RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2686
         (139 letters)



>gnl|CDD|219240 pfam06957, COPI_C, Coatomer (COPI) alpha subunit C-terminus.  This
           family represents the C-terminus (approximately 500
           residues) of the eukaryotic coatomer alpha subunit.
           Coatomer (COPI) is a large cytosolic protein complex
           which forms a coat around vesicles budding from the
           Golgi apparatus. Such coatomer-coated vesicles have been
           proposed to play a role in many distinct steps of
           intracellular transport. Note that many family members
           also contain the pfam04053 domain.
          Length = 421

 Score =  217 bits (553), Expect = 2e-70
 Identities = 89/139 (64%), Positives = 100/139 (71%)

Query: 1   MGLQMETYRKEQLKSNESSQVRICELAAYFTHSKLQPVHQILTLRTATNLFFKLKNYKTT 60
           +GL MET RKE  K     Q R CELAAYFTH KLQPVH ILTLR+A NLFFKLKN+KT 
Sbjct: 259 VGLLMETKRKELPKDTLEQQKRNCELAAYFTHCKLQPVHMILTLRSALNLFFKLKNFKTA 318

Query: 61  ASFAHRLLELGPSMEVATQARKLLAICNANPTDEHTIDYDEHNPFQICARSYTPIYHGRE 120
           ASFA RLLEL P  EVA QARK+L  C  NPTD H ++YDEHNPF +C  SY PIY G+ 
Sbjct: 319 ASFARRLLELAPKPEVAQQARKVLQACEKNPTDAHQLNYDEHNPFVVCGASYVPIYRGKP 378

Query: 121 SEACVYCGASYLPKYKGEL 139
              C YCGAS+ P ++G L
Sbjct: 379 DVKCPYCGASFSPGFEGNL 397


>gnl|CDD|211426 cd11585, SATB1_N, N-terminal domain of SATB1 and similar
          proteins.  SATB1, the special AT-rich sequence-binding
          protein 1, is involved in organizing chromosomal loci
          into distinct loops, creating a "loopscape" that has a
          direct bearing on gene expression. This N-terminal
          domain, which may be involved in various interactions
          with chromatin proteins, resembles a ubiquitin domain
          and has been shown to form tetramers, a function
          critical to SATB1-DNA interactions. The related
          Drosophila homeobox gene defective proventriculus (dve)
          plays a key role in the functional specification during
          endoderm development.
          Length = 100

 Score = 27.7 bits (62), Expect = 0.91
 Identities = 12/31 (38%), Positives = 14/31 (45%)

Query: 67 LLELGPSMEVATQARKLLAICNANPTDEHTI 97
          LL LG S   A  A+ L+ I N  P     I
Sbjct: 46 LLRLGYSHSSAASAKGLIQIKNWKPLPFDQI 76


>gnl|CDD|223242 COG0164, RnhB, Ribonuclease HII [DNA replication, recombination,
           and repair].
          Length = 199

 Score = 26.4 bits (59), Expect = 5.5
 Identities = 8/26 (30%), Positives = 11/26 (42%), Gaps = 1/26 (3%)

Query: 91  PTDEHTIDYDEHNPFQICAR-SYTPI 115
           PTD HT    +        R S+ P+
Sbjct: 159 PTDPHTEALLKKGGTPGIHRRSFAPV 184


>gnl|CDD|234574 PRK00015, rnhB, ribonuclease HII; Validated.
          Length = 197

 Score = 25.9 bits (58), Expect = 7.3
 Identities = 8/25 (32%), Positives = 12/25 (48%)

Query: 91  PTDEHTIDYDEHNPFQICARSYTPI 115
            T EH     ++ P  I  RS+ P+
Sbjct: 173 GTKEHLEALAKYGPTPIHRRSFAPV 197


>gnl|CDD|180550 PRK06382, PRK06382, threonine dehydratase; Provisional.
          Length = 406

 Score = 26.0 bits (57), Expect = 7.6
 Identities = 8/18 (44%), Positives = 14/18 (77%)

Query: 49 NLFFKLKNYKTTASFAHR 66
          +++FKL+N++ T SF  R
Sbjct: 41 DIYFKLENFQKTGSFKSR 58


>gnl|CDD|221350 pfam11971, CAMSAP_CH, CAMSAP CH domain.  This domain is the
          N-terminal CH domain from the CAMSAP proteins.
          Length = 85

 Score = 24.9 bits (55), Expect = 9.2
 Identities = 10/53 (18%), Positives = 19/53 (35%), Gaps = 2/53 (3%)

Query: 23 ICELAAYFTHSKLQPVHQILTLRTATNLFFKLKNYKTTASFAHRLLELGPSME 75
          +  L  ++   +L P+H I  L+   ++   L N +    F    L       
Sbjct: 26 LAALIHFY-CPQLVPLHDI-CLKETMSVADSLYNIQLLQEFCEEHLGNRCFHL 76


>gnl|CDD|149388 pfam08313, SCA7, SCA7, zinc-binding domain.  This domain is found
           in the protein Sgf73/Sca7 which is a component of the
           multihistone acetyltransferase complexes SAGA and SILK.
           This domain is also found in Ataxin-7, a human protein
           which in its polyglutamine expanded pathological form,
           is responsible for the neurodegenerative disease
           spinocerebellar ataxia 7 (SCA7). Ataxin-7 is an integral
           component of the mammalian SAGA-like complexes, the
           TATA-binding protein-free TAF-containing complex (TFTC)
           and the SPT3/TAF9/GCN5 acetyltransferase complex
           (STAGA). This domain is a minimal domain in
           ataxin-7-like proteins that is required for interaction
           with TFTC/STAGA subunits and is conserved highly through
           evolution. The domain contains a conserved Cys(3)His
           motif that binds zinc, thus indicating this to be a new
           zinc-binding domain.
          Length = 73

 Score = 24.6 bits (54), Expect = 9.8
 Identities = 10/29 (34%), Positives = 14/29 (48%), Gaps = 5/29 (17%)

Query: 90  NPTDEHTIDYDEH----NP-FQICARSYT 113
           NP  +  +D D+      P  + CARS T
Sbjct: 11  NPKAKKPVDVDKQCGVILPEGKPCARSLT 39


  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    0.132    0.392 

Gapped
Lambda     K      H
   0.267   0.0710    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,594,312
Number of extensions: 541049
Number of successful extensions: 386
Number of sequences better than 10.0: 1
Number of HSP's gapped: 385
Number of HSP's successfully gapped: 14
Length of query: 139
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 52
Effective length of database: 7,078,804
Effective search space: 368097808
Effective search space used: 368097808
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 (24.6 bits)