RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13000
         (65 letters)



>4abm_A Charged multivesicular BODY protein 4B; cell cycle, protein
          transport, HIV-1; 1.80A {Homo sapiens}
          Length = 79

 Score = 51.1 bits (122), Expect = 8e-11
 Identities = 29/45 (64%), Positives = 36/45 (80%)

Query: 15 GPTTGEAIQKLRETEDMLIKKQEFLEKKIGEEINIARTNGTKNKR 59
          G    EAIQ+LR+TE+ML KKQEFLEKKI +E+  A+ +GTKNKR
Sbjct: 1  GAMEQEAIQRLRDTEEMLSKKQEFLEKKIEQELTAAKKHGTKNKR 45


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
           synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
          Length = 2006

 Score = 36.2 bits (83), Expect = 2e-04
 Identities = 20/86 (23%), Positives = 33/86 (38%), Gaps = 30/86 (34%)

Query: 2   SFFKNI-------F--G-KTEEKGPTTGEAIQKLRETED--------ML-IK--KQEFLE 40
           SFF ++       F  G +  E  P T      L ++ +        ML I    QE ++
Sbjct: 291 SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILEDSLENNEGVPSPMLSISNLTQEQVQ 350

Query: 41  KKI---------GEEINIARTNGTKN 57
             +         G+++ I+  NG KN
Sbjct: 351 DYVNKTNSHLPAGKQVEISLVNGAKN 376


>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic
           vesicle, membrane, Ca structural protein; 7.94A {Bos
           taurus}
          Length = 190

 Score = 27.8 bits (61), Expect = 0.17
 Identities = 10/45 (22%), Positives = 22/45 (48%), Gaps = 3/45 (6%)

Query: 20  EAIQKLRETEDMLIKKQEFLEKKIGEEINIARTNGTKNKREFDHN 64
           E+I+K RE +   +++ +   K + +E    R    K+  E++  
Sbjct: 85  ESIRKWREEQRKRLQELDAASKVMEQEW---REKAKKDLEEWNQR 126


>2id0_A Exoribonuclease 2; RNAse, exonuclease, hydrolyase, mRNA decay, RNR
           family, hydrolase; 2.35A {Escherichia coli} SCOP:
           b.40.4.5 b.40.4.5 b.40.4.5 b.40.4.16 PDB: 2ix0_A* 2ix1_A
          Length = 644

 Score = 27.1 bits (61), Expect = 0.30
 Identities = 6/21 (28%), Positives = 9/21 (42%), Gaps = 2/21 (9%)

Query: 26  RETEDMLIKKQEFLEKKIGEE 46
           R+  D       FL+ K G +
Sbjct: 543 RDVGDW--LYARFLKDKAGTD 561


>3grl_A General vesicular transport factor P115; vesicle transport,
          membrane trafficking, membrane tethering, fusion,
          snare, RAB GTPase, armadillo repeats; 2.00A {Bos
          taurus} PDB: 3gq2_A 2w3c_A
          Length = 651

 Score = 26.6 bits (58), Expect = 0.47
 Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 1/26 (3%)

Query: 1  MSFFKNIFG-KTEEKGPTTGEAIQKL 25
          M+F + + G ++     T  E IQKL
Sbjct: 1  MNFLRGVMGGQSAGPQHTEAETIQKL 26


>2r7d_A Ribonuclease II family protein; structural genomics, PSI-2,
           structure initiative, northeast structural genomics
           consort NESG; 1.80A {Deinococcus radiodurans R1} SCOP:
           b.40.4.5 b.40.4.16 PDB: 2r7f_A
          Length = 469

 Score = 26.1 bits (58), Expect = 0.81
 Identities = 2/21 (9%), Positives = 5/21 (23%), Gaps = 2/21 (9%)

Query: 26  RETEDMLIKKQEFLEKKIGEE 46
           R +         F+  +    
Sbjct: 388 RLSRRH--HTLRFIAAQPERV 406


>2wp8_J Exosome complex exonuclease DIS3; nucleus, hydrolase, RNA-binding,
           exonucle binding, mitochondrion, rRNA processing; 3.00A
           {Saccharomyces cerevisiae}
          Length = 977

 Score = 24.0 bits (52), Expect = 3.9
 Identities = 2/21 (9%), Positives = 6/21 (28%), Gaps = 2/21 (9%)

Query: 26  RETEDMLIKKQEFLEKKIGEE 46
           R + +      + +      E
Sbjct: 872 RASIEY--YVGQVMRNNESTE 890


>2vnu_D Exosome complex exonuclease RRP44; hydrolase-RNA complex, RNA
           degradation, RNA-binding, RNA Pro; HET: 1PE; 2.30A
           {Saccharomyces cerevisiae} SCOP: b.40.4.5 b.40.4.5
           b.40.4.5 b.40.4.16
          Length = 760

 Score = 23.9 bits (52), Expect = 4.6
 Identities = 2/21 (9%), Positives = 6/21 (28%), Gaps = 2/21 (9%)

Query: 26  RETEDMLIKKQEFLEKKIGEE 46
           R + +      + +      E
Sbjct: 655 RASIEY--YVGQVMRNNESTE 673


>2w84_A Peroxisomal membrane protein PEX14; zellweger syndrome,
          alternative splicing, phosphoprotein, protein complex,
          disease mutation, peroxisome; NMR {Homo sapiens} PDB:
          2w85_A
          Length = 70

 Score = 22.6 bits (48), Expect = 8.1
 Identities = 9/21 (42%), Positives = 14/21 (66%), Gaps = 2/21 (9%)

Query: 32 LIKKQEFLEKK--IGEEINIA 50
          L  ++ FL+KK    EEI++A
Sbjct: 35 LATRRAFLKKKGLTDEEIDMA 55


>1hfe_L Protein (Fe-only hydrogenase (E.C.1.18.99.1) (larger subunit));
           hydrogene metabolism, periplasm; 1.60A {Desulfovibrio
           vulgaris subsp} SCOP: c.96.1.1 d.58.1.5 PDB: 1e08_A*
           1gx7_A*
          Length = 421

 Score = 23.1 bits (50), Expect = 9.6
 Identities = 5/26 (19%), Positives = 12/26 (46%)

Query: 36  QEFLEKKIGEEINIARTNGTKNKREF 61
           +E      G ++ +A  +G K  ++ 
Sbjct: 334 KEATVNVGGTDVKVAVVHGAKRFKQV 359


  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
   0.311    0.131    0.354 

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: 959,060
Number of extensions: 44930
Number of successful extensions: 131
Number of sequences better than 10.0: 1
Number of HSP's gapped: 130
Number of HSP's successfully gapped: 18
Length of query: 65
Length of database: 6,701,793
Length adjustment: 36
Effective length of query: 29
Effective length of database: 5,696,637
Effective search space: 165202473
Effective search space used: 165202473
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 51 (23.7 bits)