RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6045
         (105 letters)



>gnl|CDD|240296 PTZ00157, PTZ00157, 60S ribosomal protein L36a; Provisional.
          Length = 84

 Score = 97.6 bits (243), Expect = 3e-28
 Identities = 60/83 (72%), Positives = 70/83 (84%)

Query: 4  VNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
          VNVPK R+T+CKKC  H  HKV+QYKK KE    QG+RRYDRKQ+GYGGQTKPIFRKKAK
Sbjct: 2  VNVPKNRKTYCKKCGKHTSHKVSQYKKGKESLFAQGKRRYDRKQSGYGGQTKPIFRKKAK 61

Query: 64 TTKKIVLRMECTECKYRKQLPLK 86
          TTKKIVL++ECT+CK ++Q  LK
Sbjct: 62 TTKKIVLKLECTKCKSKRQKVLK 84


>gnl|CDD|144512 pfam00935, Ribosomal_L44, Ribosomal protein L44. 
          Length = 77

 Score = 89.2 bits (222), Expect = 4e-25
 Identities = 51/76 (67%), Positives = 54/76 (71%)

Query: 20 HKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTTKKIVLRMECTECKY 79
          H  HKV QYKK K     QG+RRYDRKQ GYGGQTKP+  KKAK TKKIVLR+ CTECK 
Sbjct: 2  HTEHKVEQYKKGKASLLAQGKRRYDRKQKGYGGQTKPVPGKKAKPTKKIVLRLRCTECKK 61

Query: 80 RKQLPLKRCKHFELGG 95
            Q P KRCK FEL  
Sbjct: 62 AHQRPGKRCKKFELVE 77


>gnl|CDD|224546 COG1631, RPL42A, Ribosomal protein L44E [Translation, ribosomal
          structure and biogenesis].
          Length = 94

 Score = 87.5 bits (217), Expect = 3e-24
 Identities = 47/93 (50%), Positives = 61/93 (65%), Gaps = 1/93 (1%)

Query: 4  VNVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAK 63
          + +PK+RRT+C  CK H +HKV + KK K  +   G+RRY RKQ+GYGGQ +P+ + KAK
Sbjct: 1  MKIPKKRRTYCPYCKKHTIHKVERVKKGKASELAWGQRRYRRKQSGYGGQPRPVPKGKAK 60

Query: 64 TTKKIVLRMECTECKYRKQL-PLKRCKHFELGG 95
           TKK+ LR+ CTEC    Q  P  R K FEL  
Sbjct: 61 PTKKVDLRLRCTECGKAHQRTPGFRAKRFELVE 93


>gnl|CDD|180247 PRK05767, rpl44e, 50S ribosomal protein L44e; Validated.
          Length = 92

 Score = 66.9 bits (164), Expect = 4e-16
 Identities = 39/89 (43%), Positives = 50/89 (56%), Gaps = 1/89 (1%)

Query: 5  NVPKQRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKT 64
           +PK+ RT+C  CK H  H+V + KK K  +   G+R+Y RK  GYGG+  P+    AK 
Sbjct: 2  KMPKKIRTYCPYCKTHTEHEVEKVKKGKRSELKWGQRQYRRKTIGYGGKFSPVP-GGAKP 60

Query: 65 TKKIVLRMECTECKYRKQLPLKRCKHFEL 93
          TKK+ LR  CTEC         R K FEL
Sbjct: 61 TKKVDLRYRCTECGKAHTREGFRAKKFEL 89


>gnl|CDD|180519 PRK06298, PRK06298, type III secretion system protein; Validated.
          Length = 356

 Score = 26.4 bits (58), Expect = 3.6
 Identities = 13/57 (22%), Positives = 25/57 (43%)

Query: 9   QRRTFCKKCKIHKVHKVTQYKKSKERKACQGRRRYDRKQAGYGGQTKPIFRKKAKTT 65
           QR  F K+ K+ K     ++K ++     +GRRR   ++  Y   +  +    A  +
Sbjct: 206 QRHNFAKELKMEKFEVKQEFKDTEGNPEIKGRRRQIAQEIAYEDTSSQVKHASAVVS 262


>gnl|CDD|130194 TIGR01124, ilvA_2Cterm, threonine ammonia-lyase, biosynthetic, long
           form.  This model describes a form of threonine
           ammonia-lyase, a pyridoxal-phosphate dependent enzyme,
           with two copies of the threonine dehydratase C-terminal
           domain (pfam00585). Members with known function
           participate in isoleucine biosynthesis and are inhibited
           by isoleucine. Alternate name: threonine deaminase,
           threonine dehydratase. Forms scoring between the trusted
           and noise cutoff tend to branch with this subgroup of
           threonine ammonia-lyase phylogenetically but have only a
           single copy of the C-terminal domain [Amino acid
           biosynthesis, Pyruvate family].
          Length = 499

 Score = 26.2 bits (58), Expect = 3.7
 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 7/51 (13%)

Query: 4   VNVPKQRRTFCKKCKIHKVHKVTQ--YKKSKERKAC-----QGRRRYDRKQ 47
           V +P+Q  +F K C++     +T+  Y+ +  + A      Q     +R++
Sbjct: 330 VTIPEQPGSFLKFCELLGNRNITEFNYRYADRKDAHIFVGVQLSNPQERQE 380


>gnl|CDD|128930 smart00688, DM7, Domain of unknown function in Drosophila
          CG15332, CG15333 and CG18293. 
          Length = 95

 Score = 24.7 bits (54), Expect = 6.9
 Identities = 7/15 (46%), Positives = 9/15 (60%)

Query: 44 DRKQAGYGGQTKPIF 58
          D  QA + G T P+F
Sbjct: 52 DLIQAQHNGITPPLF 66


  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
   0.322    0.134    0.410 

Gapped
Lambda     K      H
   0.267   0.0650    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,898,719
Number of extensions: 377230
Number of successful extensions: 296
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 27
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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 (22.0 bits)
S2: 53 (24.4 bits)