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= 040027
         (595 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 = 41.2 bits (95), Expect = 0.001,   Method: Compositional matrix adjust.
 Identities = 31/109 (28%), Positives = 49/109 (44%), Gaps = 14/109 (12%)

Query: 83  YD-TRLNATGLFPNLYTYNILINCFCKIGR----------VSLGFIAFGRILRSCFTPNA 131
           YD  R N   L  + Y YN+L+   C +            +S GF  F +++     PN 
Sbjct: 49  YDEARRNGVQL--SQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVPNE 105

Query: 132 ATFNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG 180
           ATF +  +   A+     A  +  ++KAFG +P + +Y   + G CR G
Sbjct: 106 ATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKG 154



 Score = 29.6 bits (65), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 27/123 (21%), Positives = 47/123 (38%), Gaps = 9/123 (7%)

Query: 260 EAKRLFIEMMDQGVQPSVVTFNVIM---------DELCKNRKMDEASRLLDLMVQRGVRP 310
           EA RL+ E    GVQ S   +NV++          E   N  +     +   M+   V P
Sbjct: 44  EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVP 103

Query: 311 NACTYNTLMDGFCLMGKINRAEELFGSMESMGCKHDDVSYNILINGYCKNKEVEEALSLY 370
           N  T+               A ++   M++ G +    SY   + G+C+  + ++A  + 
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD 163

Query: 371 REM 373
             M
Sbjct: 164 AHM 166



 Score = 29.3 bits (64), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 27/125 (21%), Positives = 49/125 (39%), Gaps = 9/125 (7%)

Query: 359 KNKEVEEALSLYREMVSKGIKPTVVTYNTLFL--GLFEIHQ-------VEHALKLFDEMQ 409
           K  +V EAL LY E    G++ +   YN L     L E          +     +F +M 
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97

Query: 410 RDGVAADTRTYTTFIDGLCKNGYIIEAVELFRTLRILKCELDIQAYNCLIDGLCKSGRLK 469
            D V  +  T+T              A ++ + ++    +  +++Y   + G C+ G   
Sbjct: 98  VDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDAD 157

Query: 470 FAWEL 474
            A+E+
Sbjct: 158 KAYEV 162


>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 = 38.5 bits (88), Expect = 0.011,   Method: Compositional matrix adjust.
 Identities = 29/107 (27%), Positives = 45/107 (42%), Gaps = 13/107 (12%)

Query: 84  DTRLNATGLFPNLYTYNILINCFCKIGR----------VSLGFIAFGRILRSCFTPNAAT 133
           + R N   L  + Y YN+L+   C +            +S GF  F + +     PN AT
Sbjct: 51  EARRNGVQL--SQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQXIVDKVVPNEAT 107

Query: 134 FNSLIKGLHAESRIMEAAALFTKLKAFGCEPNVITYNTLINGLCRTG 180
           F +  +   A+     A     + KAFG +P + +Y   + G CR G
Sbjct: 108 FTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154


  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
   0.324    0.139    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 16,457,132
Number of Sequences: 62578
Number of extensions: 664697
Number of successful extensions: 1449
Number of sequences better than 100.0: 3
Number of HSP's better than 100.0 without gapping: 0
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1424
Number of HSP's gapped (non-prelim): 21
length of query: 595
length of database: 14,973,337
effective HSP length: 104
effective length of query: 491
effective length of database: 8,465,225
effective search space: 4156425475
effective search space used: 4156425475
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (25.4 bits)