RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16695
         (101 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 = 77.0 bits (190), Expect = 1e-19
 Identities = 28/45 (62%), Positives = 33/45 (73%)

Query: 57  GLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101
             D +L+K YELY+DY LKNPFYSLEMPIRCELFD  L   ++  
Sbjct: 91  NRDSLLRKYYELYSDYVLKNPFYSLEMPIRCELFDEKLDQYVRSL 135


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

 Score = 66.1 bits (161), Expect = 3e-15
 Identities = 25/40 (62%), Positives = 31/40 (77%)

Query: 62  LKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101
           L+KIY LY+DY  KNPFYS EMPI+C LFD HL+ + + H
Sbjct: 95  LQKIYSLYSDYVTKNPFYSPEMPIQCSLFDEHLKRMFEGH 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 = 34.5 bits (80), Expect = 0.002
 Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 1/43 (2%)

Query: 55  SSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNL 97
              +    ++++ELY    + NPFY    PIR   FD  ++ L
Sbjct: 83  DDDIKQFFREVHELYIKTLM-NPFYEPNDPIRSPAFDAKVRRL 124


>gnl|CDD|219673 pfam07970, COPIIcoated_ERV, Endoplasmic reticulum vesicle
           transporter.  This family is conserved from plants and
           fungi to humans. Erv46 works in close conjunction with
           Erv41 and together they form a complex which cycles
           between the endoplasmic reticulum and Golgi complex.
           Erv46-41 interacts strongly with the endoplasmic
           reticulum glucosidase II. Mammalian glucosidase II
           comprises a catalytic alpha-subunit and a 58 kDa beta
           subunit, which is required for ER localisation. All
           proteins identified biochemically as Erv41p-Erv46p
           interactors are localised to the early secretory pathway
           and are involved in protein maturation and processing in
           the ER and/or sorting into COPII vesicles for transport
           to the Golgi.
          Length = 222

 Score = 29.2 bits (66), Expect = 0.30
 Identities = 9/39 (23%), Positives = 15/39 (38%), Gaps = 5/39 (12%)

Query: 16  YHPVDNTHLIQQQEQHRH-----IDVAPTNYQRSGSNEP 49
            +P+D T    Q ++  H     + V PT Y+       
Sbjct: 117 TNPLDGTTKFVQTDKGYHMYSYFLKVVPTRYESLNGLIV 155


>gnl|CDD|177399 PHA02570, dexA, exonuclease; Provisional.
          Length = 220

 Score = 28.1 bits (63), Expect = 0.74
 Identities = 11/55 (20%), Positives = 25/55 (45%)

Query: 25  IQQQEQHRHIDVAPTNYQRSGSNEPGRNLASSGLDLILKKIYELYADYALKNPFY 79
           ++ Q+  R  D +   + ++ S E  +NL  S  D+   + ++ + +Y   N   
Sbjct: 51  LKSQKGKRLFDKSTIEWWKNQSPEARKNLKPSDEDVSTYEGHKKFFEYLEANGVD 105


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

 Score = 27.6 bits (62), Expect = 0.96
 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 8/40 (20%)

Query: 69  YADYALKNPFYSLEMPIRCEL--------FDTHLQNLLQQ 100
           Y D    N   S+EM +   L        FD HL+NL+++
Sbjct: 277 YQDALRNNLEQSIEMAVTDGLTGLHNRRYFDMHLKNLIER 316


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

 Score = 27.2 bits (60), Expect = 0.99
 Identities = 15/50 (30%), Positives = 26/50 (52%), Gaps = 1/50 (2%)

Query: 52  NLASSGLDLILKKIYELYADYALKNPFYSLEMPIRCELFDTHLQNLLQQH 101
           N +       L++++ELYA   L +PFY  + PIR + FD  ++   +  
Sbjct: 87  NQSRKNARSFLQEVHELYAK-TLMSPFYEPDEPIRSQAFDDGVREAARVC 135


>gnl|CDD|216231 pfam00995, Sec1, Sec1 family. 
          Length = 554

 Score = 27.6 bits (62), Expect = 0.99
 Identities = 10/33 (30%), Positives = 20/33 (60%), Gaps = 1/33 (3%)

Query: 53  LASSGLDLILKKIYELYADYALKNP-FYSLEMP 84
           LA + +  ++K++ E+Y D+       +SLE+P
Sbjct: 88  LAEADVAELVKQVKEIYLDFIPLESDLFSLELP 120


