RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16948
         (297 letters)



>gnl|CDD|217320 pfam03016, Exostosin, Exostosin family.  The EXT family is a family
           of tumour suppressor genes. Mutations of EXT1 on 8q24.1,
           EXT2 on 11p11-13, and EXT3 on 19p have been associated
           with the autosomal dominant disorder known as hereditary
           multiple exostoses (HME). This is the most common known
           skeletal dysplasia. The chromosomal locations of other
           EXT genes suggest association with other forms of
           neoplasia. EXT1 and EXT2 have both been shown to encode
           a heparan sulphate polymerase with both D-glucuronyl
           (GlcA) and N-acetyl-D-glucosaminoglycan (GlcNAC)
           transferase activities. The nature of the defect in
           heparan sulphate biosynthesis in HME is unclear.
          Length = 292

 Score =  110 bits (277), Expect = 2e-28
 Identities = 50/227 (22%), Positives = 79/227 (34%), Gaps = 33/227 (14%)

Query: 83  IGDNFKVYIYP------------SNPDEEPNTISSLYQKVLDVVKESRYYTDDPSQACIF 130
                KVY+Y                        +    +   +  SR  T DP +A +F
Sbjct: 1   SCKGLKVYVYDLPRRFNLLEDVLPETSWYLTHQYAAESILHKSILNSRCRTLDPDEADLF 60

Query: 131 ILAIDTLDRD----PLSSNYVHNVPSKLLKLKHWN--NGKNHIVFNL--FSGTWPDYLEE 182
            +   T                 +   L  L +WN   G++HI+ N   F G+  D L  
Sbjct: 61  FVPFYTSLSVGTNAVERDLLPSELVEWLESLPYWNRSGGRDHIIVNSHPFGGSAFDRL-P 119

Query: 183 DLGFDTGQAILAKASMSVTHFRTGFDVSIPLFQKDLPERGGEPGAVISNNFPLRKKYILA 242
            L  +T  A+LA    S   FR GFDV +P +         E   +  +    ++K +L 
Sbjct: 120 ALNNNTILAVLAGGGFSEDQFRPGFDVPLPAYFHPNSVDDLESDGMPPS----KRKTLLF 175

Query: 243 FKGKRYVYGIGSEVRNSLYHLHNGADMVLVTTCKHGKNWAENKDGRC 289
           F G     G G+        L N    +L+  CK+  ++    +  C
Sbjct: 176 FAGGPRPAGKGA--------LANAIRDLLIEECKNSPDFQCEGNQSC 214


>gnl|CDD|130997 TIGR01942, pcnB, poly(A) polymerase.  This model describes the pcnB
           family of poly(A) polymerases (also known as plasmid
           copy number protein). These enzymes sequentially add
           adenosine nucleotides to the 3' end of RNAs, targeting
           them for degradation by the cell. This was originally
           described for anti-sense RNAs, but was later
           demonstrated for mRNAs as well. Members of this family
           are as yet limited to the gamma- and
           beta-proteobacteria, with putative members in the
           Chlamydiacae and spirochetes. This family has homology
           to tRNA nucleotidyltransferase (cca).
          Length = 410

 Score = 29.8 bits (67), Expect = 1.6
 Identities = 12/37 (32%), Positives = 18/37 (48%)

Query: 257 RNSLYHLHNGADMVLVTTCKHGKNWAENKDGRCSVDN 293
           R  L H+  G  ++ V T + G   + N +GR   DN
Sbjct: 75  RFRLVHVSFGRQIIEVATFRSGHKSSVNAEGRILKDN 111


>gnl|CDD|197563 smart00187, INB, Integrin beta subunits (N-terminal portion of
           extracellular region).  Portion of beta integrins that
           lies N-terminal to their EGF-like repeats. Integrins are
           cell adhesion molecules that mediate cell-extracellular
           matrix and cell-cell interactions. They contain both
           alpha and beta subunits. Beta integrins are proposed to
           have a von Willebrand factor type-A "insert" or "I"
           -like domain (although this remains to be confirmed).
          Length = 423

 Score = 30.0 bits (68), Expect = 1.7
 Identities = 25/97 (25%), Positives = 38/97 (39%), Gaps = 24/97 (24%)

Query: 59  RLGGDVLPNNQKCRMETCFDFTKCIGDNFKVYIYPSNPDEEPNTISSLYQKVLD------ 112
           +LGG V PN+ +C ++   ++T           YPS        I  L QK+ +      
Sbjct: 248 KLGGIVTPNDGQCHLDNNGEYTM-----STTQDYPS--------IGQLAQKLAENNINPI 294

Query: 113 --VVKESRYYTDDPSQACIFILAIDTLDRDPLSSNYV 147
             V K+      + S   I   ++  L  D  SSN V
Sbjct: 295 FAVTKKQVSLYKELSAL-IPGSSVGELSED--SSNVV 328


>gnl|CDD|202335 pfam02662, FlpD, Methyl-viologen-reducing hydrogenase, delta
           subunit.  This family consist of
           methyl-viologen-reducing hydrogenase, delta subunit /
           heterodisulphide reductase. No specific functions have
           been assigned to this subunit. The aligned region
           corresponds to almost the entire delta chain sequence
           and contains 4 conserved cysteine residues. However, in
           two Archaeoglobus sequences this region corresponds to
           only the C-terminus of these proteins.
          Length = 124

 Score = 27.9 bits (63), Expect = 3.5
 Identities = 10/19 (52%), Positives = 10/19 (52%)

Query: 260 LYHLHNGADMVLVTTCKHG 278
           L  L  GAD VLV  C  G
Sbjct: 46  LKALEKGADGVLVLGCHPG 64


  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
   0.321    0.139    0.436 

Gapped
Lambda     K      H
   0.267   0.0724    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,529,219
Number of extensions: 1485812
Number of successful extensions: 1261
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1257
Number of HSP's successfully gapped: 14
Length of query: 297
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 201
Effective length of database: 6,679,618
Effective search space: 1342603218
Effective search space used: 1342603218
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: 59 (26.5 bits)