLWEDSAGEKWLYGCWFYRPNETFHLATRKFLE---KE 85

Query: 131 IFYSFHKDEIPAASLLHPCKVAFLPKGIEL-PSGIGS---FVCRKVYDITNK 178
           +F S + +++P + +L  C V F+ +  +L P        +VC   Y    K
Sbjct: 86  VFKSDYYNKVPVSKILGKCVVMFVKEYFKLCPENFRDEDVYVCESRYSAKTK 137


>pdb|1EO0|A Chain A, Conserved Domain Common To Transcription Factors Tfiis,
           Elongin A, Crsp70
          Length = 77

 Score = 32.3 bits (72), Expect = 2.5,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 3/62 (4%)

Query: 374 DKSVEEFLLILLRALDK--LPVNLNALQMCNIGKSVNHLRTHKNVEIQKKARSLVDTWKK 431
           +KS +  +L +L  LDK  +P     L+   +G  VN  +   NVEI K  + ++ +WK 
Sbjct: 16  NKSNDAAVLEILHVLDKEFVPTE-KLLRETKVGVEVNKFKKSTNVEISKLVKKMISSWKD 74

Query: 432 RV 433
            +
Sbjct: 75  AI 76


>pdb|1WEK|A Chain A, Crystal Structure Of The Conserved Hypothetical Protein
            Tt1465 From Thermus Thermophilus Hb8
 pdb|1WEK|B Chain B, Crystal Structure Of The Conserved Hypothetical Protein
            Tt1465 From Thermus Thermophilus Hb8
 pdb|1WEK|C Chain C, Crystal Structure Of The Conserved Hypothetical Protein
            Tt1465 From Thermus Thermophilus Hb8
 pdb|1WEK|D Chain D, Crystal Structure Of The Conserved Hypothetical Protein
            Tt1465 From Thermus Thermophilus Hb8
 pdb|1WEK|E Chain E, Crystal Structure Of The Conserved Hypothetical Protein
            Tt1465 From Thermus Thermophilus Hb8
 pdb|1WEK|F Chain F, Crystal Structure Of The Conserved Hypothetical Protein
            Tt1465 From Thermus Thermophilus Hb8
          Length = 217

 Score = 32.0 bits (71), Expect = 3.0,   Method: Composition-based stats.
 Identities = 14/27 (51%), Positives = 19/27 (70%)

Query: 984  GVSEGLNSGVKREQKPSPITTHSESVK 1010
            GVS GLN  +  EQKP+P  TH+ S++
Sbjct: 93   GVSVGLNIELPHEQKPNPYQTHALSLR 119


>pdb|1WJT|A Chain A, Solution Structure Of The N-Terminal Domain I Of Mouse
           Transcription Elongation Factor S-Ii Protein 3
          Length = 103

 Score = 31.2 bits (69), Expect = 5.2,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 40/76 (52%), Gaps = 10/76 (13%)

Query: 384 LLRALDKLPVNLNALQMCNIGKSVNHLRTH-KNVEIQKKARSLVDTWKKRVEAEMDARPR 442
           LL+ L+   +++  LQ   IG +VN +R H  + E+   A+ L+  WK+ +++     PR
Sbjct: 36  LLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLLDS-----PR 90

Query: 443 LPEVPHSGNRQTGAST 458
                  G R++G S+
Sbjct: 91  ----TTKGERESGPSS 102


  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
   0.310    0.129    0.377 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 48,060,139
Number of Sequences: 62578
Number of extensions: 2058811
Number of successful extensions: 2993
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 2988
Number of HSP's gapped (non-prelim): 11
length of query: 1646
length of database: 14,973,337
effective HSP length: 112
effective length of query: 1534
effective length of database: 7,964,601
effective search space: 12217697934
effective search space used: 12217697934
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.7 bits)
S2: 58 (26.9 bits)