>gnl|CDD|233032 TIGR00580, mfd, transcription-repair coupling factor (mfd).  All
           proteins in this family for which functions are known
           are DNA-dependent ATPases that function in the process
           of transcription-coupled DNA repair in which the repair
           of the transcribed strand of actively transcribed genes
           is repaired at a higher rate than the repair of
           non-transcribed regions of the genome and than the
           non-transcribed strand of the same gene. This family is
           based on the phylogenomic analysis of JA Eisen (1999,
           Ph.D. Thesis, Stanford University). This family is
           closely related to the RecG and UvrB families [DNA
           metabolism, DNA replication, recombination, and repair].
          Length = 926

 Score = 26.5 bits (59), Expect = 2.5
 Identities = 16/67 (23%), Positives = 23/67 (34%), Gaps = 9/67 (13%)

Query: 16  YHPVDNTHLIQQQEQHRHIDVAPTNYQR----SGSNEPGRNLASSGLDLILKKIYELYAD 71
           Y PV+  HLI      R++  +  N         S E  +      +  I  K+ ELYA 
Sbjct: 371 YVPVEQLHLIS-----RYVGGSGKNPALDKLGGKSWEKTKAKVKKSVREIAAKLIELYAK 425

Query: 72  YALKNPF 78
                  
Sbjct: 426 RKAIKGH 432


>gnl|CDD|234933 PRK01285, PRK01285, pyruvoyl-dependent arginine decarboxylase;
          Reviewed.
          Length = 155

 Score = 26.0 bits (58), Expect = 3.5
 Identities = 11/19 (57%), Positives = 15/19 (78%)

Query: 38 PTNYQRSGSNEPGRNLASS 56
          PT Y R+ SNEPGR +A++
Sbjct: 64 PTVYARNSSNEPGRLIAAA 82


>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 = 26.1 bits (58), Expect = 3.6
 Identities = 12/25 (48%), Positives = 14/25 (56%)

Query: 61  ILKKIYELYADYALKNPFYSLEMPI 85
           ILK    LY  Y LK  FYS  +P+
Sbjct: 232 ILKVAESLYQKYGLKRVFYSAYVPV 256


>gnl|CDD|239287 cd02989, Phd_like_TxnDC9, Phosducin (Phd)-like family, Thioredoxin
           (TRX) domain containing protein 9 (TxnDC9) subfamily;
           composed of predominantly uncharacterized eukaryotic
           proteins, containing a TRX-like domain without the redox
           active CXXC motif. The gene name for the human protein
           is TxnDC9. The two characterized members are described
           as Phd-like proteins, PLP1 of Saccharomyces cerevisiae
           and PhLP3 of Dictyostelium discoideum. Gene disruption
           experiments show that both PLP1 and PhLP3 are
           non-essential proteins. Unlike Phd and most Phd-like
           proteins, members of this group do not contain the Phd
           N-terminal helical domain which is implicated in binding
           to the G protein betagamma subunit.
          Length = 113

 Score = 25.6 bits (57), Expect = 3.9
 Identities = 7/16 (43%), Positives = 12/16 (75%)

Query: 86  RCELFDTHLQNLLQQH 101
           RC++ D HL+ L ++H
Sbjct: 36  RCKIMDKHLEILAKKH 51


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

 Score = 25.5 bits (56), Expect = 5.5
 Identities = 10/25 (40%), Positives = 14/25 (56%)

Query: 61  ILKKIYELYADYALKNPFYSLEMPI 85
           IL +   LY  Y+LK  +YS   P+
Sbjct: 234 ILSRSENLYGRYSLKRVYYSAFSPV 258


>gnl|CDD|214474 smart00022, PLAc, Cytoplasmic phospholipase A2, catalytic subunit. 
           Cytosolic phospholipases A2 hydrolyse arachidonyl
           phospholipids. Family includes phospholipases B
           isoforms.
          Length = 549

 Score = 25.1 bits (55), Expect = 8.6
 Identities = 8/34 (23%), Positives = 12/34 (35%)

Query: 5   NYLVPSLRWNEYHPVDNTHLIQQQEQHRHIDVAP 38
            +LV +L  N + PV     I  +         P
Sbjct: 126 TWLVGTLASNNFTPVKGPEEINSEWMFSVSINNP 159


  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    0.135    0.432 

Gapped
Lambda     K      H
   0.267   0.0694    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,177,257
Number of extensions: 417463
Number of successful extensions: 333
Number of sequences better than 10.0: 1
Number of HSP's gapped: 333
Number of HSP's successfully gapped: 18
Length of query: 101
Length of database: 10,937,602
Length adjustment: 67
Effective length of query: 34
Effective length of database: 7,965,884
Effective search space: 270840056
Effective search space used: 270840056
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: 53 (24.3 bits)