RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6549
         (109 letters)



>2nps_C Vesicle transport through interaction with T- snares homolog 1A;
          vesicle fusion, snare complex, early endosomal snare
          complex, VTI1A, VAMP4, transport protein; 2.50A {Rattus
          norvegicus}
          Length = 81

 Score = 64.4 bits (157), Expect = 2e-15
 Identities = 25/79 (31%), Positives = 43/79 (54%)

Query: 5  HRETLRETNQALVRTGESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLH 64
           R  L +  + L R+   +    Q A+E E IG  ++  L   RE + RAR+RL +TD +
Sbjct: 3  MRAHLLDNTERLERSSRRLEAGYQIAVETEQIGQEMLENLSHDRERIQRARERLRETDAN 62

Query: 65 VSRSRRMIQAIRRRVFYNK 83
          + +S R++  + RR+  N+
Sbjct: 63 LGKSSRILTGMLRRIIQNR 81


>1gl2_C VTI1B, vesicle transport V-snare protein VTI1-like 1; membrane
          protein, membrane fusion protein complex, coiled coil,
          transmembrane; 1.9A {Mus musculus} SCOP: h.1.15.1
          Length = 65

 Score = 58.2 bits (141), Expect = 4e-13
 Identities = 26/62 (41%), Positives = 44/62 (70%)

Query: 16 LVRTGESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLHVSRSRRMIQAI 75
          + R  +SI RS + A E + IGT +I ELG QR+ L R + RLV+T+ ++S+SR++++++
Sbjct: 4  MNRATQSIERSHRIATETDQIGTEIIEELGEQRDQLERTKSRLVNTNENLSKSRKILRSM 63

Query: 76 RR 77
           R
Sbjct: 64 SR 65


>1l4a_C S-SNAP25 fusion protein; snare, snare complex, membrane fusion,
          neurotransmission, endocytosis/exocytosis complex;
          2.95A {Loligo pealei} SCOP: h.1.15.1
          Length = 83

 Score = 29.2 bits (65), Expect = 0.085
 Identities = 14/72 (19%), Positives = 29/72 (40%)

Query: 6  RETLRETNQALVRTGESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLHV 65
           E  ++ NQ    + ES  R      E++  G   +  L  Q E L R  + L   +  +
Sbjct: 12 EEIQQQCNQVTDDSLESTRRMLNMCEESKEAGIRTLVMLDEQGEQLDRIEEGLDQINQDM 71

Query: 66 SRSRRMIQAIRR 77
            + + ++ + +
Sbjct: 72 KDAEKNLEGMEK 83


>1n7s_C SNAP-25A; neuronal snare protein complex, four helix bundle,
          transport protein; 1.45A {Rattus norvegicus} SCOP:
          h.1.15.1 PDB: 1sfc_C 1urq_C 3hd7_C* 3hd9_C 3ipd_C
          3rk2_C 3rk3_C 3rl0_C 1kil_C 1jth_A
          Length = 79

 Score = 28.4 bits (63), Expect = 0.18
 Identities = 14/72 (19%), Positives = 29/72 (40%)

Query: 6  RETLRETNQALVRTGESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRLVDTDLHV 65
           E  R  +Q    + ES  R  Q   E++  G   +  L  Q E L R  + +   +  +
Sbjct: 8  EEMQRRADQLADESLESTRRMLQLVEESKDAGIRTLVMLDEQGEQLDRVEEGMNHINQDM 67

Query: 66 SRSRRMIQAIRR 77
            + + ++ + +
Sbjct: 68 KEAEKNLKDLGK 79


>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
           programmed cell death; HET: DTP; 6.90A {Drosophila
           melanogaster} PDB: 3iz8_A*
          Length = 1221

 Score = 29.1 bits (64), Expect = 0.30
 Identities = 18/95 (18%), Positives = 33/95 (34%), Gaps = 22/95 (23%)

Query: 16  LVRTGESIVRSEQAALE----------AEAIGTGVISELGVQREALVRARDRL-----VD 60
           L+   E +V   Q  +E             I T       +     +  RDRL     V 
Sbjct: 71  LLSKQEEMV---QKFVEEVLRINYKFLMSPIKTEQRQP-SMMTRMYIEQRDRLYNDNQVF 126

Query: 61  TDLHVSRSRRMIQAIRRRVFYNKLFLIMIIVIESM 95
              +VSR  +    +R+ +   +L     ++I+ +
Sbjct: 127 AKYNVSRL-QPYLKLRQALL--ELRPAKNVLIDGV 158


>3gcf_A Terminal oxygenase component of carbazole 1,9A- dioxygenase; rieske
           oxygenase, 2Fe-2S, electron transfer, oxidoreductase;
           2.30A {Nocardioides aromaticivorans}
          Length = 394

 Score = 25.0 bits (54), Expect = 6.1
 Identities = 5/27 (18%), Positives = 13/27 (48%)

Query: 53  RARDRLVDTDLHVSRSRRMIQAIRRRV 79
            ++++L   D+ + + R +     R V
Sbjct: 354 WSKEQLFPPDMCIVKWRTLASERGRGV 380


>3b5n_C Protein transport protein SEC9; snare complex, syntaxin,
          synaptobrevin, SNAP-25, SSO1P, SNC1P, SEC9P, SSO1,
          SNC1, coiled coil; 1.60A {Saccharomyces cerevisiae}
          SCOP: h.1.15.1
          Length = 70

 Score = 24.0 bits (52), Expect = 6.5
 Identities = 11/38 (28%), Positives = 15/38 (39%)

Query: 21 ESIVRSEQAALEAEAIGTGVISELGVQREALVRARDRL 58
           S   + + A +AE  G   +  LG Q E L      L
Sbjct: 12 ASTRNTLKMAQDAERAGMNTLGMLGHQSEQLNNVEGNL 49


>3pm9_A Putative oxidoreductase; putative D-2-hydroxyglutarate
           dehydrogenase, putative D-LACT dehydrogenase; HET: FAD;
           2.57A {Rhodopseudomonas palustris}
          Length = 476

 Score = 24.8 bits (55), Expect = 8.0
 Identities = 9/63 (14%), Positives = 21/63 (33%), Gaps = 12/63 (19%)

Query: 29  AALEAEAIGTGVISELGVQREALVRARDRL----------VDTDLHVSRSR--RMIQAIR 76
              E   +    I+    Q++A  + R+ +          +  D+ V  +   + I+   
Sbjct: 312 RGFEDGIVVDAAIANSVQQQQAFWKLREEISPAQKPEGGSIKHDISVPVAAVPQFIEQAN 371

Query: 77  RRV 79
             V
Sbjct: 372 AAV 374


  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    0.137    0.354 

Gapped
Lambda     K      H
   0.267   0.0639    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,647,110
Number of extensions: 96723
Number of successful extensions: 233
Number of sequences better than 10.0: 1
Number of HSP's gapped: 232
Number of HSP's successfully gapped: 24
Length of query: 109
Length of database: 6,701,793
Length adjustment: 73
Effective length of query: 36
Effective length of database: 4,663,560
Effective search space: 167888160
Effective search space used: 167888160
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 (21.7 bits)
S2: 51 (23.6 bits)