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= 036577
         (470 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 = 40.8 bits (94), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 28/123 (22%), Positives = 50/123 (40%), Gaps = 11/123 (8%)

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

Query: 176 DAVTFNSLIKGLCAESRIMEAAALFTKLKAFGCEPNVITYSTLINGLCRTGHTIVALNLF 235
           +  TF +  +   A+     A  +  ++KAFG +P + +Y   + G CR G    A  + 
Sbjct: 104 NEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVD 163

Query: 236 EEM 238
             M
Sbjct: 164 AHM 166



 Score = 29.3 bits (64), Expect = 4.8,   Method: Compositional matrix adjust.
 Identities = 32/147 (21%), Positives = 60/147 (40%), Gaps = 8/147 (5%)

Query: 201 TKLKAFGCEPNVITYSTLINGLC-RTGHTIVALNLFEEMANGNGEIGVVCEPNTVTYTTI 259
            K KA    P  +    L   +C + G  + AL L++E A  NG        N + Y   
Sbjct: 16  AKKKAIQQSPEALLKQKL--DMCSKKGDVLEALRLYDE-ARRNGVQLSQYHYNVLLYVCS 72

Query: 260 IDGLCKEGF----VDKAKELFLKMKDENINPNVVTYNSLIHGFCYANDWNEAKCLLIEMM 315
           +     E      + +  ++F +M  + + PN  T+ +        +D   A  ++ +M 
Sbjct: 73  LAEAATESSPNPGLSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMK 132

Query: 316 DQGVQPNVVTFNVIMDELCKNGKMDEA 342
             G+QP + ++   +   C+ G  D+A
Sbjct: 133 AFGIQPRLRSYGPALFGFCRKGDADKA 159



 Score = 28.5 bits (62), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 29/134 (21%), Positives = 52/134 (38%), Gaps = 9/134 (6%)

Query: 260 IDGLCKEGFVDKAKELFLKMKDENINPNVVTYNSLIHGFCYANDWNEAKC---------L 310
           +D   K+G V +A  L+ + +   +  +   YN L++    A    E+           +
Sbjct: 33  LDMCSKKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDI 92

Query: 311 LIEMMDQGVQPNVVTFNVIMDELCKNGKMDEASRLLDLMIQIGVRPNAFVYNTLMDGFCL 370
             +M+   V PN  TF             + A  ++  M   G++P    Y   + GFC 
Sbjct: 93  FKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCR 152

Query: 371 TGRVNRAKELFVSM 384
            G  ++A E+   M
Sbjct: 153 KGDADKAYEVDAHM 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 = 37.7 bits (86), Expect = 0.014,   Method: Compositional matrix adjust.
 Identities = 26/111 (23%), Positives = 44/111 (39%), Gaps = 11/111 (9%)

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

Query: 176 DAVTFNSLIKGLCAESRIMEAAALFTKLKAFGCEPNVITYSTLINGLCRTG 226
           +  TF +  +   A+     A     + KAFG +P + +Y   + G CR G
Sbjct: 104 NEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKG 154


>pdb|4A1F|A Chain A, Crystal Structure Of C-Terminal Domain Of Helicobacter
           Pylori Dnab Helicase
 pdb|4A1F|B Chain B, Crystal Structure Of C-Terminal Domain Of Helicobacter
           Pylori Dnab Helicase
          Length = 338

 Score = 29.3 bits (64), Expect = 4.9,   Method: Compositional matrix adjust.
 Identities = 12/23 (52%), Positives = 19/23 (82%)

Query: 260 IDGLCKEGFVDKAKELFLKMKDE 282
           ID L KEG +++A+EL+LK+ +E
Sbjct: 253 IDKLKKEGKIEEAQELYLKVNEE 275


  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    0.138    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,394,761
Number of Sequences: 62578
Number of extensions: 542016
Number of successful extensions: 1629
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 1610
Number of HSP's gapped (non-prelim): 21
length of query: 470
length of database: 14,973,337
effective HSP length: 102
effective length of query: 368
effective length of database: 8,590,381
effective search space: 3161260208
effective search space used: 3161260208
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: 53 (25.0 bits)