RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

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



>gnl|CDD|178952 PRK00270, rpsU, 30S ribosomal protein S21; Reviewed.
          Length = 64

 Score = 51.4 bits (124), Expect = 5e-08
 Identities = 28/59 (47%), Positives = 42/59 (71%), Gaps = 1/59 (1%)

Query: 22 VLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRK 79
          V VR+N  +++ALR  K+K++  G+LREL+ R  YEKPS+KR R K+ A +R RK + +
Sbjct: 4  VKVRENESIDKALRRFKRKVEKAGILRELRRREFYEKPSEKRKRKKAAARKRRRKKLAR 62


>gnl|CDD|129141 TIGR00030, S21p, ribosomal protein S21.  This model describes
          bacterial ribosomal protein S21 and most mitochondrial
          and chloroplast equivalents.
          Length = 58

 Score = 43.0 bits (102), Expect = 2e-05
 Identities = 26/55 (47%), Positives = 39/55 (70%), Gaps = 1/55 (1%)

Query: 22 VLVRDNN-VEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRK 75
          V V++   ++ ALR  K+K++ EG+LRELK R +YEKPS++R R +  A +R RK
Sbjct: 3  VKVKEGESIDSALRRFKRKLEKEGILRELKKRRYYEKPSERRRRKEKAAAKRIRK 57


>gnl|CDD|180177 PRK05636, PRK05636, replicative DNA helicase; Provisional.
          Length = 505

 Score = 28.7 bits (64), Expect = 0.33
 Identities = 13/33 (39%), Positives = 20/33 (60%), Gaps = 3/33 (9%)

Query: 2   LVFNAFRGIFSEGREISAVYV---LVRDNNVEQ 31
           L+F A   +FS+ +EI  V V   L R N++E+
Sbjct: 110 LIFQAIIDLFSDNKEIDPVIVAGRLDRTNDLER 142


>gnl|CDD|168661 PRK06753, PRK06753, hypothetical protein; Provisional.
          Length = 373

 Score = 28.5 bits (64), Expect = 0.41
 Identities = 14/33 (42%), Positives = 21/33 (63%), Gaps = 1/33 (3%)

Query: 60  QKRVRLKSEAIRRSRKLMRKIAQREGAPVSRLR 92
           + RV+  ++ I+RSRK+  KIAQ E   +  LR
Sbjct: 318 KIRVKHTAKVIKRSRKI-GKIAQIESKLLVALR 349


>gnl|CDD|162257 TIGR01219, Pmev_kin_ERG8, phosphomevalonate kinase, ERG8-type,
           eukaryotic branch.  This enzyme is part of the
           mevalonate pathway, one of two alternative pathways for
           the biosynthesis of IPP. In an example of nonorthologous
           gene displacement, two different types of
           phosphomevalonate kinase are found - the animal type and
           this ERG8 type. This model represents plant and fungal
           forms of the ERG8 type of phosphomevalonate kinase.
          Length = 454

 Score = 27.2 bits (60), Expect = 0.91
 Identities = 9/26 (34%), Positives = 14/26 (53%)

Query: 68  EAIRRSRKLMRKIAQREGAPVSRLRQ 93
           EA+ R R+LMR+I +     +    Q
Sbjct: 359 EAMLRIRRLMRQITEEASVDIEPESQ 384


>gnl|CDD|150324 pfam09618, Cas_Csy4, CRISPR-associated protein (Cas_Csy4).  CRISPR
           (Clustered Regularly Interspaced Short Palindromic
           Repeats) is a widespread family of prokaryotic direct
           repeats with spacers of unique sequence between
           consecutive repeats. This protein family, typified by
           YPO2462 of Yersinia pestis, is a CRISPR-associated (Cas)
           family strictly associated with the Ypest subtype of
           CRISPR/Cas locus. It is designated Csy4, for CRISPR/Cas
           Subtype Ypest protein 4.
          Length = 182

 Score = 26.0 bits (58), Expect = 2.1
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 61  KRVRLKSEAIRRSRKLMRK 79
            RV+ KS   R  R+LM++
Sbjct: 96  SRVQAKSSPARLRRRLMKR 114


>gnl|CDD|168970 PRK07486, PRK07486, amidase; Provisional.
          Length = 484

 Score = 25.7 bits (57), Expect = 2.5
 Identities = 8/20 (40%), Positives = 11/20 (55%), Gaps = 1/20 (5%)

Query: 51  MRGHYEKPSQKRVRLKSEAI 70
           +   Y  P+ +R  LK EAI
Sbjct: 331 LLALYRDPA-RRALLKPEAI 349


>gnl|CDD|180152 PRK05589, PRK05589, peptide chain release factor 2; Provisional.
          Length = 325

 Score = 25.5 bits (56), Expect = 3.4
 Identities = 14/30 (46%), Positives = 17/30 (56%), Gaps = 6/30 (20%)

