RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy10782
         (105 letters)



>1t77_A Lipopolysaccharide-responsive and beige-like anchor protein,
           CDC4-like protein; PH-beach domains, vesicle
           trafficking, signal transduction; 2.40A {Homo sapiens}
           SCOP: a.169.1.1 b.55.1.6 PDB: 1mi1_A
          Length = 414

 Score =  107 bits (268), Expect = 2e-29
 Identities = 44/104 (42%), Positives = 63/104 (60%), Gaps = 8/104 (7%)

Query: 1   MAGRSYNDLMQYPVLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNYL 60
           +AGRSYNDL QYPV P+++++Y+S  LDLT P +FR+L KP+   + K  + +   Y   
Sbjct: 157 IAGRSYNDLNQYPVFPWVITNYESEELDLTLPTNFRDLSKPIGALNPKRAAFFAERYESW 216

Query: 61  AREMCDAVGGVNQEPYHYGSHYSNSGTVLHFLVRIPPFTSMFLN 104
                          +HYG+HYS +  VL +L+RI PFT+ FLN
Sbjct: 217 E--------DDQVPKFHYGTHYSTASFVLAWLLRIEPFTTYFLN 252


>2ihr_1 Peptide chain release factor 2; mixed alpha-beta, translation;
           2.50A {Thermus thermophilus} PDB: 2b9m_Y* 3f1e_X 3f1g_X
           2x9r_Y* 2x9t_Y* 2jl5_Y 2jl7_Y 2wh1_Y 2wh3_Y
          Length = 365

 Score = 26.4 bits (59), Expect = 1.8
 Identities = 9/26 (34%), Positives = 11/26 (42%), Gaps = 2/26 (7%)

Query: 75  PYHYGSHYSNSGTVLHFLVRIPPFTS 100
              YG     +G   H LVR  PF +
Sbjct: 174 ENAYGLLSPEAGV--HRLVRPSPFDA 197


>1s2x_A CAG-Z; CAG pathogenicity island, type IV secretion system, unknown
           function; 1.90A {Helicobacter pylori} SCOP: a.47.3.1
          Length = 206

 Score = 25.4 bits (55), Expect = 4.0
 Identities = 18/77 (23%), Positives = 32/77 (41%)

Query: 19  LSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYNYLAREMCDAVGGVNQEPYHY 78
           + +Y ++  D  DP+ F    + + +  +KN   +   YNYL   +  +     QE    
Sbjct: 39  IQNYATSLKDSNDPQDFLRRVQELRINMQKNFISFDAYYNYLNNLVLASYNRCKQEKTFA 98

Query: 79  GSHYSNSGTVLHFLVRI 95
            S   N  T+  F+  I
Sbjct: 99  ESTIKNELTLGEFVAEI 115


>1gqe_A Release factor 2, RF2; protein synthesis, ribosome, macromolecular
           mimicry, translation; 1.81A {Escherichia coli} SCOP:
           e.38.1.1 PDB: 1mi6_A 1ml5_Z*
          Length = 365

 Score = 25.3 bits (56), Expect = 4.3
 Identities = 11/26 (42%), Positives = 14/26 (53%), Gaps = 2/26 (7%)

Query: 75  PYHYGSHYSNSGTVLHFLVRIPPFTS 100
            Y YG   + +G  +H LVR  PF S
Sbjct: 186 DYAYGWLRTETG--VHRLVRKSPFDS 209


>3ihp_A Ubiquitin carboxyl-terminal hydrolase 5; hydrolase, protease, thiol
           protease, UBL conjugation pathway, metal-binding,
           zinc-finger,structural genomics; 2.80A {Homo sapiens}
          Length = 854

 Score = 25.6 bits (55), Expect = 4.6
 Identities = 15/83 (18%), Positives = 24/83 (28%), Gaps = 11/83 (13%)

Query: 32  PKSFRNLKKPMAVQDKKNESHYVNNYNYLAREMCDAVGGVNQEPYHYG---------SHY 82
                ++ K         E     N      E+    G   +  +  G         S Y
Sbjct: 296 SHFGIDMLKMQKTDKTMTELEIDMNQRIGEWELIQESGVPLKPLFGPGYTGIRNLGNSCY 355

Query: 83  SNSGTVLHFLVRIPPFTSMFLNS 105
            NS  V+  L  IP F   +++ 
Sbjct: 356 LNS--VVQVLFSIPDFQRKYVDK 376


>1cb8_A Protein (chondroitinase AC); lyase, chondroitin degradation; HET:
           MAN RAM GCU MFU; 1.90A {Pedobacter heparinus} SCOP:
           a.102.3.2 b.24.1.1 b.30.5.2 PDB: 1hm2_A* 1hm3_A* 1hmu_A*
           1hmw_A*
          Length = 678

 Score = 25.1 bits (54), Expect = 6.1
 Identities = 13/52 (25%), Positives = 19/52 (36%)

Query: 7   NDLMQYPVLPFILSDYKSATLDLTDPKSFRNLKKPMAVQDKKNESHYVNNYN 58
           N    Y VLP I    +    + T PK   N  +  AV  ++ +      Y 
Sbjct: 553 NAQYAYIVLPGINKPEEIKKYNGTAPKVLANTNQLQAVYHQQLDMVQAIFYT 604


>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 = 6.7
 Identities = 6/13 (46%), Positives = 9/13 (69%)

Query: 28  DLTDPKSFRNLKK 40
           D+T+  SF N+K 
Sbjct: 90  DVTNASSFENIKS 102


>1vg8_A RAS-related protein RAB-7; GTP-binding protein, protein transport;
           HET: GNP; 1.70A {Rattus norvegicus} SCOP: c.37.1.8 PDB:
           1vg0_B* 3law_A* 1t91_A* 1yhn_A* 1vg1_A* 1vg9_B*
          Length = 207

 Score = 24.5 bits (54), Expect = 7.6
 Identities = 5/13 (38%), Positives = 8/13 (61%)

Query: 28  DLTDPKSFRNLKK 40
           D+T P +F+ L  
Sbjct: 89  DVTAPNTFKTLDS 101


>3nco_A Endoglucanase fncel5A; fncel5A, F. nodosum RT17-B1, hydrolase;
           1.50A {Fervidobacterium nodosum} PDB: 3rjx_A 3rjy_A*
          Length = 320

 Score = 24.5 bits (53), Expect = 8.9
 Identities = 9/50 (18%), Positives = 15/50 (30%), Gaps = 9/50 (18%)

Query: 49  NESHYV---NNYNYLAREMCDAVGGVNQEPYHY----GSHYSNSGTVLHF 91
           NE         +N L  ++   +   N  P         ++SN   V   
Sbjct: 143 NEPAQNLTPTKWNELYPKVLGEIRKTN--PSRIVIIDVPNWSNYSYVREL 190


  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
   0.319    0.134    0.404 

Gapped
Lambda     K      H
   0.267   0.0601    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,605,251
Number of extensions: 80233
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 221
Number of HSP's successfully gapped: 16
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 51 (23.7 bits)