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= 006566
         (640 letters)

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

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



>pdb|3NOY|A Chain A, Crystal Structure Of Ispg (Gcpe)
 pdb|3NOY|B Chain B, Crystal Structure Of Ispg (Gcpe)
 pdb|3NOY|C Chain C, Crystal Structure Of Ispg (Gcpe)
 pdb|3NOY|D Chain D, Crystal Structure Of Ispg (Gcpe)
          Length = 366

 Score =  167 bits (423), Expect = 2e-41,   Method: Compositional matrix adjust.
 Identities = 110/285 (38%), Positives = 156/285 (54%), Gaps = 35/285 (12%)

Query: 85  RRKTRTVMVGNVAIGSEHPIRVQTMTTNDTKDVAGTVEEVMRIADQGADLVRITVQGKRE 144
           +RKTR + VGNV IG + PI VQ+MT+  T DV  T+ ++ R+ + G ++VR+ V  K +
Sbjct: 13  KRKTRQIRVGNVKIGGDAPIVVQSMTSTKTHDVEATLNQIKRLYEAGCEIVRVAVPHKED 72

Query: 145 ADACFEIKNSLVQKNYNIPLVADIHFAPSVA-LRVAECFDKIRVNPGNFADRRAQFEQLE 203
            +A  EI      K   +P++ADIHFAPS A L + +    IR+NPGN        E +E
Sbjct: 73  VEALEEI-----VKKSPMPVIADIHFAPSYAFLSMEKGVHGIRINPGNIGKEEIVREIVE 127

Query: 204 YTDDEYQKELQHIEEVFSPLVEKCKKYGRAVRIGTNHGSLSDRIMSYYG-DSPRGMVESA 262
                                   K+ G AVRIG N GSL   ++  YG  S   + ESA
Sbjct: 128 EA----------------------KRRGVAVRIGVNSGSLEKDLLEKYGYPSAEALAESA 165

Query: 263 FEFARICRKLDFHNFLFSMKASNPVVMVQAYRLLVAEMYVHGWDYPLHLGVTEAGEGEDG 322
             ++    K  F N+  S+K S+ +  V+A  L+ AE      D PLH+G+TEAG G  G
Sbjct: 166 LRWSEKFEKWGFTNYKVSIKGSDVLQNVRA-NLIFAERT----DVPLHIGITEAGMGTKG 220

Query: 323 RMKSAIGIGTLLQDGLGDTIRVSLTEPPEKEIDPCRR-LANLGMR 366
            +KS++GIG LL  G+GDT+RVSLT+ P  E++     L +LG+R
Sbjct: 221 IIKSSVGIGILLYMGIGDTVRVSLTDDPVVEVETAYEILKSLGLR 265


>pdb|2Y0F|A Chain A, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
 pdb|2Y0F|B Chain B, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
 pdb|2Y0F|C Chain C, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
 pdb|2Y0F|D Chain D, Structure Of Gcpe (Ispg) From Thermus Thermophilus Hb27
 pdb|4G9P|A Chain A, Structure Of The Gcpe-Mecpp (Ispg) Complex From Thermus
           Thermophilus
          Length = 406

 Score =  143 bits (360), Expect = 4e-34,   Method: Compositional matrix adjust.
 Identities = 111/309 (35%), Positives = 150/309 (48%), Gaps = 48/309 (15%)

Query: 84  VRRKTRTVMVGNVAIGSEHPIRVQTMTTNDTKDVAGTVEEVMRIADQGADLVRITVQGKR 143
           +RR T TV VG V IG  HPI VQ+MT   T+DV  T  +V+ +   G+++VR+TV  + 
Sbjct: 4   MRRPTPTVYVGRVPIGGAHPIAVQSMTNTPTRDVEATTAQVLELHRAGSEIVRLTVNDEE 63

Query: 144 EADACFEIKNSLVQKNYNIPLVADIHFAPSVALR----VAECFDKIRVNPGNFADRRAQF 199
            A A  EIK  L+ +   +PLV D HF   + LR    +AE  DK R+NPG     R   
Sbjct: 64  AAKAVPEIKRRLLAEGVEVPLVGDFHFNGHLLLRKYPKMAEALDKFRINPGTLGRGR--- 120

Query: 200 EQLEYTDDEYQKELQHIEEVFSPLVEKCKKYGRAVRIGTNHGSLSDRIMSYYGD------ 253
                          H +E F+ ++      G+ VRIG N GSL   +++   D      
Sbjct: 121 ---------------HKDEHFAEMIRIAMDLGKPVRIGANWGSLDPALLTELMDRNASRP 165

Query: 254 SPR--------GMVESAFEF--ARICRKLDFHNFLFSMKASNPVVMVQAYRLLVAEMYVH 303
            P+         +VESA     A +   L     + S K S    +V  YR L       
Sbjct: 166 EPKSAHEVVLEALVESAVRAYEAALEMGLGEDKLVLSAKVSKARDLVWVYRELARRT--- 222

Query: 304 GWDYPLHLGVTEAGEGEDGRMKSAIGIGTLLQDGLGDTIRVSLT----EPPEKEIDPCRR 359
               PLHLG+TEAG G  G + SA  +  LL +G+GDTIRVSLT    EP  KE++  + 
Sbjct: 223 --QAPLHLGLTEAGMGVKGIVASAAALAPLLLEGIGDTIRVSLTPSPKEPRTKEVEVAQE 280

Query: 360 -LANLGMRA 367
            L  LG+RA
Sbjct: 281 ILQALGLRA 289


>pdb|3RCW|A Chain A, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|B Chain B, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|C Chain C, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|D Chain D, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|E Chain E, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|F Chain F, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|G Chain G, Crystal Structure Of The Bromodomain Of Human Brd1
 pdb|3RCW|H Chain H, Crystal Structure Of The Bromodomain Of Human Brd1
          Length = 135

 Score = 30.0 bits (66), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 8/63 (12%)

Query: 170 FAPSVALR-VAECFDKIRVNPGNFADRRAQFEQLEYTDDEYQKELQHIEEVFSPLVEKCK 228
           FA  V+L+ V +  D I+ +P +FA  R + E   Y      K L   EE F  +++ C 
Sbjct: 34  FAQPVSLKEVPDYLDHIK-HPMDFATMRKRLEAQGY------KNLHEFEEDFDLIIDNCM 86

Query: 229 KYG 231
           KY 
Sbjct: 87  KYN 89


  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    0.398 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,389,899
Number of Sequences: 62578
Number of extensions: 761571
Number of successful extensions: 1731
Number of sequences better than 100.0: 7
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 5
Number of HSP's that attempted gapping in prelim test: 1723
Number of HSP's gapped (non-prelim): 7
length of query: 640
length of database: 14,973,337
effective HSP length: 105
effective length of query: 535
effective length of database: 8,402,647
effective search space: 4495416145
effective search space used: 4495416145
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: 55 (25.8 bits)