Query: 28  NVEQALRVLKKKMQGEGVLRELKMRGHYEK 57
           N E A+++LK K      L ELK R H EK
Sbjct: 242 NKETAMKMLKSK------LVELKERAHKEK 265


>gnl|CDD|184698 PRK14476, PRK14476, nitrogenase molybdenum-cofactor biosynthesis
          protein NifN; Provisional.
          Length = 455

 Score = 25.2 bits (56), Expect = 3.9
 Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 2/26 (7%)

Query: 16 EISAVYVLVRDNNVEQALRVLKKKMQ 41
          E++ +  L  D NVE+A+  + KK +
Sbjct: 69 EVTTI--LGGDENVEEAILNICKKAK 92


>gnl|CDD|151389 pfam10942, DUF2619, Protein of unknown function (DUF2619).  This
          bacterial family of proteins has no known function.
          Length = 69

 Score = 24.5 bits (54), Expect = 6.0
 Identities = 8/26 (30%), Positives = 18/26 (69%)

Query: 10 IFSEGREISAVYVLVRDNNVEQALRV 35
          + S   E++A  ++++ N+VE+AL +
Sbjct: 2  LLSASIELTAALLMLKYNDVEKALAI 27


>gnl|CDD|180641 PRK06635, PRK06635, aspartate kinase; Reviewed.
          Length = 404

 Score = 24.3 bits (54), Expect = 6.6
 Identities = 8/23 (34%), Positives = 14/23 (60%), Gaps = 1/23 (4%)

Query: 16  EISAVYVLVRDNNVEQALRVLKK 38
           EI  + VL+ +  +E A+R L +
Sbjct: 378 EIK-ISVLIDEKYLELAVRALHE 399


>gnl|CDD|182217 PRK10062, PRK10062, hypothetical protein; Provisional.
          Length = 303

 Score = 24.3 bits (53), Expect = 7.3
 Identities = 13/37 (35%), Positives = 20/37 (54%)

Query: 43  EGVLRELKMRGHYEKPSQKRVRLKSEAIRRSRKLMRK 79
           E VL  L+ R H E P+Q++ RL+  A +   K  + 
Sbjct: 104 EKVLHMLEARKHKEDPAQRQQRLEKLAAQDPLKFEKD 140


>gnl|CDD|183991 PRK13352, PRK13352, thiamine biosynthesis protein ThiC;
          Provisional.
          Length = 431

 Score = 24.3 bits (54), Expect = 7.4
 Identities = 5/17 (29%), Positives = 10/17 (58%)

Query: 77 MRKIAQREGAPVSRLRQ 93
          M  +A++EG     +R+
Sbjct: 16 MEYVAKKEGVDPEFIRE 32


>gnl|CDD|151314 pfam10865, DUF2703, Protein of unknown function (DUF2703).  This
          family of protein has no known function.
          Length = 120

 Score = 24.3 bits (53), Expect = 7.8
 Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 1/46 (2%)

Query: 26 DNNVEQALRVLKKKMQGEGVLRELKMRGHYEKPSQKRVRLKSEAIR 71
             +E A+  L++ ++  G+   L+     +     R  L+S  I 
Sbjct: 22 GEALEAAVNELREALEPLGIEVVLEET-ELDPEEFARAPLESNRIW 66


>gnl|CDD|177793 PLN00203, PLN00203, glutamyl-tRNA reductase.
          Length = 519

 Score = 24.3 bits (53), Expect = 7.9
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 71  RRSRKLMRKIAQREGAPVSRLRQHR 95
           R  +++   +++  G PVS LRQH 
Sbjct: 146 RGVKEVTEWMSKTSGIPVSELRQHL 170


>gnl|CDD|148491 pfam06898, YqfD, Putative stage IV sporulation protein YqfD.  This
           family consists of several putative bacterial stage IV
           sporulation (SpoIV) proteins. YqfD of Bacillus subtilis
           is known to be essential for efficient sporulation
           although its exact function is unknown.
          Length = 383

 Score = 23.9 bits (52), Expect = 9.2
 Identities = 8/25 (32%), Positives = 13/25 (52%)

Query: 55  YEKPSQKRVRLKSEAIRRSRKLMRK 79
           YE   +     K EA+ + +KL +K
Sbjct: 319 YEVQDKVVKLTKEEAVEKGKKLAKK 343


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.323    0.136    0.367 

Gapped
Lambda     K      H
   0.267   0.0699    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,561,561
Number of extensions: 89118
Number of successful extensions: 393
Number of sequences better than 10.0: 1
Number of HSP's gapped: 392
Number of HSP's successfully gapped: 54
Length of query: 95
Length of database: 5,994,473
Length adjustment: 63
Effective length of query: 32
Effective length of database: 4,633,169
Effective search space: 148261408
Effective search space used: 148261408
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: 50 (23.1 bits)