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= 041816
         (396 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 = 42.4 bits (98), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 28/123 (22%), Positives = 50/123 (40%), Gaps = 11/123 (8%)

Query: 126 VLSLFKRLNSTGLFPDLYTYNILINCFCKMGR----------VSHGFVVLGRILRSCFTP 175
            L L+      G+    Y YN+L+   C +            +S GF +  +++     P
Sbjct: 45  ALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQMIVDKVVP 103

Query: 176 DAVAFTSLIKGLCAESRIMEAAALFTKLKAFGCKPNVITYSTLINGLCRTGHTIVALNLF 235
           +   FT+  +   A+     A  +  ++KAFG +P + +Y   + G CR G    A  + 
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD 163

Query: 236 EEM 238
             M
Sbjct: 164 AHM 166


>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 = 39.3 bits (90), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 26/111 (23%), Positives = 44/111 (39%), Gaps = 11/111 (9%)

Query: 126 VLSLFKRLNSTGLFPDLYTYNILINCFCKMGR----------VSHGFVVLGRILRSCFTP 175
            L L+      G+    Y YN+L+   C +            +S GF +  + +     P
Sbjct: 45  ALRLYDEARRNGVQLSQYHYNVLL-YVCSLAEAATESSPNPGLSRGFDIFKQXIVDKVVP 103

Query: 176 DAVAFTSLIKGLCAESRIMEAAALFTKLKAFGCKPNVITYSTLINGLCRTG 226
           +   FT+  +   A+     A     + KAFG +P + +Y   + G CR G
Sbjct: 104 NEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154


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

 Score = 32.7 bits (73), Expect = 0.40,   Method: Compositional matrix adjust.
 Identities = 26/138 (18%), Positives = 62/138 (44%), Gaps = 7/138 (5%)

Query: 256 YTTIIDGLCKEGFVDKAKELFLQMKDKNINPDVVTYNSLIHGFCYANDWNEANCL---LI 312
           Y  ++ G  ++G   +   +   +KD  + PD+++Y + +   C      +A  +   L 
Sbjct: 168 YNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQ--CMGRQDQDAGTIERCLE 225

Query: 313 EMMDQGVQPDVVTFNVIMDELCKNGKMDEASRLLELMIL-RGVNPNTSTFSTLMDGFCLT 371
           +M  +G++   +   V++ E  +   +    ++     L   + P  +T   L D +   
Sbjct: 226 QMSQEGLKLQALFTAVLLSEEDRATVLKAVHKVKPTFSLPPQLPPPVNTSKLLRDVYAKD 285

Query: 372 GRVNHAKELFVSMESMGC 389
           GRV++ K L + ++++ C
Sbjct: 286 GRVSYPK-LHLPLKTLQC 302


>pdb|2Y94|A Chain A, Structure Of An Active Form Of Mammalian Ampk
          Length = 476

 Score = 28.5 bits (62), Expect = 7.1,   Method: Compositional matrix adjust.
 Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 322 DVVTFNVIMDELCKNGKMDE-ASRLLELMILRGVN 355
           + V+   + D +CKNG++DE  SR L   IL GV+
Sbjct: 96  EYVSGGELFDYICKNGRLDEKESRRLFQQILSGVD 130


  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
   0.323    0.136    0.414 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,140,792
Number of Sequences: 62578
Number of extensions: 438105
Number of successful extensions: 1438
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1426
Number of HSP's gapped (non-prelim): 13
length of query: 396
length of database: 14,973,337
effective HSP length: 101
effective length of query: 295
effective length of database: 8,652,959
effective search space: 2552622905
effective search space used: 2552622905
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 52 (24.6 bits)