RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17868
         (208 letters)



>gnl|CDD|239200 cd02801, DUS_like_FMN, Dihydrouridine synthase-like (DUS-like)
           FMN-binding domain. Members of this family catalyze the
           reduction of the 5,6-double bond of a uridine residue on
           tRNA. Dihydrouridine modification of tRNA is widely
           observed in prokaryotes and eukaryotes, and also in some
           archaea. Most dihydrouridines are found in the D loop of
           t-RNAs. The role of dihydrouridine in tRNA is currently
           unknown, but may increase conformational flexibility of
           the tRNA. It is likely that different family members
           have different substrate specificities, which may
           overlap. 1VHN, a putative flavin oxidoreductase, has
           high sequence similarity to DUS.  The enzymatic
           mechanism of 1VHN is not known at the present.
          Length = 231

 Score = 31.3 bits (72), Expect = 0.24
 Identities = 8/20 (40%), Positives = 8/20 (40%)

Query: 1   MAARGLLKNPGLFSGANRTP 20
           M  RG L NP LF       
Sbjct: 211 MIGRGALGNPWLFREIKELL 230


>gnl|CDD|216365 pfam01207, Dus, Dihydrouridine synthase (Dus).  Members of this
           family catalyze the reduction of the 5,6-double bond of
           a uridine residue on tRNA. Dihydrouridine modification
           of tRNA is widely observed in prokaryotes and
           eukaryotes, and also in some archae. Most
           dihydrouridines are found in the D loop of t-RNAs. The
           role of dihydrouridine in tRNA is currently unknown, but
           may increase conformational flexibility of the tRNA. It
           is likely that different family members have different
           substrate specificities, which may overlap. Dus 1 from
           Saccharomyces cerevisiae acts on pre-tRNA-Phe, while Dus
           2 acts on pre-tRNA-Tyr and pre-tRNA-Leu. Dus 1 is active
           as a single subunit, requiring NADPH or NADH, and is
           stimulated by the presence of FAD. Some family members
           may be targeted to the mitochondria and even have a role
           in mitochondria.
          Length = 309

 Score = 31.1 bits (71), Expect = 0.36
 Identities = 8/26 (30%), Positives = 11/26 (42%)

Query: 1   MAARGLLKNPGLFSGANRTPMSCIEE 26
           M  RG L NP LF+  +       + 
Sbjct: 211 MIGRGALGNPWLFAEQHTVKTGEFDP 236


>gnl|CDD|215165 PLN02292, PLN02292, ferric-chelate reductase.
          Length = 702

 Score = 29.4 bits (66), Expect = 1.6
 Identities = 33/120 (27%), Positives = 51/120 (42%), Gaps = 15/120 (12%)

Query: 35  FMTFLHHLVFMCDKLL---SSQEKDQLNS---LYSGVEILDFIENKFHVQSPCRSHFVNL 88
            ++F    +F+ D+ L    S+   +L S   L      L+F +N   + SP    FVN+
Sbjct: 303 LISFPGFYIFLVDRFLRFLQSRNNVKLVSARVLPCDTVELNFSKNPMLMYSPTSIMFVNI 362

Query: 89  NKGSKYEEE-----SEGKFFQEEMSSVKKQVAKDLMEDILDNCLSSQEKDQLNSLYSGVE 143
              SK +       S  K   E++S + K   K      L + LSS   DQ++ L   VE
Sbjct: 363 PSISKLQWHPFTITSSSKLEPEKLSVMIKSQGK--WSTKLYHMLSSS--DQIDRLAVSVE 418


>gnl|CDD|181392 PRK08332, PRK08332, ribonucleotide-diphosphate reductase subunit
            alpha; Validated.
          Length = 1740

 Score = 28.6 bits (63), Expect = 2.8
 Identities = 20/60 (33%), Positives = 29/60 (48%)

Query: 149  ENKFHVQSSCRSHFVNLNKGSKYEEESEGKFFQEEMSSVKKQVAKDLTEDILDNCFNIYE 208
            E   +   SC    +NL K  KY+E  +  F  +E + V ++VAK L   I  N F + E
Sbjct: 1299 EEPLYEYESCNLASINLAKFVKYDENGKPYFDWDEYAYVIQKVAKYLDNAIDVNKFPLPE 1358


>gnl|CDD|236747 PRK10736, PRK10736, hypothetical protein; Provisional.
          Length = 374

 Score = 27.6 bits (62), Expect = 5.3
 Identities = 8/44 (18%), Positives = 15/44 (34%), Gaps = 7/44 (15%)

Query: 4  RGLLKNPGL-------FSGANRTPMSCIEEWVSMKHNHFMTFLH 40
            +L+  GL       F    R  +     W+   ++H +T   
Sbjct: 36 AVVLQATGLTLRQAQQFLQLPRKSLESTLRWLEQPNHHLLTADS 79


>gnl|CDD|227354 COG5021, HUL4, Ubiquitin-protein ligase [Posttranslational
           modification, protein turnover, chaperones].
          Length = 872

 Score = 27.4 bits (61), Expect = 6.3
 Identities = 14/95 (14%), Positives = 25/95 (26%), Gaps = 5/95 (5%)

Query: 94  YEEESEGKFFQEEMSSVKKQVAKDLMEDILDNCLSSQEKDQLNS-----LYSGVEILDFI 148
              ++       +  SV         E    +   +   ++        L S + I    
Sbjct: 71  DGLQNRDCLRSLDPLSVLSVDGLQTSETSFRSSALNPYVNEFLCENDVRLSSSITIQVSD 130

Query: 149 ENKFHVQSSCRSHFVNLNKGSKYEEESEGKFFQEE 183
           E+K +V     S   NL        E+       E
Sbjct: 131 ESKQNVIEDVFSGLENLGSVDVLSTEATKGIDFLE 165


  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
   0.316    0.132    0.378 

Gapped
Lambda     K      H
   0.267   0.0689    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,020,042
Number of extensions: 887810
Number of successful extensions: 795
Number of sequences better than 10.0: 1
Number of HSP's gapped: 792
Number of HSP's successfully gapped: 24
Length of query: 208
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 115
Effective length of database: 6,812,680
Effective search space: 783458200
Effective search space used: 783458200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 57 (25.8 bits)