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= 006010
         (664 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 = 38.9 bits (89), Expect = 0.009,   Method: Compositional matrix adjust.
 Identities = 38/181 (20%), Positives = 67/181 (37%), Gaps = 44/181 (24%)

Query: 274 KNGELGRAAKLVDNMFLKGCLPNEVTYNTLIHGLCL---------KGNLDKAVSLLDRMV 324
           K G++  A +L D     G   ++  YN L++   L            L +   +  +M+
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMI 97

Query: 325 ASKCMPNEVTYGTIINGLVKLGRAVDGARVLMSMEERKFHVNEYIYSTLISGLFKEGKAE 384
             K +PNE T+              +GAR+ ++ ++                       E
Sbjct: 98  VDKVVPNEATF-------------TNGARLAVAKDD----------------------PE 122

Query: 385 DAMKLWKQMMEKGCKPNTVVYSALIDGLCRVGKPDEAEEILFEMINNGCAANAFTYSSLM 444
            A  + KQM   G +P    Y   + G CR G  D+A E+   M+ +         ++L+
Sbjct: 123 MAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEVDAHMVESEVVPEEPELAALL 182

Query: 445 K 445
           K
Sbjct: 183 K 183



 Score = 32.0 bits (71), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 29/120 (24%), Positives = 44/120 (36%), Gaps = 9/120 (7%)

Query: 206 GLVDNAIQLFREMPVRNCEPDIYTY------CTLMDGLCKENR---LDEAVLLLDEMQVD 256
           G V  A++L+ E      +   Y Y      C+L +   + +    L     +  +M VD
Sbjct: 40  GDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQMIVD 99

Query: 257 GCFPTPVTFNVLINGLCKNGELGRAAKLVDNMFLKGCLPNEVTYNTLIHGLCLKGNLDKA 316
              P   TF           +   A  +V  M   G  P   +Y   + G C KG+ DKA
Sbjct: 100 KVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 159


>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 = 33.9 bits (76), Expect = 0.33,   Method: Compositional matrix adjust.
 Identities = 33/160 (20%), Positives = 56/160 (35%), Gaps = 44/160 (27%)

Query: 274 KNGELGRAAKLVDNMFLKGCLPNEVTYNTLIHGLCL---------KGNLDKAVSLLDRMV 324
           K G++  A +L D     G   ++  YN L++   L            L +   +  + +
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGLSRGFDIFKQXI 97

Query: 325 ASKCMPNEVTYGTIINGLVKLGRAVDGARVLMSMEERKFHVNEYIYSTLISGLFKEGKAE 384
             K +PNE T+              +GAR+ ++ ++                       E
Sbjct: 98  VDKVVPNEATF-------------TNGARLAVAKDD----------------------PE 122

Query: 385 DAMKLWKQMMEKGCKPNTVVYSALIDGLCRVGKPDEAEEI 424
            A    KQ    G +P    Y   + G CR G  D+A E+
Sbjct: 123 XAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162


>pdb|1GAX|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1GAX|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1IVS|A Chain A, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1IVS|B Chain B, Crystal Structure Of Thermus Thermophilus Valyl-Trna
           Synthetase Complexed With Trna(Val) And Valyl-Adenylate
           Analogue
 pdb|1IYW|A Chain A, Preliminary Structure Of Thermus Thermophilus Ligand-Free
           Valyl-Trna Synthetase
 pdb|1IYW|B Chain B, Preliminary Structure Of Thermus Thermophilus Ligand-Free
           Valyl-Trna Synthetase
          Length = 862

 Score = 30.0 bits (66), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 30/59 (50%), Gaps = 4/59 (6%)

Query: 331 NEVTYGTIINGLVKLGRAVDGARVLMSMEERKFHVNEYIYSTLISGLFKEGKAEDAMKL 389
            E + GTI+  L +LG + D +R   +M+E++     Y +S      + EG A  A +L
Sbjct: 118 KEESGGTILKQLKRLGASADWSREAFTMDEKRSRAVRYAFSR----YYHEGLAYRAPRL 172


  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
   0.322    0.136    0.409 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,108,679
Number of Sequences: 62578
Number of extensions: 772357
Number of successful extensions: 1640
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1618
Number of HSP's gapped (non-prelim): 24
length of query: 664
length of database: 14,973,337
effective HSP length: 105
effective length of query: 559
effective length of database: 8,402,647
effective search space: 4697079673
effective search space used: 4697079673
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.8 bits)