RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5946
         (63 letters)



>gnl|CDD|235404 PRK05319, rplD, 50S ribosomal protein L4; Provisional.
          Length = 205

 Score = 28.5 bits (65), Expect = 0.13
 Identities = 13/30 (43%), Positives = 16/30 (53%), Gaps = 2/30 (6%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPK 34
           L L S LS K  +  L +V DL L  + PK
Sbjct: 107 LALRSALSEKAREGRLVVVDDLSL--EAPK 134


>gnl|CDD|182889 PRK10996, PRK10996, thioredoxin 2; Provisional.
          Length = 139

 Score = 28.1 bits (63), Expect = 0.16
 Identities = 22/71 (30%), Positives = 29/71 (40%), Gaps = 17/71 (23%)

Query: 2   SIVLGLTSTLSIKLMQDDLHIVKDLVLPVDDP-----KYLENLVEERCSQV--------- 47
            ++     TL  KL+QDDL +V D   P   P        E++  ER  +V         
Sbjct: 36  EVINATGETLD-KLLQDDLPVVIDFWAPWCGPCRNFAPIFEDVAAERSGKVRFVKVNTEA 94

Query: 48  --SLSARLGIR 56
              LSAR  IR
Sbjct: 95  ERELSARFRIR 105


>gnl|CDD|237734 PRK14500, PRK14500, putative bifunctional molybdopterin-guanine
           dinucleotide biosynthesis protein MoaC/MobA;
           Provisional.
          Length = 346

 Score = 27.2 bits (60), Expect = 0.44
 Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 7/52 (13%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDP--KYLENLVEERCSQVSLSARLG 54
           L LT   S ++ +D     K L+     P  +YL +L+ + C QV LSAR  
Sbjct: 164 LVLTGGKSRRMGKD-----KALLNYQGQPHAQYLYDLLAKYCEQVFLSARPS 210


>gnl|CDD|234414 TIGR03953, rplD_bact, 50S ribosomal protein L4,
           bacterial/organelle.  Members of this protein family are
           ribosomal protein L4. This model recognizes bacterial
           and most organellar forms, but excludes homologs from
           the eukaryotic cytoplasm and from archaea [Protein
           synthesis, Ribosomal proteins: synthesis and
           modification].
          Length = 188

 Score = 27.1 bits (61), Expect = 0.44
 Identities = 20/63 (31%), Positives = 27/63 (42%), Gaps = 17/63 (26%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPK------YLENL---------VEERCSQVSL 49
           L L S LS K  +  L +V D  L  ++PK       L+NL          +E    + L
Sbjct: 92  LALRSALSEKAREGKLVVVDDFDL--EEPKTKDLAKILKNLGLDKKVLIVTDEVDENLYL 149

Query: 50  SAR 52
           SAR
Sbjct: 150 SAR 152


>gnl|CDD|184731 PRK14536, cysS, cysteinyl-tRNA synthetase; Provisional.
          Length = 490

 Score = 27.2 bits (60), Expect = 0.45
 Identities = 8/45 (17%), Positives = 20/45 (44%)

Query: 1   MSIVLGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVEERCS 45
           +S++  + + L + L+Q+    +   V      + +  L+E R  
Sbjct: 410 LSVLQAMDTVLGLGLIQEATASLSAQVPAGPSEEEIGQLIEARAH 454


>gnl|CDD|215999 pfam00573, Ribosomal_L4, Ribosomal protein L4/L1 family.  This
           family includes Ribosomal L4/L1 from eukaryotes and
           archaebacteria and L4 from eubacteria. L4 from yeast has
           been shown to bind rRNA.
          Length = 190

 Score = 26.7 bits (60), Expect = 0.61
 Identities = 12/37 (32%), Positives = 17/37 (45%)

Query: 5   LGLTSTLSIKLMQDDLHIVKDLVLPVDDPKYLENLVE 41
           L L S LS K  +  L +V D  L +   K    L++
Sbjct: 92  LALRSALSAKAREGKLVVVDDFELEIPKTKDAVKLLK 128


>gnl|CDD|203280 pfam05579, Peptidase_S32, Equine arteritis virus serine
           endopeptidase S32.  Serine peptidases involved in
           processing nidovirus polyprotein.
          Length = 425

 Score = 25.1 bits (55), Expect = 2.2
 Identities = 7/22 (31%), Positives = 10/22 (45%)

Query: 6   GLTSTLSIKLMQDDLHIVKDLV 27
            LT+ L+  L  DDL  +    
Sbjct: 368 SLTAALACTLSDDDLDFLSRHT 389


>gnl|CDD|237458 PRK13654, PRK13654, magnesium-protoporphyrin IX monomethyl ester
           cyclase; Provisional.
          Length = 355

 Score = 25.2 bits (56), Expect = 2.3
 Identities = 10/24 (41%), Positives = 15/24 (62%), Gaps = 2/24 (8%)

Query: 26  LVLPVDDPKYLENLVEERCSQVSL 49
           +VL VDDP++   L  ERC + + 
Sbjct: 285 VVLDVDDPRFYARL--ERCVENNE 306


>gnl|CDD|217540 pfam03408, Foamy_virus_ENV, Foamy virus envelope protein.
           Expression of the envelope (Env) glycoprotein is
           essential for viral particle egress. This feature is
           unique to the Spumavirinae, a subclass of the
           Retroviridae.
          Length = 985

 Score = 24.3 bits (53), Expect = 5.1
 Identities = 9/31 (29%), Positives = 17/31 (54%)

Query: 16  MQDDLHIVKDLVLPVDDPKYLENLVEERCSQ 46
           MQ    ++ D  LP+ DP+  +  + ++C Q
Sbjct: 196 MQSLSDVMIDFELPLGDPRDQDQYIHKKCYQ 226


  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    0.138    0.374 

Gapped
Lambda     K      H
   0.267   0.0652    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,106,066
Number of extensions: 219880
Number of successful extensions: 160
Number of sequences better than 10.0: 1
Number of HSP's gapped: 160
Number of HSP's successfully gapped: 9
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
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 (21.7 bits)
S2: 53 (24.4 bits)