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= psy2085
         (358 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

Searching..................................................done



>pdb|2XZM|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 1
 pdb|2XZN|R Chain R, Crystal Structure Of The Eukaryotic 40s Ribosomal Subunit
           In Complex With Initiation Factor 1. This File Contains
           The 40s Subunit And Initiation Factor For Molecule 2
          Length = 343

 Score = 33.9 bits (76), Expect = 0.15,   Method: Compositional matrix adjust.
 Identities = 23/73 (31%), Positives = 38/73 (52%), Gaps = 14/73 (19%)

Query: 51  VRISPDGQYVLSTGIYKPRVRCYETDNLSMKFERCFDSEVVTFEILSDDYSSELNSIAIN 110
           + ISP+G+Y+ +TG    ++  ++  NL+   +R FD+             S +N IA N
Sbjct: 219 LSISPNGKYI-ATGGKDKKLLIWDILNLTYP-QREFDA------------GSTINQIAFN 264

Query: 111 PVHQLICVGTIEG 123
           P  Q + VGT +G
Sbjct: 265 PKLQWVAVGTDQG 277


>pdb|1QNI|A Chain A, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|B Chain B, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|C Chain C, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|D Chain D, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|E Chain E, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
 pdb|1QNI|F Chain F, Crystal Structure Of Nitrous Oxide Reductase From
           Pseudomonas Nautica, At 2.4a Resolution
          Length = 581

 Score = 31.6 bits (70), Expect = 0.66,   Method: Compositional matrix adjust.
 Identities = 18/61 (29%), Positives = 25/61 (40%)

Query: 23  GRYLLPTNDIRRRIELIQDFEMPGVSTSVRISPDGQYVLSTGIYKPRVRCYETDNLSMKF 82
           G   +P  D R   E  +   +P     +  SPDG+Y ++ G   P V     D L   F
Sbjct: 244 GDSKVPVVDGRGESEFTRYIPVPKNPHGLNTSPDGKYFIANGKLSPTVSVIAIDKLDDLF 303

Query: 83  E 83
           E
Sbjct: 304 E 304


>pdb|2W5R|A Chain A, Structure-Based Mechanism Of Lipoteichoic Acid Synthesis
           By Staphylococcus Aureus Ltas
          Length = 424

 Score = 31.6 bits (70), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 25/38 (65%), Gaps = 1/38 (2%)

Query: 316 ETESRKKKKKLQLSANLLEDDRFSKLFENPDFQVIEPS 353
           E   ++ +K L++S N+L  D F + ++NPDF+ + PS
Sbjct: 379 EKNKKQVEKDLEMSDNVLNGDLF-RFYKNPDFKKVNPS 415


>pdb|2W5Q|A Chain A, Structure-Based Mechanism Of Lipoteichoic Acid Synthesis
           By Staphylococcus Aureus Ltas.
 pdb|2W5S|A Chain A, Structure-Based Mechanism Of Lipoteichoic Acid Synthesis
           By Staphylococcus Aureus Ltas.
 pdb|2W5T|A Chain A, Structure-Based Mechanism Of Lipoteichoic Acid Synthesis
           By Staphylococcus Aureus Ltas
          Length = 424

 Score = 31.6 bits (70), Expect = 0.68,   Method: Compositional matrix adjust.
 Identities = 14/38 (36%), Positives = 25/38 (65%), Gaps = 1/38 (2%)

Query: 316 ETESRKKKKKLQLSANLLEDDRFSKLFENPDFQVIEPS 353
           E   ++ +K L++S N+L  D F + ++NPDF+ + PS
Sbjct: 379 EKNKKQVEKDLEMSDNVLNGDLF-RFYKNPDFKKVNPS 415


>pdb|1QGN|A Chain A, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|B Chain B, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|C Chain C, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|D Chain D, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|E Chain E, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|F Chain F, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|G Chain G, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1QGN|H Chain H, Cystathionine Gamma-Synthase From Nicotiana Tabacum
 pdb|1I41|A Chain A, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|B Chain B, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|C Chain C, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|D Chain D, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|E Chain E, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|F Chain F, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|G Chain G, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|H Chain H, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|I Chain I, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|J Chain J, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|K Chain K, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I41|L Chain L, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Appa
 pdb|1I43|A Chain A, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|B Chain B, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|C Chain C, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|D Chain D, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|E Chain E, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|F Chain F, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|G Chain G, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|H Chain H, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|I Chain I, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|J Chain J, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|K Chain K, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I43|L Chain L, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ppca
 pdb|1I48|A Chain A, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|B Chain B, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|C Chain C, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|D Chain D, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|E Chain E, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|F Chain F, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|G Chain G, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|H Chain H, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|I Chain I, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|J Chain J, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|K Chain K, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
 pdb|1I48|L Chain L, Cystathionine Gamma-Synthase In Complex With The Inhibitor
           Ctcpo
          Length = 445

