RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2725
         (143 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 =  159 bits (405), Expect = 1e-51
 Identities = 54/135 (40%), Positives = 77/135 (57%)

Query: 3   VYNFYLFDSFGTLLYYAEWNRLKHSGMPREEEGKLMYGMLFSLKSFVSKISPLDSKTGFL 62
           +++ Y+F+  G L+YY EW+R K  G     E KL+ GML SL +  SK+SPL   +G  
Sbjct: 1   IHSLYIFNRAGGLIYYKEWHRPKQEGKLTTNEYKLLAGMLHSLHAISSKLSPLPGSSGIE 60

Query: 63  SYKTTKYALHLYETPTGLKFVLNTDVQAQDVRKFLASVYSKVYVEYVVKNPLINPREPIK 122
           S +T  + LH  +T TG+KFVL TD      R  L   Y ++Y +YV+KNP  +   PI+
Sbjct: 61  SLETDTFKLHCLQTLTGIKFVLVTDPGTGPNRDSLLRKYYELYSDYVLKNPFYSLEMPIR 120

Query: 123 SDLFQNALDALVKES 137
            +LF   LD  V+  
Sbjct: 121 CELFDEKLDQYVRSL 135


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

 Score = 58.8 bits (142), Expect = 5e-12
 Identities = 32/134 (23%), Positives = 61/134 (45%), Gaps = 3/134 (2%)

Query: 1   MTVYNFYLFDSFGTLLYYAEWNRLKHSGMPREEEGKLMYGMLFSLKSFVSKISPLDSKTG 60
           M V  F++ +  G L++  +    +        E  ++   L  + + +++  PL   +G
Sbjct: 1   MAVEQFFIINKSGGLIF--QREFGEGETELNSNEYLILASTLHGVSAILTQTIPLPGSSG 58

Query: 61  FLSYKTTKYALHLYETPTGLKFVLNTDVQAQDVRKFLASVYSKVYVEYVVKNPLINPREP 120
            L      + + +++T TG KFV   + +  +    L  +YS +Y +YV KNP  +P  P
Sbjct: 59  RLVLYFRNFVMTIFQTTTGTKFVFVAEKRTVNALFQLQKIYS-LYSDYVTKNPFYSPEMP 117

Query: 121 IKSDLFQNALDALV 134
           I+  LF   L  + 
Sbjct: 118 IQCSLFDEHLKRMF 131


>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 = 41.4 bits (98), Expect = 1e-05
 Identities = 20/75 (26%), Positives = 39/75 (52%), Gaps = 5/75 (6%)

Query: 64  YKTTKYALHLYETPTGLKFVL---NTDVQAQDVRKFLASVYSKVYVEYVVKNPLINPREP 120
                 A+  Y T T +KF+L   ++  +  D+++F   V+ ++Y++ ++ NP   P +P
Sbjct: 54  DSFNDLAVSGYVTNTHIKFILLHDSSTERDDDIKQFFREVH-ELYIKTLM-NPFYEPNDP 111

Query: 121 IKSDLFQNALDALVK 135
           I+S  F   +  L K
Sbjct: 112 IRSPAFDAKVRRLAK 126


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

 Score = 31.0 bits (70), Expect = 0.11
 Identities = 18/63 (28%), Positives = 34/63 (53%), Gaps = 3/63 (4%)

Query: 74  YETPTGLKFVLNTDVQAQD-VRKFLASVYSKVYVEYVVKNPLINPREPIKSDLFQNALDA 132
           Y  P+G+KF+     Q++   R FL  V+ ++Y + ++ +P   P EPI+S  F + +  
Sbjct: 73  YIMPSGMKFLFIHQNQSRKNARSFLQEVH-ELYAKTLM-SPFYEPDEPIRSQAFDDGVRE 130

Query: 133 LVK 135
             +
Sbjct: 131 AAR 133


>gnl|CDD|237362 PRK13356, PRK13356, aminotransferase; Provisional.
          Length = 286

 Score = 29.2 bits (66), Expect = 0.68
 Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 10/61 (16%)

Query: 19  AEWNRLKHSGMPREEEGKLMY--GMLFSLKSFVSKISPLDSKTGFLSYKTTKYALHLYET 76
            E   L   G+ R +    +Y   M ++   F S ++P    T F        AL L E 
Sbjct: 73  EEIEALAREGLKRFDPDTALYIRPMYWAEDGFASGVAPDPESTRF--------ALCLEEA 124

Query: 77  P 77
           P
Sbjct: 125 P 125


>gnl|CDD|206730 cd04167, Snu114p, Snu114p, a spliceosome protein, is a GTPase.
           Snu114p subfamily. Snu114p is one of several proteins
           that make up the U5 small nuclear ribonucleoprotein
           (snRNP) particle. U5 is a component of the spliceosome,
           which catalyzes the splicing of pre-mRNA to remove
           introns. Snu114p is homologous to EF-2, but typically
           contains an additional N-terminal domain not found in
           Ef-2. This protein is part of the GTP translation factor
           family and the Ras superfamily, characterized by five
           G-box motifs.
          Length = 213

 Score = 27.2 bits (61), Expect = 3.1
 Identities = 8/24 (33%), Positives = 13/24 (54%)

Query: 39  YGMLFSLKSFVSKISPLDSKTGFL 62
           +G  F+L+SF  K   +DS    +
Sbjct: 187 FGFCFTLESFAKKYGLVDSILSHI 210


>gnl|CDD|226841 COG4412, COG4412, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 760

 Score = 27.3 bits (60), Expect = 4.0
 Identities = 20/107 (18%), Positives = 37/107 (34%), Gaps = 20/107 (18%)

Query: 52  ISPLDSKTGFLSYKTTKYALHL-----YETPTGLKFV-----------LNTDVQAQDVRK 95
           ++  D+   +L YK++ Y  ++     Y  PT    +            + D        
Sbjct: 155 LTAPDTGMLYLQYKSSHYQDYVFVPEGYNGPTSENEISLSAYYGQQSGFSYDESGAKEGW 214

Query: 96  FLASVYSKVYVEYVVKNPLINPREPIKSDLFQNALDALVKESSISLK 142
           ++A   +     Y  KN L          L + AL+   K  +I L+
Sbjct: 215 YIADKSAA----YYGKNKLGVENPSGARKLVKEALNTAAKHQAIQLQ 257


  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
   0.319    0.136    0.387 

Gapped
Lambda     K      H
   0.267   0.0801    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,080,114
Number of extensions: 609092
Number of successful extensions: 469
Number of sequences better than 10.0: 1
Number of HSP's gapped: 467
Number of HSP's successfully gapped: 13
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
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: 54 (24.4 bits)