RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy16694
         (164 letters)



>gnl|CDD|146632 pfam04099, Sybindin, Sybindin-like family.  Sybindin is a
           physiological syndecan-2 ligand on dendritic spines, the
           small protrusions on the surface of dendrites that
           receive the vast majority of excitatory synapses.
          Length = 135

 Score =  167 bits (425), Expect = 3e-54
 Identities = 66/109 (60%), Positives = 79/109 (72%), Gaps = 1/109 (0%)

Query: 43  RMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDT 102
           ++TTNE   LA M + L AI+S+LSP P SSGIE LE DTFKLHC QTLTG+KF++V D 
Sbjct: 27  KLTTNEYKLLAGMLHSLHAISSKLSPLPGSSGIESLETDTFKLHCLQTLTGIKFVLVTDP 86

Query: 103 NQS-GLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 150
                 D +L+K YELY+DY LKNPFYSLEMPIRCELFD  L   ++  
Sbjct: 87  GTGPNRDSLLRKYYELYSDYVLKNPFYSLEMPIRCELFDEKLDQYVRSL 135


>gnl|CDD|227451 COG5122, TRS23, Transport protein particle (TRAPP) complex subunit
           [Intracellular trafficking and secretion].
          Length = 134

 Score =  120 bits (302), Expect = 1e-35
 Identities = 48/108 (44%), Positives = 64/108 (59%)

Query: 43  RMTTNEKIFLASMFYPLFAIASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVGDT 102
            + +NE + LAS  + + AI +Q  P P SSG  VL    F +  +QT TG KF+ V + 
Sbjct: 27  ELNSNEYLILASTLHGVSAILTQTIPLPGSSGRLVLYFRNFVMTIFQTTTGTKFVFVAEK 86

Query: 103 NQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 150
                   L+KIY LY+DY  KNPFYS EMPI+C LFD HL+ + + H
Sbjct: 87  RTVNALFQLQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEGH 134


>gnl|CDD|218183 pfam04628, Sedlin_N, Sedlin, N-terminal conserved region.
           Mutations in this protein are associated with the
           X-linked spondyloepiphyseal dysplasia tarda syndrome
           (OMIM:313400). This family represents an N-terminal
           conserved region.
          Length = 127

 Score = 46.5 bits (111), Expect = 4e-07
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 4/62 (6%)

Query: 88  YQTLTGVKFMIVGDT---NQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQ 144
           Y T T +KF+++ D+       +    ++++ELY    + NPFY    PIR   FD  ++
Sbjct: 64  YVTNTHIKFILLHDSSTERDDDIKQFFREVHELYIKTLM-NPFYEPNDPIRSPAFDAKVR 122

Query: 145 NL 146
            L
Sbjct: 123 RL 124


>gnl|CDD|188431 TIGR03916, rSAM_link_UDG, putative DNA modification/repair radical
           SAM protein.  This uncharacterized protein of about 400
           amino acids in length contains a radical SAM protein in
           the N-terminal half. Members are present in about twenty
           percent of prokaryotic genomes, always paired with a
           member of the conserved hypothetical protein TIGR03915.
           Roughly forty percent of the members of that family
           exist as fusions with a uracil-DNA glycosylase-like
           region, TIGR03914. In DNA, uracil results from
           deamidation of cytosine, forming U/G mismatches that
           lead to mutation, and so uracil-DNA glycosylase is a DNA
           repair enzyme. This indirect connection, and the
           recurring role or radical SAM protein in modification
           chemistries, suggest that this protein may act in DNA
           modification, repair, or both [Unknown function, Enzymes
           of unknown specificity].
          Length = 415

 Score = 36.5 bits (85), Expect = 0.003
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 97  MIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPI 134
           MI+G T ++    ILK    LY  Y LK  FYS  +P+
Sbjct: 220 MIIGATGETDYQ-ILKVAESLYQKYGLKRVFYSAYVPV 256


>gnl|CDD|227890 COG5603, TRS20, Subunit of TRAPP, an ER-Golgi tethering complex
           [Cell motility and secretion].
          Length = 136

