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= 005178
         (710 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 = 0.21,   Method: Compositional matrix adjust.
 Identities = 35/169 (20%), Positives = 76/169 (44%), Gaps = 10/169 (5%)

Query: 231 CAKRCNLFDEAIEWFERMYKTGLMPDEVTYSAILDVYAKSGKVEEV---------LSLYE 281
           C+K+ ++  EA+  ++   + G+   +  Y+ +L V + +    E            +++
Sbjct: 36  CSKKGDVL-EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFK 94

Query: 282 RGVASGWKPDPIAFSVLGKMFGESGDYDGIRYVLQEMKSLGVQPNLVVYNTLLEAMGKAG 341
           + +     P+   F+   ++     D +    ++++MK+ G+QP L  Y   L    + G
Sbjct: 95  QMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154

Query: 342 KPGLARSLFDEMVESGLTPDEKTLTALIKIYGKARWAKDALELWERMRE 390
               A  +   MVES + P+E  L AL+K+    + A    +  +R+R+
Sbjct: 155 DADKAYEVDAHMVESEVVPEEPELAALLKVSMDTKNADKVYKTLQRLRD 203


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

 Score = 31.2 bits (69), Expect = 1.9,   Method: Compositional matrix adjust.
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 1/58 (1%)

Query: 302 FGESGDYDGIRYVLQEMKSLGVQPNLVVYNTLLEAMGKAGK-PGLARSLFDEMVESGL 358
           +   G +  + YVL  +K  G+ P+L+ Y   L+ MG+  +  G      ++M + GL
Sbjct: 175 WARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGRQDQDAGTIERCLEQMSQEGL 232


>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana With Mn
 pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
           A. Thaliana, Semet Substituted Form With Sr
          Length = 501

 Score = 30.8 bits (68), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 33/169 (19%), Positives = 73/169 (43%), Gaps = 10/169 (5%)

Query: 231 CAKRCNLFDEAIEWFERMYKTGLMPDEVTYSAILDVYAKSGKVEEV---------LSLYE 281
           C+K+ ++  EA+  ++   + G+   +  Y+ +L V + +    E            +++
Sbjct: 36  CSKKGDVL-EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFK 94

Query: 282 RGVASGWKPDPIAFSVLGKMFGESGDYDGIRYVLQEMKSLGVQPNLVVYNTLLEAMGKAG 341
           + +     P+   F+   ++     D +     +++ K+ G+QP L  Y   L    + G
Sbjct: 95  QXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154

Query: 342 KPGLARSLFDEMVESGLTPDEKTLTALIKIYGKARWAKDALELWERMRE 390
               A  +    VES + P+E  L AL+K+    + A    +  +R+R+
Sbjct: 155 DADKAYEVDAHXVESEVVPEEPELAALLKVSXDTKNADKVYKTLQRLRD 203


>pdb|1JR2|A Chain A, Structure Of Uroporphyrinogen Iii Synthase
 pdb|1JR2|B Chain B, Structure Of Uroporphyrinogen Iii Synthase
          Length = 286

 Score = 29.6 bits (65), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 2/48 (4%)

Query: 383 ELWERMRENKWPMD--FILYNTLLNMCADIGLVEEAERLFEDMKLSDY 428
           E+WER  + KW     +++ N   ++ + IGL  E E      KL++Y
Sbjct: 102 EVWERSLKEKWNAKSVYVVGNATASLVSKIGLDTEGETCGNAEKLAEY 149


  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
   0.318    0.133    0.395 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,518,795
Number of Sequences: 62578
Number of extensions: 764942
Number of successful extensions: 2130
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 2118
Number of HSP's gapped (non-prelim): 20
length of query: 710
length of database: 14,973,337
effective HSP length: 106
effective length of query: 604
effective length of database: 8,340,069
effective search space: 5037401676
effective search space used: 5037401676
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 55 (25.8 bits)