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= 001911
         (997 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 = 0.001,   Method: Compositional matrix adjust.
 Identities = 29/124 (23%), Positives = 56/124 (45%), Gaps = 11/124 (8%)

Query: 501 KAFLLFQEMKRNGLIPDVYTYTILI----------DNFCKAGLIEQARNWFDEMVKEGCD 550
           +A  L+ E +RNG+    Y Y +L+          ++    GL  +  + F +M+ +   
Sbjct: 44  EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL-SRGFDIFKQMIVDKVV 102

Query: 551 PNVVTYTALIHAYLKARKPSQANELFETMLSKGCIPNIVTFTALIDGHCKAGDIERACRI 610
           PN  T+T      +    P  A ++ + M + G  P + ++   + G C+ GD ++A  +
Sbjct: 103 PNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162

Query: 611 YARM 614
            A M
Sbjct: 163 DAHM 166



 Score = 41.2 bits (95), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 32/154 (20%), Positives = 63/154 (40%), Gaps = 32/154 (20%)

Query: 384 RSGDYSYAYKLLSKMRKCGFQPGYVVYNILIGGICGNEDLPASDVFELAEKAYAEMLNAG 443
           + GD   A +L  + R+ G Q     YN+L+  +C            LAE A     N G
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCS-----------LAEAATESSPNPG 85

Query: 444 VVLNKINVSNFVQCLCGAGKYEKAYNVIREMMSKGFIPDTSTYSKVIGYLCDASEAEKAF 503
           +                     + +++ ++M+    +P+ +T++          + E AF
Sbjct: 86  L--------------------SRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAF 125

Query: 504 LLFQEMKRNGLIPDVYTYTILIDNFCKAGLIEQA 537
            + ++MK  G+ P + +Y   +  FC+ G  ++A
Sbjct: 126 DMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKA 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 = 34.7 bits (78), Expect = 0.31,   Method: Compositional matrix adjust.
 Identities = 26/122 (21%), Positives = 52/122 (42%), Gaps = 11/122 (9%)

Query: 501 KAFLLFQEMKRNGLIPDVYTYTILI----------DNFCKAGLIEQARNWFDEMVKEGCD 550
           +A  L+ E +RNG+    Y Y +L+          ++    GL  +  + F + + +   
Sbjct: 44  EALRLYDEARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPGL-SRGFDIFKQXIVDKVV 102

Query: 551 PNVVTYTALIHAYLKARKPSQANELFETMLSKGCIPNIVTFTALIDGHCKAGDIERACRI 610
           PN  T+T      +    P  A +  +   + G  P + ++   + G C+ GD ++A  +
Sbjct: 103 PNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFCRKGDADKAYEV 162

Query: 611 YA 612
            A
Sbjct: 163 DA 164



 Score = 33.5 bits (75), Expect = 0.61,   Method: Compositional matrix adjust.
 Identities = 30/135 (22%), Positives = 51/135 (37%), Gaps = 27/135 (20%)

Query: 384 RSGDYSYAYKLLSKMRKCGFQPGYVVYNILIGGICGNEDLPASDVFELAEKAYAEMLNAG 443
           + GD   A +L  + R+ G Q     YN+L+  +C            LAE A     N G
Sbjct: 38  KKGDVLEALRLYDEARRNGVQLSQYHYNVLLY-VCS-----------LAEAATESSPNPG 85

Query: 444 ---------------VVLNKINVSNFVQCLCGAGKYEKAYNVIREMMSKGFIPDTSTYSK 488
                          VV N+   +N  +        E A++ +++  + G  P   +Y  
Sbjct: 86  LSRGFDIFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGP 145

Query: 489 VIGYLCDASEAEKAF 503
            +   C   +A+KA+
Sbjct: 146 ALFGFCRKGDADKAY 160


>pdb|4ARZ|B Chain B, The Crystal Structure Of Gtr1p-Gtr2p Complexed With
           Gtp-Gdp
          Length = 341

 Score = 31.6 bits (70), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 33/145 (22%), Positives = 65/145 (44%), Gaps = 12/145 (8%)

Query: 366 EGCYPSPRIFHS---LIHAYCRSGDYSYAYKLLSKMRKCGFQPG-YVVYNILIGGICG-N 420
           E  Y S R+F S   L++      +Y  A   L+ + +  ++    +   +LI  + G +
Sbjct: 71  EPSYDSERLFKSVGALVYVIDSQDEYINAITNLAMIIEYAYKVNPSINIEVLIHKVDGLS 130

Query: 421 EDLPASDVFELAEKAYAEMLNAGVVLNKINVSNFVQCLCGAGKYEKAYNVIREMMSKGFI 480
           ED       ++ ++   E+L  G  L+ + VS ++  +     YE    +++++     I
Sbjct: 131 EDFKVDAQRDIMQRTGEELLELG--LDGVQVSFYLTSIFDHSIYEAFSRIVQKL-----I 183

Query: 481 PDTSTYSKVIGYLCDASEAEKAFLL 505
           P+ S    ++  L   S+ EKAFL 
Sbjct: 184 PELSFLENMLDNLIQHSKIEKAFLF 208


  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    0.139    0.422 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 28,631,754
Number of Sequences: 62578
Number of extensions: 1215635
Number of successful extensions: 2269
Number of sequences better than 100.0: 4
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 2248
Number of HSP's gapped (non-prelim): 18
length of query: 997
length of database: 14,973,337
effective HSP length: 108
effective length of query: 889
effective length of database: 8,214,913
effective search space: 7303057657
effective search space used: 7303057657
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: 56 (26.2 bits)