RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780437|ref|YP_003064850.1| 30S ribosomal protein S21
[Candidatus Liberibacter asiaticus str. psy62]
         (95 letters)



>gnl|CDD|144672 pfam01165, Ribosomal_S21, Ribosomal protein S21. 
          Length = 57

 Score = 48.7 bits (117), Expect = 3e-07
 Identities = 30/55 (54%), Positives = 40/55 (72%), Gaps = 1/55 (1%)

Query: 22 VLVRDN-NVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRK 75
          V V++N N+E ALR  K+K++  G+LREL+ R  YEKPS+KR R + EA RR RK
Sbjct: 3  VKVKENENIESALRRFKRKVEKNGILRELRRRRFYEKPSEKRKRKRREARRRRRK 57


>gnl|CDD|31170 COG0828, RpsU, Ribosomal protein S21 [Translation, ribosomal
          structure and biogenesis].
          Length = 67

 Score = 41.0 bits (96), Expect = 7e-05
 Identities = 29/63 (46%), Positives = 43/63 (68%)

Query: 22 VLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIA 81
           +  +  +++ALR  K+K++ EG+LRE+K R  YEKPS+KR R K+ A +R  K +RK  
Sbjct: 5  KVRENEPLDKALRRFKRKVEKEGILREMKEREFYEKPSEKRKRKKAAARKRKFKRLRKEQ 64

Query: 82 QRE 84
          QRE
Sbjct: 65 QRE 67


>gnl|CDD|35534 KOG0313, KOG0313, KOG0313, Microtubule binding protein YTM1
           (contains WD40 repeats) [Cytoskeleton].
          Length = 423

 Score = 27.6 bits (61), Expect = 0.81
 Identities = 10/46 (21%), Positives = 18/46 (39%)

Query: 50  KMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR 95
            M   +   + +   L+S + RR +K  R+       P+  L  H 
Sbjct: 215 TMLKIWSVETDEEDELESSSNRRRKKQKREKEGGTRTPLVTLEGHT 260


>gnl|CDD|31883 COG1697, COG1697, DNA topoisomerase VI, subunit A [DNA replication,
           recombination, and repair].
          Length = 356

 Score = 27.2 bits (60), Expect = 1.0
 Identities = 12/47 (25%), Positives = 24/47 (51%)

Query: 43  EGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVS 89
           + V + L   G +EK +   V LK +  R +R+ ++++ +    PV 
Sbjct: 192 DAVFQRLVEEGFWEKENAILVTLKGQPDRATRRFLKRLNEELDLPVY 238


>gnl|CDD|143991 pfam00240, ubiquitin, Ubiquitin family.  This family contains a
          number of ubiquitin-like proteins: SUMO (smt3
          homologue), Nedd8, Elongin B, Rub1, and Parkin. A
          number of them are thought to carry a distinctive
          five-residue motif termed the proteasome-interacting
          motif (PIM), which may have a biologically significant
          role in protein delivery to proteasomes and recruitment
          of proteasomes to transcription sites.
          Length = 69

 Score = 25.3 bits (56), Expect = 3.6
 Identities = 8/19 (42%), Positives = 11/19 (57%)

Query: 74 RKLMRKIAQREGAPVSRLR 92
           +L  KI  +EG PV + R
Sbjct: 19 SELKEKIEDKEGIPVDQQR 37


>gnl|CDD|99995 cd04299, GT1_Glycogen_Phosphorylase_like, This family is most
           closely related to the oligosaccharide phosphorylase
           domain family and other unidentified sequences.
           Oligosaccharide phosphorylase catalyzes the breakdown of
           oligosaccharides into glucose-1-phosphate units. They
           are important allosteric enzymes in carbohydrate
           metabolism. The members of this family are found in
           bacteria and Archaea..
          Length = 778

 Score = 25.2 bits (56), Expect = 3.8
 Identities = 8/34 (23%), Positives = 15/34 (44%)

Query: 62  RVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQHR 95
           R +L+   I   R+ +R+   R GA    + +  
Sbjct: 438 RQQLRRRLIEFVRRRLRRQWLRRGASAEEIGEAD 471


>gnl|CDD|145371 pfam02181, FH2, Formin Homology 2 Domain. 
          Length = 372

 Score = 24.9 bits (55), Expect = 4.6
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 7/59 (11%)

Query: 20  VYVLVRDNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMR 78
           +  L +   +E+ LR L  K   E  + ELK       PS + +   SE +R SRK  +
Sbjct: 150 LLELSKIPRLEERLRALLFKSTFEEEVEELK-------PSLETLEAASEELRESRKFKK 201


>gnl|CDD|36363 KOG1148, KOG1148, KOG1148, Glutaminyl-tRNA synthetase [Translation,
           ribosomal structure and biogenesis].
          Length = 764

 Score = 24.5 bits (53), Expect = 6.6
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 1/44 (2%)

Query: 50  KMRGHYEKPSQKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLRQ 93
           + RG  E+ S  R R   E++R     MR     EG    R++Q
Sbjct: 352 ERRGFNERLSPWRDRPIEESLRLFED-MRDGKYEEGEATLRMKQ 394


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.323    0.136    0.367 

Gapped
Lambda     K      H
   0.267   0.0684    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,070,152
Number of extensions: 47987
Number of successful extensions: 249
Number of sequences better than 10.0: 1
Number of HSP's gapped: 248
Number of HSP's successfully gapped: 24
Length of query: 95
Length of database: 6,263,737
Length adjustment: 63
Effective length of query: 32
Effective length of database: 4,902,370
Effective search space: 156875840
Effective search space used: 156875840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 51 (23.5 bits)