RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4875
         (100 letters)



>gnl|CDD|238076 cd00131, PAX, Paired Box domain.
          Length = 128

 Score =  114 bits (286), Expect = 3e-34
 Identities = 48/61 (78%), Positives = 51/61 (83%)

Query: 13  RYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIP 72
           RYYETGSIRP AIGGSKPRVAT EVV KI  YK+E P +FAWEIRDRLLQEGVC   N+P
Sbjct: 56  RYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVP 115

Query: 73  S 73
           S
Sbjct: 116 S 116


>gnl|CDD|109353 pfam00292, PAX, 'Paired box' domain. 
          Length = 125

 Score =  112 bits (283), Expect = 6e-34
 Identities = 48/61 (78%), Positives = 51/61 (83%)

Query: 13  RYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIP 72
           RY ETGSIRP  IGGSKP+VAT EVV KI+ YKRE P IFAWEIRDRLL EGVC NDN+P
Sbjct: 56  RYQETGSIRPGVIGGSKPKVATPEVVKKIAEYKRENPGIFAWEIRDRLLAEGVCDNDNVP 115

Query: 73  S 73
           S
Sbjct: 116 S 116


>gnl|CDD|128645 smart00351, PAX, Paired Box domain. 
          Length = 125

 Score =  110 bits (277), Expect = 6e-33
 Identities = 47/62 (75%), Positives = 52/62 (83%)

Query: 13  RYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIP 72
           RYYETGSIRP AIGGSKP+VAT +VV KI+ YK+E P IFAWEIRDRLL EGVC  DN+P
Sbjct: 56  RYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVCDKDNVP 115

Query: 73  SR 74
           S 
Sbjct: 116 SV 117


>gnl|CDD|132511 TIGR03471, HpnJ, hopanoid biosynthesis associated radical SAM
           protein HpnJ.  The sequences represented by this model
           are members of the radical SAM superfamily of enzymes
           (pfam04055). These enzymes utilize an iron-sulfur redox
           cluster and S-adenosylmethionine to carry out diverse
           radical mediated reactions. The member of this clade
           from Acidithiobacillus ferrooxidans ATCC 23270
           (AFE_0975) is found in the same locus as squalene-hopene
           cyclase (SHC, TIGR01507) and other genes associated with
           the biosynthesis of hopanoid natural products.
           Similarly, in Ralstonia eutropha JMP134 (Reut_B4901)
           this gene is adjacent to HpnAB, IspH and HpnH
           (TIGR03470), although SHC itself is elsewhere in the
           genome. Notably, this gene (here named HpnJ) and three
           others form a conserved set (HpnIJKL) which occur in a
           subset of all genomes containing the SHC enzyme. This
           relationship was discerned using the method of partial
           phylogenetic profiling. This group includes Zymomonas
           mobilis, the organism where the initial hopanoid
           biosynthesis locus was described consisting of the genes
           HpnA-E and SHC (HpnF). Continuing past SHC are found a
           phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and
           another radical SAM enzyme (ZMO0874), HpnH. Although
           discontinuous in Z. mobilis, we continue the gene symbol
           sequence with HpnIJKL. One of the well-described
           hopanoid intermediates is bacteriohopanetetrol. In the
           conversion from hopene several reactions must occur in
           the side chain for which a radical mechanism might be
           reasonable. These include the four (presumably
           anaerobic) hydroxylations and a methyl shift.
          Length = 472

 Score = 26.2 bits (58), Expect = 3.1
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 18/55 (32%)

Query: 11  VHRYYETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGV 65
           V R+Y+    RP+ IG          +V ++         +F W++  R L+EGV
Sbjct: 425 VERFYKRFYFRPKKIG---------RIVREM---------LFDWDMMKRRLREGV 461


>gnl|CDD|167141 PRK01021, lpxB, lipid-A-disaccharide synthase; Reviewed.
          Length = 608

