RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2587
         (210 letters)



>1mkc_A Protein (midkine); heparin-binding growth factor; NMR {Synthetic}
           SCOP: g.5.1.2
          Length = 43

 Score = 39.4 bits (91), Expect = 3e-05
 Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 60  CKYDKSSWSECDPNTHMKNRTLTLKKG-SPTTCEATKSISRKC 101
           CKY   +W  CD  T  K R  TLKK      C+ T  +++ C
Sbjct: 1   CKYKFENWGACDGGTGTKVRQGTLKKARYNAQCQETIRVTKPC 43



 Score = 32.8 bits (74), Expect = 0.005
 Identities = 14/43 (32%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 105 CRYEKGSWSQCSVA-GDMTRTDMLKEANSDANCEKSRTLTKKC 146
           C+Y+  +W  C    G   R   LK+A  +A C+++  +TK C
Sbjct: 1   CKYKFENWGACDGGTGTKVRQGTLKKARYNAQCQETIRVTKPC 43


>3t5o_A Complement component C6; macpf, MAC, membrane attack complex,
           innate IMMU system, blood, membrane, cytolysin, immune
           SYST; HET: NAG FUL FUC BGC MAN; 2.87A {Homo sapiens}
           PDB: 4a5w_B* 4e0s_B*
          Length = 913

 Score = 30.2 bits (67), Expect = 0.53
 Identities = 25/148 (16%), Positives = 45/148 (30%), Gaps = 13/148 (8%)

Query: 50  RNTRGAEKQPCKYDK-----SSWSECDPNTHMKNRTLTLKKGSP---TTCEATKSISRKC 101
           + TR    Q C  +        WS+CDP    +++  ++ + S      C A     + C
Sbjct: 47  QETRECNWQRCPINCLLGDFGPWSDCDPCIEKQSKVRSVLRPSQFGGQPCTAPLVAFQPC 106

Query: 102 --KKACRYEKGSWSQCSVAGDMTRTDMLKEANSDANCEKSRTLTKKCKAKNSGRKNKANN 159
              K C+ E+                   E N + +C  +       + K    +     
Sbjct: 107 IPSKLCKIEEADCKNKFRCDSGRCIARKLECNGENDCGDNSDERDCGRTKAVCTRKYNPI 166

Query: 160 DCLTDLGLG---LSDGRTCVVYKARHLG 184
             +  +G G   L+      V      G
Sbjct: 167 PSVQLMGNGFHFLAGEPRGEVLDNSFTG 194


>1vex_A F-spondin; TSR, cell adhesion; NMR {Rattus norvegicus}
          Length = 56

 Score = 25.8 bits (57), Expect = 2.7
 Identities = 14/40 (35%), Positives = 17/40 (42%), Gaps = 3/40 (7%)

Query: 110 GSWSQCSV---AGDMTRTDMLKEANSDANCEKSRTLTKKC 146
             WS CSV    G  TR  MLK      +C +     +KC
Sbjct: 11  SEWSDCSVTCGKGMRTRQRMLKSLAELGDCNEDLEQAEKC 50


>3ojy_B Complement component C8 beta chain; macpf, lipocalin, immune
           system; HET: TPO BMA; 2.51A {Homo sapiens}
          Length = 537

 Score = 26.8 bits (58), Expect = 6.5
 Identities = 20/115 (17%), Positives = 36/115 (31%), Gaps = 6/115 (5%)

Query: 65  SSWSECDPNTHMKNRTLTLKKGSP---TTCEATKSISRKCK--KACRYEKG-SWSQCSVA 118
           SSW+ CDP    + R   L + S      C  +      C   + CR +       C+  
Sbjct: 17  SSWTTCDPCQKKRYRYAYLLQPSQFHGEPCNFSDKEVEDCVTNRPCRSQVRCEGFVCAQT 76

Query: 119 GDMTRTDMLKEANSDANCEKSRTLTKKCKAKNSGRKNKANNDCLTDLGLGLSDGR 173
           G      +L   ++D   +      ++   K     ++         G+ L    
Sbjct: 77  GRCVNRRLLCNGDNDCGDQSDEANCRRIYKKCQHEMDQYWGIGSLASGINLFTNS 131


>1ee8_A MUTM (FPG) protein; beta sandwich, zinc finger, helix two-turns
           helix, riken STR genomics/proteomics initiative, RSGI,
           structural genomics; 1.90A {Thermus thermophilus} SCOP:
           a.156.1.2 b.113.1.1 g.39.1.8
          Length = 266

 Score = 26.3 bits (59), Expect = 6.9
 Identities = 11/34 (32%), Positives = 13/34 (38%), Gaps = 7/34 (20%)

Query: 165 LGLGLSDGRTCVVYKARHLGLSGSLI---DRHTR 195
           L   L  G   V     HLG++G        HTR
Sbjct: 54  LLFALEGGVELVA----HLGMTGGFRLEPTPHTR 83


>2xzf_A Formamidopyrimidine-DNA glycosylase; hydrolase-DNA complex; HET:
           VET; 1.80A {Lactococcus lactis subsp} PDB: 1pm5_A*
           1xc8_A* 1pji_A* 2xzu_A* 3c58_A* 1tdz_A* 1nnj_A 1kfv_A
           1pjj_A*
          Length = 271

 Score = 25.9 bits (58), Expect = 9.6
 Identities = 5/35 (14%), Positives = 10/35 (28%), Gaps = 12/35 (34%)

Query: 169 LSDGRTCVVYKARHLGLSGSL--------IDRHTR 195
           + D    +     HL + G           ++H  
Sbjct: 63  IGDDFRLIS----HLRMEGKYRLATLDAPREKHDH 93


>3twl_A Formamidopyrimidine-DNA glycosylase 1; helix two turns helix,
           zinc-LESS finger, hydrolase, DNA DAMA repair,
           DNA-binding, glycosidase, lyase; 1.70A {Arabidopsis
           thaliana} PDB: 3twm_A* 3twk_A
          Length = 310

 Score = 26.1 bits (58), Expect = 9.7
 Identities = 7/45 (15%), Positives = 12/45 (26%), Gaps = 6/45 (13%)

Query: 167 LGLSDGRTCVVYKARHLGLSGSL--IDRHTRSNGRPTRSSERDWP 209
           L L              G++G++           R       +WP
Sbjct: 64  LELDSPPFPSF----QFGMAGAIYIKGVAVTKYKRSAVKDSEEWP 104


  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
   0.314    0.128    0.401 

Gapped
Lambda     K      H
   0.267   0.0757    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,033,667
Number of extensions: 157887
Number of successful extensions: 318
Number of sequences better than 10.0: 1
Number of HSP's gapped: 310
Number of HSP's successfully gapped: 23
Length of query: 210
Length of database: 6,701,793
Length adjustment: 89
Effective length of query: 121
Effective length of database: 4,216,824
Effective search space: 510235704
Effective search space used: 510235704
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 (21.6 bits)
S2: 55 (24.9 bits)