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= 008097
         (577 letters)

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

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



>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Ca
          Length = 501

 Score = 34.7 bits (78), Expect = 0.13,   Method: Compositional matrix adjust.
 Identities = 18/70 (25%), Positives = 32/70 (45%)

Query: 364 FDQMIEEGGVPNVVIYDCLIHAYCQEERVREASELMKEMTGHGYLPIASTFNTVLSGLCR 423
           F QMI +  VPN   +         ++    A +++K+M   G  P   ++   L G CR
Sbjct: 93  FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152

Query: 424 QGNVGTALKL 433
           +G+   A ++
Sbjct: 153 KGDADKAYEV 162



 Score = 31.6 bits (70), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 32/132 (24%), Positives = 50/132 (37%), Gaps = 21/132 (15%)

Query: 212 GRLGKVKGGCRFLKEMERKGCLPNVDTYNIL--ISSYCETGV-------LDSALDVFNDM 262
            + G V    R   E  R G   +   YN+L  + S  E          L    D+F  M
Sbjct: 37  SKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQM 96

Query: 263 KIDGISWNFVTYDTLIRGLCSGGRI----DDGLKILQLMEDSKE-GSKGRISPYNSVLYG 317
            +D +  N  T+        +G R+    DD      +++  K  G + R+  Y   L+G
Sbjct: 97  IVDKVVPNEATF-------TNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFG 149

Query: 318 LYRENQQDEALE 329
             R+   D+A E
Sbjct: 150 FCRKGDADKAYE 161


>pdb|1SDO|A Chain A, Crystal Structure Of Restriction Endonuclease Bstyi
 pdb|1VRR|A Chain A, Crystal Structure Of The Restriction Endonuclease Bstyi
           Complex With Dna
 pdb|1VRR|B Chain B, Crystal Structure Of The Restriction Endonuclease Bstyi
           Complex With Dna
 pdb|2P0J|A Chain A, Structure Of Restriction Endonuclease Bstyi Bound To
           Non-Cognate Dna
 pdb|2P0J|B Chain B, Structure Of Restriction Endonuclease Bstyi Bound To
           Non-Cognate Dna
          Length = 203

 Score = 34.7 bits (78), Expect = 0.14,   Method: Compositional matrix adjust.
 Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 269 WNFVTYDTLIRGLC--SGGRIDDGLKILQLMEDSKEGSKGRISPYNSVLYGLYRE 321
           ++FV YD  ++ +      +ID G++IL + E SKE S G IS Y   LY + R+
Sbjct: 134 YSFVAYDLFVKHMAFYVSDKIDVGVEILPMKELSKEMSSG-ISYYEGELYNVIRQ 187


>pdb|2AFR|A Chain A, The Crystal Structure Of Putative Precorrin Isomerase Cbic
           In Cobalamin Biosynthesis
 pdb|2AFV|A Chain A, The Crystal Structure Of Putative Precorrin Isomerase Cbic
           In Cobalamin Biosynthesis
 pdb|2AFV|B Chain B, The Crystal Structure Of Putative Precorrin Isomerase Cbic
           In Cobalamin Biosynthesis
          Length = 231

 Score = 30.0 bits (66), Expect = 3.2,   Method: Compositional matrix adjust.
 Identities = 29/114 (25%), Positives = 51/114 (44%), Gaps = 11/114 (9%)

Query: 332 KQMEKLFPRAVDRSLKIL--GFCVDGNVEDAKRCFDQMIEEGGVPN-VVIYDCLIHAYCQ 388
           K + K+ P+A+D  ++ L  G  +         C  QMI  G  P  + +Y C  + +  
Sbjct: 52  KNITKIHPQAIDSGIQALKKGCPI--------VCDVQMILSGLNPERLKVYGCKTYCFIS 103

Query: 389 EERVREASELMKEMTGHGYLPIASTFNTVLSGLCRQGNVGTALKLVEEDMRGIG 442
           +E V E ++          +  A++FN +   +   GN  TAL  +E+ +R  G
Sbjct: 104 DEDVIENAKRKNSTRAIESIQKANSFNLLNESIIVIGNAPTALLEIEKLIRQEG 157


>pdb|1H2M|S Chain S, Factor Inhibiting Hif-1 Alpha In Complex With Hif-1 Alpha
           Fragment Peptide
          Length = 52

 Score = 29.3 bits (64), Expect = 6.3,   Method: Composition-based stats.
 Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 360 AKRCFDQMIEEGGVPNVVIYDCLIHAYCQEER-VREASELMKEM 402
           A R   Q ++E G+P +  YDC ++A  Q  R + +  EL++ +
Sbjct: 5   ACRLLGQSMDESGLPQLTSYDCEVNAPIQGSRNLLQGEELLRAL 48


>pdb|1L8C|B Chain B, Structural Basis For Hif-1alphaCBP RECOGNITION IN THE
           Cellular Hypoxic Response
          Length = 51

 Score = 28.9 bits (63), Expect = 7.2,   Method: Composition-based stats.
 Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 1/44 (2%)

Query: 360 AKRCFDQMIEEGGVPNVVIYDCLIHAYCQEER-VREASELMKEM 402
           A R   Q ++E G+P +  YDC ++A  Q  R + +  EL++ +
Sbjct: 4   ACRLLGQSMDESGLPQLTSYDCEVNAPIQGSRNLLQGEELLRAL 47


  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    0.139    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,507,088
Number of Sequences: 62578
Number of extensions: 675414
Number of successful extensions: 1598
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 1592
Number of HSP's gapped (non-prelim): 12
length of query: 577
length of database: 14,973,337
effective HSP length: 104
effective length of query: 473
effective length of database: 8,465,225
effective search space: 4004051425
effective search space used: 4004051425
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: 54 (25.4 bits)