 Score = 29.6 bits (65), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 18/76 (23%), Positives = 39/76 (51%), Gaps = 3/76 (3%)

Query: 19  VIIGGRYLLPTNDIRRRIELIQDFEMP--GVSTSVRISPDGQYVLSTGIYKPRVRCYETD 76
           ++  G +++ T D  R+  +  +  +P  G++ +V I P     L   + + +V  + T+
Sbjct: 149 LVPAGGHIVTTTDCYRKTRIFIETILPKMGITATV-IDPADVGALELALNQKKVNLFFTE 207

Query: 77  NLSMKFERCFDSEVVT 92
           + +  F RC D E+V+
Sbjct: 208 SPTNPFLRCVDIELVS 223


>pdb|3TMG|A Chain A, Crystal Structure Of Glycine Betaine, L-Proline Abc
           Transporter, GlycineBETAINEL-Proline-Binding Protein
           (Prox) From Borrelia Burgdorferi
 pdb|3TMG|B Chain B, Crystal Structure Of Glycine Betaine, L-Proline Abc
           Transporter, GlycineBETAINEL-Proline-Binding Protein
           (Prox) From Borrelia Burgdorferi
 pdb|3TMG|C Chain C, Crystal Structure Of Glycine Betaine, L-Proline Abc
           Transporter, GlycineBETAINEL-Proline-Binding Protein
           (Prox) From Borrelia Burgdorferi
 pdb|3TMG|D Chain D, Crystal Structure Of Glycine Betaine, L-Proline Abc
           Transporter, GlycineBETAINEL-Proline-Binding Protein
           (Prox) From Borrelia Burgdorferi
          Length = 280

 Score = 29.3 bits (64), Expect = 3.8,   Method: Compositional matrix adjust.
 Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 91  VTFEILSDDYSSELNSIAINPVHQLICVGTIEGKVEAWDP 130
           V FE +   Y++E+ S+  + ++Q +  G I+G V +W P
Sbjct: 37  VVFEKMG--YNAEIFSVTTSIMYQYLASGKIDGTVSSWVP 74


>pdb|4HNK|A Chain A, Crystal Structure Of An Enzyme
 pdb|4HNK|B Chain B, Crystal Structure Of An Enzyme
 pdb|4HNK|C Chain C, Crystal Structure Of An Enzyme
 pdb|4HNK|D Chain D, Crystal Structure Of An Enzyme
 pdb|4HNK|E Chain E, Crystal Structure Of An Enzyme
 pdb|4HNK|F Chain F, Crystal Structure Of An Enzyme
 pdb|4HNK|G Chain G, Crystal Structure Of An Enzyme
 pdb|4HNK|H Chain H, Crystal Structure Of An Enzyme
 pdb|4HNK|I Chain I, Crystal Structure Of An Enzyme
 pdb|4HNK|J Chain J, Crystal Structure Of An Enzyme
 pdb|4HNK|K Chain K, Crystal Structure Of An Enzyme
 pdb|4HNK|L Chain L, Crystal Structure Of An Enzyme
 pdb|4HNK|M Chain M, Crystal Structure Of An Enzyme
 pdb|4HNK|N Chain N, Crystal Structure Of An Enzyme
          Length = 219

 Score = 28.9 bits (63), Expect = 4.4,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%)

Query: 306 KLMDEKQKAEETESRKKKKKLQLSANLLEDDRFSKLFENPDFQVIE 351
           ++M+ K+K  E  S+  +K   + +N+LE D++    E  DF++I+
Sbjct: 168 EIMNTKKKVIEIISKNTEKDTNVISNVLERDKYFNADEAVDFKLID 213


>pdb|4GM2|A Chain A, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
 pdb|4GM2|B Chain B, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
 pdb|4GM2|C Chain C, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
 pdb|4GM2|D Chain D, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
 pdb|4GM2|E Chain E, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
 pdb|4GM2|F Chain F, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
 pdb|4GM2|G Chain G, The Crystal Structure Of A Peptidase From Plasmodium
           Falciparum
          Length = 205

