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= 045814
         (427 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 = 35.0 bits (79), Expect = 0.081,   Method: Compositional matrix adjust.
 Identities = 28/125 (22%), Positives = 52/125 (41%), Gaps = 11/125 (8%)

Query: 286 LEAYRVFNDLKERGYVPDTVMYTTVIHGLCKMG----------WLGDARKMWFEMIHKGL 335
           LEA R++++ +  G       Y  +++ +C +            L     ++ +MI   +
Sbjct: 43  LEALRLYDEARRNGVQLSQYHYNVLLY-VCSLAEAATESSPNPGLSRGFDIFKQMIVDKV 101

Query: 336 LPNEYTYNSMIHGYCRIDNLEEAKRLHKEMLDKGYGETTVTYNTLIAGLCLHGRTDEAYH 395
           +PNE T+ +        D+ E A  + K+M   G      +Y   + G C  G  D+AY 
Sbjct: 102 VPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFCRKGDADKAYE 161

Query: 396 LFEEM 400
           +   M
Sbjct: 162 VDAHM 166



 Score = 29.3 bits (64), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 17/77 (22%), Positives = 33/77 (42%)

Query: 215 VSEGYELLRQVLEDGLVPENTAFNKLISRFCEKKNFGRVSELLHTMVARNRAPDNFTYEE 274
           +S G+++ +Q++ D +VP    F         K +     +++  M A    P   +Y  
Sbjct: 86  LSRGFDIFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGP 145

Query: 275 VINGLCKSRKRLEAYRV 291
            + G C+     +AY V
Sbjct: 146 ALFGFCRKGDADKAYEV 162


>pdb|2BTU|A Chain A, Crystal Structure Of Phosphoribosylformylglycinamidine
           Cyclo-Ligase From Bacillus Anthracis At 2.3a Resolution.
 pdb|2BTU|B Chain B, Crystal Structure Of Phosphoribosylformylglycinamidine
           Cyclo-Ligase From Bacillus Anthracis At 2.3a Resolution
          Length = 346

 Score = 31.2 bits (69), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 37/169 (21%), Positives = 70/169 (41%), Gaps = 15/169 (8%)

Query: 64  DIPSFNFNDPLFFREFLKQQNNVLLSIRFFQWLHSHYGFSPDLVSCNVLFDSLVEARAFK 123
           D+  F   +P+           ++L+  F    H   G     +  N   D +V+     
Sbjct: 46  DLSKFALEEPVLVSGTDGVGTKLMLA--FMADKHDTIGIDAVAMCVN---DIVVQGAEPL 100

Query: 124 VAMDFLDSTGFSPNPNSLELYIQCLCESGLIEEAFCAF--SKLKEMGVFGSIKTWNSALL 181
             +D++        P+ +E  ++ + E     +A CA    +  EM    S + ++ A  
Sbjct: 101 FFLDYIACG--KAEPSKIENIVKGISEG--CRQAGCALIGGETAEMPGMYSTEEYDLAGF 156

Query: 182 GCIKIDRTDLVWKLYHDLIESGYLIQAFCNDGKVSEGYELLRQV-LEDG 229
               +D+  +V     + IE+G+++    + G  S GY L+R+V LEDG
Sbjct: 157 TVGIVDKKKIVT---GEKIEAGHVLIGLASSGIHSNGYSLVRKVLLEDG 202


>pdb|4G6Z|A Chain A, Crystal Structure Of A Glutamyl-Trna Synthetase Glurs From
           Burkholderia Thailandensis Bound To L-Glutamate
          Length = 490

 Score = 30.8 bits (68), Expect = 1.6,   Method: Compositional matrix adjust.
 Identities = 22/73 (30%), Positives = 35/73 (47%), Gaps = 14/73 (19%)

Query: 281 KSRKRLEAYRVFNDLKERGYVPDTVMYTTVIHGLCKMGWL-GDARKM-------WFEMIH 332
           K  KR  A  V    ++ GY+P+ V+     + L ++GW  GDA          WF++ H
Sbjct: 264 KMSKRHGAMSVMG-YRDAGYLPEAVL-----NYLARLGWSHGDAEIFTREQFVEWFDLEH 317

Query: 333 KGLLPNEYTYNSM 345
            G  P +Y +N +
Sbjct: 318 LGKSPAQYDHNKL 330


>pdb|3MKR|A Chain A, Crystal Structure Of Yeast AlphaEPSILON-Cop Subcomplex Of
           The Copi Vesicular Coat
          Length = 291

 Score = 29.6 bits (65), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 351 RIDNLEEAKRLHKEMLDKGYGETTVTYNTLIAGLCLHG-RTDEAYHLFEEMAQK 403
           ++D L+ A++  K+M D+    T     T    L   G +  +AY++F+EMA K
Sbjct: 142 KLDRLDLARKELKKMQDQDEDATLTQLATAWVSLAAGGEKLQDAYYIFQEMADK 195


>pdb|1YTF|C Chain C, Yeast TfiiaTBPDNA COMPLEX
 pdb|1NH2|C Chain C, Crystal Structure Of A Yeast TfiiaTBPDNA COMPLEX
          Length = 79

 Score = 28.9 bits (63), Expect = 6.3,   Method: Composition-based stats.
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 49 KITRTKPRWEQTLLSDIPSFNFNDPLF 75
          K+TRTK RW+ +L   + + N ND  F
Sbjct: 43 KVTRTKARWKCSLKDGVVTINRNDYTF 69


>pdb|1RM1|C Chain C, Structure Of A Yeast TfiiaTBPTATA-Box Dna Complex
          Length = 286

 Score = 28.1 bits (61), Expect = 9.4,   Method: Compositional matrix adjust.
 Identities = 12/29 (41%), Positives = 18/29 (62%)

Query: 49  KITRTKPRWEQTLLSDIPSFNFNDPLFFR 77
           K+TRTK RW+ +L   + + N ND  F +
Sbjct: 250 KVTRTKARWKCSLKDGVVTINRNDYTFQK 278


  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    0.427 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,232,562
Number of Sequences: 62578
Number of extensions: 556507
Number of successful extensions: 1298
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1289
Number of HSP's gapped (non-prelim): 13
length of query: 427
length of database: 14,973,337
effective HSP length: 102
effective length of query: 325
effective length of database: 8,590,381
effective search space: 2791873825
effective search space used: 2791873825
T: 11
A: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (25.0 bits)