RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12389
         (104 letters)



>gnl|CDD|216146 pfam00843, Arena_nucleocap, Arenavirus nucleocapsid protein. 
          Length = 533

 Score = 31.2 bits (71), Expect = 0.063
 Identities = 22/61 (36%), Positives = 30/61 (49%), Gaps = 14/61 (22%)

Query: 55  TRKEPADSDLPLSKVSAPHPIINIVTQPQS--------YSISGSLDPGAPPQDG----ET 102
           T K P  SDL   K++  HP + I+TQ +S         S+S ++  GA   DG    ET
Sbjct: 203 TVKYPNLSDL--EKLTQKHPCLKIITQEESQINISGYNLSLSAAVKAGACLLDGGNMLET 260

Query: 103 I 103
           I
Sbjct: 261 I 261


>gnl|CDD|129349 TIGR00246, tRNA_RlmH_YbeA, rRNA large subunit m3Psi
           methyltransferase RlmH.  This protein, in the SPOUT
           methyltransferase family, previously designated YbeA in
           E. coli, was shown to be responsible for a further
           modification, a methylation, to a pseudouridine base in
           ribosomal large subunit RNA [Protein synthesis, tRNA and
           rRNA base modification].
          Length = 153

 Score = 27.2 bits (60), Expect = 1.2
 Identities = 10/32 (31%), Positives = 17/32 (53%)

Query: 54  DTRKEPADSDLPLSKVSAPHPIINIVTQPQSY 85
            T K  A+    LSK++ PHP++ ++     Y
Sbjct: 109 PTCKAAAEQSWSLSKLTLPHPLVRVIVAESLY 140


>gnl|CDD|224126 COG1205, COG1205, Distinct helicase family with a unique C-terminal
           domain including a metal-binding cysteine cluster
           [General function prediction only].
          Length = 851

 Score = 26.6 bits (59), Expect = 2.4
 Identities = 5/29 (17%), Positives = 8/29 (27%)

Query: 13  LHIRTAQIYRWWADENPETEMSSLWSQGW 41
           L I    +    A   P   + S   +  
Sbjct: 376 LGIDIGSLDAVIAYGYPGVSVLSFRQRAG 404


>gnl|CDD|220096 pfam09052, SipA, Salmonella invasion protein A.  Salmonella
           invasion protein A is an actin-binding protein that
           contributes to host cytoskeletal rearrangements by
           stimulating actin polymerisation and counteracting
           F-actin destabilising proteins. Members of this family
           possess an all-helical fold consisting of eight
           alpha-helices arranged so that six long, amphipathic
           helices form a compact fold that surrounds a final,
           predominantly hydrophobic helix in the middle of the
           molecule.
          Length = 674

 Score = 26.9 bits (59), Expect = 2.5
 Identities = 11/31 (35%), Positives = 17/31 (54%)

Query: 65  PLSKVSAPHPIINIVTQPQSYSISGSLDPGA 95
           P S  +  H ++  VT    +SISG++D  A
Sbjct: 366 PASPAAGQHALVQKVTSVLPHSISGTVDTFA 396


>gnl|CDD|223066 PHA03379, PHA03379, EBNA-3A; Provisional.
          Length = 935

 Score = 26.6 bits (58), Expect = 3.4
 Identities = 11/24 (45%), Positives = 13/24 (54%)

Query: 17  TAQIYRWWADENPETEMSSLWSQG 40
           T  I   W DENP TE +  W+ G
Sbjct: 300 TTSIQTPWLDENPSTETAQAWNAG 323


>gnl|CDD|235952 PRK07187, PRK07187, ribonucleotide-diphosphate reductase subunit
           alpha; Validated.
          Length = 721

 Score = 25.4 bits (56), Expect = 6.0
 Identities = 10/23 (43%), Positives = 14/23 (60%), Gaps = 3/23 (13%)

Query: 72  PHPIINIVTQPQSY---SISGSL 91
           P PII+IV   Q +   +IS +L
Sbjct: 641 PKPIIDIVAAAQKHVDQAISLTL 663


>gnl|CDD|180341 PRK05990, PRK05990, precorrin-2 C(20)-methyltransferase; Reviewed.
          Length = 241

 Score = 25.3 bits (56), Expect = 6.4
 Identities = 14/45 (31%), Positives = 16/45 (35%), Gaps = 16/45 (35%)

Query: 10  MHTLHIRTAQIYRWWADENPETE-------MSSLWSQGWCPLLQG 47
           M+ LH R A  Y        ETE       M   WS    PL+  
Sbjct: 116 MY-LHDRLAPRY--------ETEVIPGVCSMLGCWSVLGAPLVYR 151


>gnl|CDD|215187 PLN02328, PLN02328, lysine-specific histone demethylase 1
          homolog.
          Length = 808

 Score = 25.3 bits (55), Expect = 7.2
 Identities = 15/74 (20%), Positives = 23/74 (31%), Gaps = 7/74 (9%)

Query: 26 DENPETEMSSLWSQGWCPLLQGIARLCCDTRKEPADSDLPLSKVSAPHPIINIVTQPQSY 85
            +PET++S   SQ    +         D +  P           +P P    +  P S 
Sbjct: 22 ASSPETDLSLSPSQSEQNIEN-------DGQNSPETQSPLTELQPSPLPPNTTLDAPVSD 74

Query: 86 SISGSLDPGAPPQD 99
          S          PQ+
Sbjct: 75 SQGDESSSEQQPQN 88


>gnl|CDD|238570 cd01164, FruK_PfkB_like, 1-phosphofructokinase (FruK), minor
           6-phosphofructokinase (pfkB) and related sugar kinases.
           FruK plays an important role in the predominant pathway
           for fructose utilisation.This group also contains
           tagatose-6-phophate kinase, an enzyme of the tagatose
           6-phosphate pathway, which responsible for breakdown of
           the galactose moiety during lactose metabolism by
           bacteria such as L. lactis.
          Length = 289

 Score = 24.8 bits (55), Expect = 9.3
 Identities = 8/18 (44%), Positives = 10/18 (55%)

Query: 87  ISGSLDPGAPPQDGETIV 104
           +SGSL PG P      +V
Sbjct: 134 LSGSLPPGVPADFYAELV 151


  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
   0.318    0.134    0.436 

Gapped
Lambda     K      H
   0.267   0.0548    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,213,279
Number of extensions: 408951
Number of successful extensions: 269
Number of sequences better than 10.0: 1
Number of HSP's gapped: 269
Number of HSP's successfully gapped: 10
Length of query: 104
Length of database: 10,937,602
Length adjustment: 69
Effective length of query: 35
Effective length of database: 7,877,176
Effective search space: 275701160
Effective search space used: 275701160
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 (21.7 bits)
S2: 53 (24.6 bits)