 Score = 28.9 bits (63), Expect = 4.6,   Method: Compositional matrix adjust.
 Identities = 14/46 (30%), Positives = 28/46 (60%)

Query: 306 KLMDEKQKAEETESRKKKKKLQLSANLLEDDRFSKLFENPDFQVIE 351
           ++M+ K+K  E  S+  +K   + +N+LE D++    E  DF++I+
Sbjct: 154 EIMNTKKKVIEIISKNTEKDTNVISNVLERDKYFNADEAVDFKLID 199


>pdb|3MMY|A Chain A, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
 pdb|3MMY|C Chain C, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
 pdb|3MMY|E Chain E, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
 pdb|3MMY|G Chain G, Structural And Functional Analysis Of The Interaction
           Between The Nucleoporin Nup98 And The Mrna Export Factor
           Rae1
          Length = 368

 Score = 28.5 bits (62), Expect = 5.6,   Method: Compositional matrix adjust.
 Identities = 23/77 (29%), Positives = 31/77 (40%), Gaps = 13/77 (16%)

Query: 76  DNLSMKFERCFDSEVVTFEILSDDYSSELNSIAINPVHQLICVGTIEGKVEAWDPRMKVK 135
           DN + K   C  S         D Y+  +N IA +PVH  +     +G+   WD   + K
Sbjct: 253 DNFTFK---CHRSNGTNTSAPQDIYA--VNGIAFHPVHGTLATVGSDGRFSFWDKDARTK 307

Query: 136 AGT---LD-----CAFN 144
             T   LD     C FN
Sbjct: 308 LKTSEQLDQPISACCFN 324


>pdb|1SQ9|A Chain A, Structure Of Ski8p, A Wd Repeat Protein Involved In Mrna
           Degradation And Meiotic Recombination
          Length = 397

 Score = 28.5 bits (62), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 27/52 (51%)

Query: 100 YSSELNSIAINPVHQLICVGTIEGKVEAWDPRMKVKAGTLDCAFNCISNERD 151
           +SS + S++ N   + +C    +GK+  WD + K +  TL+   + I  E D
Sbjct: 290 HSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEED 341


>pdb|1S4U|X Chain X, Crystal Structure Analysis Of The Beta-Propeller Protein
           Ski8p
          Length = 407

 Score = 28.1 bits (61), Expect = 7.0,   Method: Compositional matrix adjust.
 Identities = 15/52 (28%), Positives = 27/52 (51%)

Query: 100 YSSELNSIAINPVHQLICVGTIEGKVEAWDPRMKVKAGTLDCAFNCISNERD 151
           +SS + S++ N   + +C    +GK+  WD + K +  TL+   + I  E D
Sbjct: 300 HSSWVMSLSFNDSGETLCSAGWDGKLRFWDVKTKERITTLNMHCDDIEIEED 351


>pdb|3OW8|A Chain A, Crystal Structure Of The Wd Repeat-Containing Protein 61
 pdb|3OW8|B Chain B, Crystal Structure Of The Wd Repeat-Containing Protein 61
 pdb|3OW8|C Chain C, Crystal Structure Of The Wd Repeat-Containing Protein 61
 pdb|3OW8|D Chain D, Crystal Structure Of The Wd Repeat-Containing Protein 61
          Length = 321

 Score = 28.1 bits (61), Expect = 8.1,   Method: Compositional matrix adjust.
 Identities = 23/99 (23%), Positives = 43/99 (43%), Gaps = 14/99 (14%)

Query: 50  SVRISPDGQYVLSTGIYKPRVRCYETDNLSMKFERCFDSEVVTFEILSDDYSSELNSIAI 109
           S+  SPDG+Y+ S  I          D +   F+      + T E     ++  + S+  
Sbjct: 169 SIAYSPDGKYLASGAI----------DGIINIFDIATGKLLHTLE----GHAMPIRSLTF 214

Query: 110 NPVHQLICVGTIEGKVEAWDPRMKVKAGTLDCAFNCISN 148
           +P  QL+   + +G ++ +D +    AGTL    + + N
Sbjct: 215 SPDSQLLVTASDDGYIKIYDVQHANLAGTLSGHASWVLN 253


  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
   0.318    0.135    0.399 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 8,713,703
Number of Sequences: 62578
Number of extensions: 294042
Number of successful extensions: 741
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 731
Number of HSP's gapped (non-prelim): 16
length of query: 358
length of database: 14,973,337
effective HSP length: 100
effective length of query: 258
effective length of database: 8,715,537
effective search space: 2248608546
effective search space used: 2248608546
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)