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= 047518
         (256 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 = 32.0 bits (71), Expect = 0.38,   Method: Compositional matrix adjust.
 Identities = 31/128 (24%), Positives = 54/128 (42%), Gaps = 7/128 (5%)

Query: 83  KMGRVSHGFVVLGRILRSCFTPDVVTFTSLIKVCK-PDAITYNTIIDGLCKQGFVDKAKE 141
           K G V     +     R+        +  L+ VC   +A T ++   GL + GF     +
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSR-GF-----D 91

Query: 142 LFLKMKDKNVKPNVVTYTSVIRGFCYANDWNEAKRLFIEMMDQGVQPNVVTFNVIMDELC 201
           +F +M    V PN  T+T+  R     +D   A  +  +M   G+QP + ++   +   C
Sbjct: 92  IFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFC 151

Query: 202 KNGKMDEA 209
           + G  D+A
Sbjct: 152 RKGDADKA 159



 Score = 30.4 bits (67), Expect = 0.92,   Method: Compositional matrix adjust.
 Identities = 20/75 (26%), Positives = 31/75 (41%)

Query: 177 LFIEMMDQGVQPNVVTFNVIMDELCKNGKMDEASSLLDLMIQHGVRPDAFTYNTLLDGFC 236
           +F +M+   V PN  TF             + A  ++  M   G++P   +Y   L GFC
Sbjct: 92  IFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFC 151

Query: 237 LTGRVNHAKELFVSM 251
             G  + A E+   M
Sbjct: 152 RKGDADKAYEVDAHM 166


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

 Score = 30.4 bits (67), Expect = 0.90,   Method: Composition-based stats.
 Identities = 31/147 (21%), Positives = 64/147 (43%), Gaps = 25/147 (17%)

Query: 123 YNTIIDGLCKQGFVDKAKELFLKMKDKNVKPNVVTYTSVIRGFCYA---NDWNEAKRLFI 179
           YN ++ G  +QG   +   +   +KD  + P++++Y + ++  C      D    +R   
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ--CMGRQDQDAGTIERCLE 225

Query: 180 EMMDQGVQPNVVTFNVIMDELCKNGKMDEASSLLDLMIQHGVRPD----------AFTYN 229
           +M  +G++   +   V++ E       D A+ L  +   H V+P             T  
Sbjct: 226 QMSQEGLKLQALFTAVLLSE------EDRATVLKAV---HKVKPTFSLPPQLPPPVNTSK 276

Query: 230 TLLDGFCLTGRVNHAKELFVSMESMGC 256
            L D +   GRV++ K L + ++++ C
Sbjct: 277 LLRDVYAKDGRVSYPK-LHLPLKTLQC 302


>pdb|1PBW|A Chain A, Structure Of Bcr-Homology (Bh) Domain
 pdb|1PBW|B Chain B, Structure Of Bcr-Homology (Bh) Domain
          Length = 216

 Score = 30.4 bits (67), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 21/90 (23%), Positives = 44/90 (48%), Gaps = 4/90 (4%)

Query: 25  YMLRMHPSPP-PVSSFNIMLGCLAKNKHYDTVLSLFKRLNSTGLFPDLY--THSILINCF 81
           Y+L + P+P  P + ++ M+    + +  +  + L K+L  +   P  Y  T   L+  F
Sbjct: 86  YLLDL-PNPVIPAAVYSEMISLAPEVQSSEEYIQLLKKLIRSPSIPHQYWLTLQYLLKHF 144

Query: 82  CKMGRVSHGFVVLGRILRSCFTPDVVTFTS 111
            K+ + S   ++  R+L   F+P +  F++
Sbjct: 145 FKLSQTSSKNLLNARVLSEIFSPMLFRFSA 174


>pdb|4FVM|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha
 pdb|4FXD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
           Dna/rna
 pdb|4FXD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
           Dna/rna
          Length = 910

 Score = 29.3 bits (64), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 13/70 (18%)

Query: 33  PPPVSSFNIMLGCLAKNKHYDTVLSLFKRLNSTGLFPDLYTHSILINCFCKMGRVSHGFV 92
           PP  +SF + L  LAK K    V  LF                 +++CFC M +V    V
Sbjct: 240 PPQSTSFPLGLAALAKQKLPGRV-RLFN------------NEKAMLSCFCAMLKVEDPDV 286

Query: 93  VLGRILRSCF 102
           ++G  L++ +
Sbjct: 287 IIGHRLQNVY 296


>pdb|4FYD|A Chain A, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
           Dna/rna And Dgtp
 pdb|4FYD|B Chain B, Crystal Structure Of Yeast Dna Polymerase Alpha Bound To
           Dna/rna And Dgtp
          Length = 910

 Score = 29.3 bits (64), Expect = 2.2,   Method: Compositional matrix adjust.
 Identities = 20/70 (28%), Positives = 31/70 (44%), Gaps = 13/70 (18%)

Query: 33  PPPVSSFNIMLGCLAKNKHYDTVLSLFKRLNSTGLFPDLYTHSILINCFCKMGRVSHGFV 92
           PP  +SF + L  LAK K    V  LF                 +++CFC M +V    V
Sbjct: 240 PPQSTSFPLGLAALAKQKLPGRV-RLFN------------NEKAMLSCFCAMLKVEDPDV 286

Query: 93  VLGRILRSCF 102
           ++G  L++ +
Sbjct: 287 IIGHRLQNVY 296


  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
   0.325    0.140    0.431 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,469,106
Number of Sequences: 62578
Number of extensions: 289513
Number of successful extensions: 1049
Number of sequences better than 100.0: 6
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1038
Number of HSP's gapped (non-prelim): 12
length of query: 256
length of database: 14,973,337
effective HSP length: 97
effective length of query: 159
effective length of database: 8,903,271
effective search space: 1415620089
effective search space used: 1415620089
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 50 (23.9 bits)