 Score = 34.1 bits (78), Expect = 0.011
 Identities = 18/64 (28%), Positives = 35/64 (54%), Gaps = 2/64 (3%)

Query: 88  YQTLTGVKFMIV-GDTNQSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNL 146
           Y   +G+KF+ +  + ++      L++++ELYA   L +PFY  + PIR + FD  ++  
Sbjct: 73  YIMPSGMKFLFIHQNQSRKNARSFLQEVHELYAK-TLMSPFYEPDEPIRSQAFDDGVREA 131

Query: 147 LQQH 150
            +  
Sbjct: 132 ARVC 135


>gnl|CDD|226727 COG4277, COG4277, Predicted DNA-binding protein with the
           Helix-hairpin-helix motif [General function prediction
           only].
          Length = 404

 Score = 30.9 bits (70), Expect = 0.27
 Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)

Query: 97  MIVGDTNQSGLDLILKKIYELYADYALKNPFYSLEMPI 134
           MIVG   ++  D IL +   LY  Y+LK  +YS   P+
Sbjct: 222 MIVGADGETDED-ILSRSENLYGRYSLKRVYYSAFSPV 258


>gnl|CDD|235788 PRK06372, PRK06372, translation initiation factor IF-2B subunit
           delta; Provisional.
          Length = 253

 Score = 26.8 bits (59), Expect = 5.5
 Identities = 36/140 (25%), Positives = 54/140 (38%), Gaps = 25/140 (17%)

Query: 2   HVLTAVNDAVIKNGQLDDGTDVLEFLSKPESFPVKLTFTRPRMTTNEKIFLASMFYPLFA 61
           H     ND+VI  G +     +  F+S  E   +K  +        E I +A +      
Sbjct: 80  HAKPLFNDSVI--GTISSSQVLKAFISSSEK--IKSVYILESRPMLEGIDMAKLL----- 130

Query: 62  IASQLSPEPKSSGIEVLEADTFKLHCYQTLTGVKFMIVG-DTNQSGLDLILKK---IYEL 117
                      SGI+V+      +   + +  V  +IVG D+      LI K       L
Sbjct: 131 ---------VKSGIDVVLLTDASM--CEAVLNVDAVIVGSDSVLYDGGLIHKNGTFPLAL 179

Query: 118 YADYALKNPFYSLEMPIRCE 137
            A Y LK PFYSL + ++ E
Sbjct: 180 CARY-LKKPFYSLTISMKIE 198


>gnl|CDD|236577 PRK09581, pleD, response regulator PleD; Reviewed.
          Length = 457

 Score = 26.8 bits (60), Expect = 6.1
 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 8/40 (20%)

Query: 118 YADYALKNPFYSLEMPIRCEL--------FDTHLQNLLQQ 149
           Y D    N   S+EM +   L        FD HL+NL+++
Sbjct: 277 YQDALRNNLEQSIEMAVTDGLTGLHNRRYFDMHLKNLIER 316


>gnl|CDD|180368 PRK06048, PRK06048, acetolactate synthase 3 catalytic subunit;
           Reviewed.
          Length = 561

 Score = 26.3 bits (58), Expect = 9.8
 Identities = 10/29 (34%), Positives = 19/29 (65%)

Query: 132 MPIRCELFDTHLQNLLQQHEKTGVTNACG 160
           +P+  EL+D+ L+++L +HE+     A G
Sbjct: 35  IPVYDELYDSDLRHILVRHEQAAAHAADG 63


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.320    0.136    0.395 

Gapped
Lambda     K      H
   0.267   0.0810    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,166,173
Number of extensions: 734063
Number of successful extensions: 610
Number of sequences better than 10.0: 1
Number of HSP's gapped: 607
Number of HSP's successfully gapped: 15
Length of query: 164
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 74
Effective length of database: 6,945,742
Effective search space: 513984908
Effective search space used: 513984908
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 (21.8 bits)
S2: 55 (24.8 bits)