 Score = 25.5 bits (56), Expect = 5.2
 Identities = 10/15 (66%), Positives = 11/15 (73%), Gaps = 2/15 (13%)

Query: 40  KISHYKRECPSIFAW 54
           KI HY   CPSI+AW
Sbjct: 338 KIVHYV--CPSIWAW 350


>gnl|CDD|213908 TIGR04295, B12_rSAM_oligo, B12-binding domain/radical SAM domain
           protein, rhizo-twelve system.  A variety of bacteria,
           including multiple species of Bradyrhizobium,
           Mesorhizobium, and Methylobacterium, have a typically
           twelve-gene cassette (hence the designation
           rhizo-twelve) for the biosynthesis of some unknown
           oligosaccaride. This family is a B12-binding
           domain/radical SAM domain protein found in roughly have
           of these cassettes, but nowhere else.
          Length = 422

 Score = 25.5 bits (56), Expect = 5.9
 Identities = 20/85 (23%), Positives = 34/85 (40%), Gaps = 15/85 (17%)

Query: 16  ETGSIRPRAIGGSKPRVATAEVVSKISHYKRECPSIFAWEIRDRLLQEGVCSNDNIPSRE 75
           E+ +   R +     R++T E+   + H KR  P + A      L+          P  +
Sbjct: 302 ESITEEGRELLAKNCRMSTEELTELLIHAKRSVPFVQA-----NLID--------SPKDD 348

Query: 76  CPSIFAWEIRDRLLQEGVCSNDNIP 100
              +  W  R RL   GV +N+ +P
Sbjct: 349 PAEVARW--RQRLQGHGVWANEPVP 371


>gnl|CDD|220622 pfam10185, Mesd, Chaperone for wingless signalling and trafficking
           of LDL receptor.  Mesd is a family of highly conserved
           proteins found from nematodes to humans. The final
           C-terminal residues, KEDL, are the endoplasmic reticulum
           retention sequence as it is an ER protein specifically
           required for the intracellular trafficking of members of
           the low-density lipoprotein family of receptors (LDLRs).
           The N- and C-terminal sequences are predicted to adopt a
           random coil conformation, with the exception of an
           isolated predicted helix within the N-terminal region,
           The central folded domain flanked by natively
           unstructured regions is the necessary structure for
           facilitating maturation of LRP6 (Low-Density Lipoprotein
           Receptor-Related Protein 6 Maturation).
          Length = 156

 Score = 24.8 bits (54), Expect = 7.4
 Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 3/40 (7%)

Query: 52  FAWEIRDRLLQEGVCSNDNIPSRECPSI---FAWEIRDRL 88
            AWE +D L+ +  C+   I  +E P      A   +D L
Sbjct: 117 QAWEAKDFLVSQERCAEVTIEGQEYPGKADARAGSGKDEL 156


>gnl|CDD|220277 pfam09521, RE_NgoPII, NgoPII restriction endonuclease.  This family
           includes the NgoPII (recognises and cleaves GG^CC)
           restriction endonuclease.
          Length = 263

 Score = 24.8 bits (54), Expect = 8.4
 Identities = 6/33 (18%), Positives = 14/33 (42%)

Query: 67  SNDNIPSRECPSIFAWEIRDRLLQEGVCSNDNI 99
            +D++ +  C +   WE +D +   G      +
Sbjct: 108 VSDSMITDACKNCEKWEEKDIIYAIGTVPKRKL 140


  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
   0.323    0.139    0.444 

Gapped
Lambda     K      H
   0.267   0.0723    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,103,461
Number of extensions: 411994
Number of successful extensions: 289
Number of sequences better than 10.0: 1
Number of HSP's gapped: 289
Number of HSP's successfully gapped: 19
Length of query: 100
Length of database: 10,937,602
Length adjustment: 66
Effective length of query: 34
Effective length of database: 8,010,238
Effective search space: 272348092
Effective search space used: 272348092
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 (21.9 bits)
S2: 53 (24.2 bits)