RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3003
         (106 letters)



>1o4w_A PIN (PILT N-terminus) domain; structural genomics, joint CEN
           structural genomics, JCSG, protein structure initiative,
           PS translation; 1.90A {Archaeoglobus fulgidus} SCOP:
           c.120.1.1
          Length = 147

 Score =  113 bits (284), Expect = 7e-34
 Identities = 21/103 (20%), Positives = 44/103 (42%), Gaps = 5/103 (4%)

Query: 1   MEQLQMGIPYITDCVLGEIEKLGQKYKVALRIIKD---PRFERIPCMHKGTYADDCIVNR 57
           + +       IT  V  E+EKL    +   ++         E    +   +  D  ++  
Sbjct: 47  LREFGFSRFLITASVKRELEKLEMSLRGKEKVAARFALKLLEHFEVVETESEGDPSLIEA 106

Query: 58  VTQHKCYIVATCDKDLKRRIRKVPGVPIMYISQHRYTIERMPD 100
             ++ C I+ T DK+LKR+ ++  G+P+ Y+ + +     + D
Sbjct: 107 AEKYGC-ILITNDKELKRKAKQ-RGIPVGYLKEDKRVFVELLD 147


>3gir_A Aminomethyltransferase; glycine cleavage system, aminotransferase,
           structural genomics; 1.60A {Bartonella henselae}
          Length = 393

 Score = 28.7 bits (65), Expect = 0.32
 Identities = 9/45 (20%), Positives = 17/45 (37%), Gaps = 3/45 (6%)

Query: 51  DDCIVNRVTQHKCYIV---ATCDKDLKRRIRKVPGVPIMYISQHR 92
           DD I+ R+ + +  +V        D     ++  G     I+  R
Sbjct: 128 DDLILTRLAECRFMLVANAGNAQADFAELEKRAFGFECQVIALER 172


>1wsr_A Aminomethyltransferase; glycine-cleavage sytem; 2.00A {Homo
           sapiens} PDB: 1wsv_A*
          Length = 375

 Score = 27.1 bits (61), Expect = 1.2
 Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 3/27 (11%)

Query: 51  DDCIVNRVTQHKCYIV---ATCDKDLK 74
           DD IV   ++   Y+V      +KDL 
Sbjct: 100 DDLIVTNTSEGHLYVVSNAGCWEKDLA 126


>2dod_A Transcription elongation regulator 1; FF domain, structural
          genomics, NPPSFA, national project on protein
          structural and functional analyses; NMR {Homo sapiens}
          SCOP: a.159.2.1
          Length = 82

 Score = 24.9 bits (54), Expect = 3.5
 Identities = 7/37 (18%), Positives = 15/37 (40%)

Query: 26 YKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHK 62
           K   +I+ DPR+  +    +    D  +  R  + +
Sbjct: 39 EKELHKIVFDPRYLLLNPKERKQVFDQYVKTRAEEER 75


>2hky_A Ribonuclease 7; RNAse, antimicrobial activity, hydrolase; NMR {Homo
           sapiens}
          Length = 129

 Score = 24.4 bits (53), Expect = 7.0
 Identities = 11/48 (22%), Positives = 17/48 (35%), Gaps = 1/48 (2%)

Query: 37  RFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLKRRIRKVPGVP 84
                 C        +C      Q+K Y+VA C    K+  ++   VP
Sbjct: 76  PVSLTMCKLTSGKYPNCRYKEKRQNKSYVVA-CKPPQKKDSQQFHLVP 122


>3hfh_A Transcription elongation regulator 1; helix bundle, activator,
          alternative splicing, coiled coil, nucleus,
          phosphoprotein, repressor; HET: MLY; 2.70A {Homo
          sapiens} PDB: 2kis_A 2e71_A 2kiq_A
          Length = 190

 Score = 24.7 bits (53), Expect = 7.2
 Identities = 6/31 (19%), Positives = 13/31 (41%)

Query: 32 IIKDPRFERIPCMHKGTYADDCIVNRVTQHK 62
          I+ DPR+  +    +    D  +  R  + +
Sbjct: 33 IVFDPRYLLLNPXERXQVFDQYVXTRAEEER 63


>3n0r_A Response regulator; sigma factor, receiver, two-component SI
           transduction, signaling protein; HET: MSE GOL; 1.25A
           {Caulobacter vibrioides} PDB: 3t0y_A
          Length = 286

 Score = 24.4 bits (53), Expect = 9.2
 Identities = 5/32 (15%), Positives = 11/32 (34%), Gaps = 4/32 (12%)

Query: 75  RRIRKVPGVPIMYISQHRYTIERM----PDAY 102
           + I     VP+++I+     +       P   
Sbjct: 226 KDILGRMDVPVIFITAFPERLLTGERPEPTFL 257


>2fe1_A Conserved hypothetical protein PAE0151; PIN domain, structural
           genomics, unknown function; 2.20A {Pyrobaculum
           aerophilum} SCOP: c.120.1.1
          Length = 156

 Score = 24.3 bits (52), Expect = 9.9
 Identities = 12/70 (17%), Positives = 22/70 (31%), Gaps = 2/70 (2%)

Query: 15  VLGEIEKLGQKYKVALRIIKDPRFERIPCMHKGTYADDCIVNRVTQHKCYIVATCDKDLK 74
           +L E+ +  +  KV            +   H  T  D   V    +     + T D+ L 
Sbjct: 89  MLEELWEFFKALKVHSYAEVLKDAFALALKHGVTVYDAAYVALAEKIGG-KLLTLDRQLA 147

Query: 75  RRIRKVPGVP 84
            +   +   P
Sbjct: 148 EKFPAL-VTP 156


  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
   0.326    0.143    0.447 

Gapped
Lambda     K      H
   0.267   0.0594    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,752,033
Number of extensions: 96124
Number of successful extensions: 312
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 15
Length of query: 106
Length of database: 6,701,793
Length adjustment: 71
Effective length of query: 35
Effective length of database: 4,719,402
Effective search space: 165179070
Effective search space used: 165179070
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 51 (23.7 bits)