RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy627
         (89 letters)



>2jya_A AGR_C_3324P, uncharacterized protein ATU1810; protein with unknown
           function ATU1810, ontario centre for ST proteomics,
           OCSP; NMR {Agrobacterium tumefaciens str}
          Length = 106

 Score =  114 bits (288), Expect = 3e-35
 Identities = 33/85 (38%), Positives = 47/85 (55%), Gaps = 1/85 (1%)

Query: 1   MQSGTHNANNWFIQFDTR-ERWENPLMGWCSTGDPLSNLALNFSSKEDAIQYCQKNGWKF 59
           MQSGT   N W ++FD    R  +P+MG+ S+ D    + L F ++E A  Y Q+ G ++
Sbjct: 16  MQSGTAKTNVWVLEFDAEVPRKIDPIMGYTSSSDMKQQVKLTFETQEQAEAYAQRKGIEY 75

Query: 60  FVEEPKWKTPKVKSYAFNFSWNKRT 84
            V  PK  T KV SY  NF +N+  
Sbjct: 76  RVILPKEATRKVVSYTDNFRFNRTQ 100


>2lju_A Putative oxidoreductase; structural genomics, seattle structural
           GENO center for infectious disease, ssgcid; NMR
           {Ehrlichia chaffeensis}
          Length = 108

 Score =  114 bits (288), Expect = 3e-35
 Identities = 25/84 (29%), Positives = 42/84 (50%), Gaps = 1/84 (1%)

Query: 1   MQSGTHNANNWFIQFDTR-ERWENPLMGWCSTGDPLSNLALNFSSKEDAIQYCQKNGWKF 59
           MQSG      W ++F+    ++  PLM W  + D    + L+F+++E AI Y   +   +
Sbjct: 24  MQSGHSKLKAWKLEFEPSCTQYTEPLMNWTGSHDTKQQVCLSFTTRELAIAYAVAHKIDY 83

Query: 60  FVEEPKWKTPKVKSYAFNFSWNKR 83
            V +   +T   KSYA NF+  + 
Sbjct: 84  TVLQDNPRTIVPKSYADNFTKPRD 107


>3t5v_A Nuclear mRNA export protein SAC3; PCI, mRNA nuclear export, mRNA,
           nuclear, transcription; 2.90A {Saccharomyces cerevisiae}
          Length = 316

 Score = 28.3 bits (62), Expect = 0.28
 Identities = 6/33 (18%), Positives = 15/33 (45%), Gaps = 2/33 (6%)

Query: 34  PLSNLA--LNFSSKEDAIQYCQKNGWKFFVEEP 64
           P   L   L F+++++ I++C     +    + 
Sbjct: 226 PFIYLENMLLFNNRQEIIEFCNYYSIEIINGDA 258


>1kor_A Argininosuccinate synthetase; ligase, riken structural
           genomics/proteomics initiative, RSGI, structural
           genomics; HET: ANP ARG; 1.95A {Thermus thermophilus}
           SCOP: c.26.2.1 d.210.1.1 PDB: 1j1z_A* 1j21_A* 1kh1_A
           1kh2_A* 1kh3_A* 1j20_A*
          Length = 400

 Score = 27.1 bits (61), Expect = 0.82
 Identities = 4/16 (25%), Positives = 10/16 (62%)

Query: 41  NFSSKEDAIQYCQKNG 56
           +F  +++ I Y + +G
Sbjct: 146 SFQGRKEMIAYAEAHG 161


>1vl2_A Argininosuccinate synthase; TM1780, structural genomics, JCS
           protein structure initiative, PSI, joint center for
           structu genomics, ligase; 1.65A {Thermotoga maritima}
           SCOP: c.26.2.1 d.210.1.1
          Length = 421

 Score = 26.4 bits (59), Expect = 1.1
 Identities = 5/20 (25%), Positives = 7/20 (35%)

Query: 37  NLALNFSSKEDAIQYCQKNG 56
                F  + D I Y  + G
Sbjct: 159 EFLAKFKGRTDLINYAMEKG 178


>2nz2_A Argininosuccinate synthase; amino-acid biosynthesis, aspartate,
           citrulline, ST genomics, structural genomics consortium,
           SGC, ligase; HET: CIR; 2.40A {Homo sapiens}
          Length = 413

 Score = 26.3 bits (59), Expect = 1.1
 Identities = 4/20 (20%), Positives = 10/20 (50%)

Query: 37  NLALNFSSKEDAIQYCQKNG 56
                F  + D ++Y +++G
Sbjct: 150 EFYNRFKGRNDLMEYAKQHG 169


>3m4p_A Ehasnrs, asparaginyl-tRNA synthetase, putative; aminoacyl-tRNA
           synthetase, tRNA ligase, AARS, translation, ATP-binding,
           nucleotide-binding; HET: 4AD; 2.83A {Entamoeba
           histolytica} PDB: 3m4q_A
          Length = 456

 Score = 26.4 bits (59), Expect = 1.4
 Identities = 6/21 (28%), Positives = 11/21 (52%)

Query: 46  EDAIQYCQKNGWKFFVEEPKW 66
            DAI+YC  +G     +  ++
Sbjct: 303 ADAIKYCNDHGILNKDKPFEY 323


>1ng7_A Poliovirus 3A-N, genome polyprotein [core protein P3A]; helical
          hairpin, unfolded domain, symmetric dimer, viral
          protein; NMR {Human poliovirus 1} SCOP: a.178.1.1
          Length = 60

 Score = 25.0 bits (54), Expect = 1.6
 Identities = 5/12 (41%), Positives = 8/12 (66%)

Query: 46 EDAIQYCQKNGW 57
          ++   YC+K GW
Sbjct: 32 QEVRDYCEKKGW 43


>2f42_A STIP1 homology and U-box containing protein 1; chaperone; 2.50A
           {Danio rerio} PDB: 2c2v_S 2oxq_C
          Length = 179

 Score = 25.7 bits (56), Expect = 1.8
 Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)

Query: 31  TGDPLSNLAL--NFSSKEDAIQYCQKNGWKF 59
           T  PL+   L  N + KE    + Q+NGW  
Sbjct: 147 TRSPLTQDQLIPNLAMKEVIDAFIQENGWVE 177


>3ss7_X D-serine dehydratase; type II fold, ALFA,beta-elimination, P
           5'-phosphate, lyase; HET: PLP; 1.55A {Escherichia coli}
           PDB: 3ss9_X* 3r0x_A* 3r0z_A
          Length = 442

 Score = 25.5 bits (56), Expect = 2.3
 Identities = 5/25 (20%), Positives = 11/25 (44%), Gaps = 2/25 (8%)

Query: 44  SKEDAIQYCQKNGWKFFV--EEPKW 66
           + E+  +  Q +   FF+  E  + 
Sbjct: 219 AVEEGRKAAQSDPNCFFIDDENSRT 243


>1ky3_A GTP-binding protein YPT7P; vesicular traffic, GTP hydrolysis,
           YPT/RAB protein, endocytosis, hydrolase,
           endocytosis/exocytosis complex; HET: GDP; 1.35A
           {Saccharomyces cerevisiae} SCOP: c.37.1.8 PDB: 1ky2_A*
          Length = 182

 Score = 24.5 bits (54), Expect = 4.6
 Identities = 3/19 (15%), Positives = 7/19 (36%)

Query: 44  SKEDAIQYCQKNGWKFFVE 62
           S++ A +  +  G      
Sbjct: 138 SEKSAQELAKSLGDIPLFL 156


>1k92_A Argininosuccinate synthase, argininosuccinate SY; N-type ATP
           pyrophosphatase, ligase; 1.60A {Escherichia coli} SCOP:
           c.26.2.1 d.210.1.1 PDB: 1k97_A* 1kp2_A* 1kp3_A*
          Length = 455

 Score = 24.5 bits (54), Expect = 5.3
 Identities = 1/15 (6%), Positives = 5/15 (33%)

Query: 42  FSSKEDAIQYCQKNG 56
              + +  ++    G
Sbjct: 165 LGGRHEMSEFMIACG 179


>2pif_A UPF0317 protein pspto_5379; UPF0317 family, structural genomics,
          PSI-2, protein structur initiative; 2.30A {Pseudomonas
          syringae PV} SCOP: d.382.1.1 PDB: 3db9_A
          Length = 276

 Score = 24.6 bits (53), Expect = 5.3
 Identities = 7/29 (24%), Positives = 11/29 (37%)

Query: 24 PLMGWCSTGDPLSNLALNFSSKEDAIQYC 52
          P++     G P + LA     + D   Y 
Sbjct: 65 PILDVSDAGSPTTLLAEGSDLRTDIPMYR 93


>1wms_A RAB-9, RAB9, RAS-related protein RAB-9A; GTPase, protein transport;
           HET: GDP; 1.25A {Homo sapiens} SCOP: c.37.1.8 PDB:
           1s8f_A* 1yzl_A* 2ocb_A*
          Length = 177

 Score = 24.0 bits (53), Expect = 7.5
 Identities = 7/19 (36%), Positives = 11/19 (57%)

Query: 44  SKEDAIQYCQKNGWKFFVE 62
           S E+A  +C+ NG   + E
Sbjct: 134 STEEAQAWCRDNGDYPYFE 152


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.317    0.129    0.443 

Gapped
Lambda     K      H
   0.267   0.0859    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,347,165
Number of extensions: 60404
Number of successful extensions: 279
Number of sequences better than 10.0: 1
Number of HSP's gapped: 277
Number of HSP's successfully gapped: 25
Length of query: 89
Length of database: 6,701,793
Length adjustment: 57
Effective length of query: 32
Effective length of database: 5,110,296
Effective search space: 163529472
Effective search space used: 163529472
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.2 bits)