RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780292|ref|YP_003064705.1| 50S ribosomal protein L13
[Candidatus Liberibacter asiaticus str. psy62]
         (155 letters)



>gnl|CDD|181703 PRK09216, rplM, 50S ribosomal protein L13; Reviewed.
          Length = 144

 Score =  234 bits (601), Expect = 5e-63
 Identities = 73/143 (51%), Positives = 101/143 (70%), Gaps = 1/143 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           TF  K +EVE+KW ++DA+G ++GRLAS++A  LRGK+KPT+TP  D GD V++INA KV
Sbjct: 3   TFSAKPAEVERKWYVIDAEGKVLGRLASEVASILRGKHKPTFTPHVDTGDFVIVINAEKV 62

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
             +GKK   K YYRH+GYPGG+K+ T  E+LA   P  +++KA+  MLP+ PL R   K 
Sbjct: 63  KLTGKKLTDKIYYRHSGYPGGLKEITFGELLA-KKPERVIEKAVKGMLPKNPLGRAMFKK 121

Query: 124 LHIYAEDHHPHEAQKPVFMDIAK 146
           L +YA   HPH AQ+P  ++I +
Sbjct: 122 LKVYAGAEHPHAAQQPEVLEIKQ 144


>gnl|CDD|162186 TIGR01066, rplM_bact, ribosomal protein L13, bacterial type.  This
           model distinguishes ribosomal protein L13 of bacteria
           and organelles from its eukarytotic and archaeal
           counterparts.
          Length = 140

 Score =  189 bits (481), Expect = 4e-49
 Identities = 74/141 (52%), Positives = 100/141 (70%), Gaps = 1/141 (0%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           T  + S + ++KW +VDA G  +GRLAS++A  LRGK+KPTYTP  D GD+V++INA KV
Sbjct: 1   TLAKASDDKKRKWYVVDAAGKTLGRLASEVARLLRGKHKPTYTPHVDCGDYVIVINAEKV 60

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
             +GKK +QK YYRH+GYPGG+K  T +E++A   P  +L+ A+  MLP+  L RK  K 
Sbjct: 61  RLTGKKLEQKVYYRHSGYPGGLKSRTFEEMIA-RKPERVLEHAVKGMLPKNRLGRKLFKK 119

Query: 124 LHIYAEDHHPHEAQKPVFMDI 144
           L +YA   HPHEAQKP+ +DI
Sbjct: 120 LKVYAGSEHPHEAQKPIVLDI 140


>gnl|CDD|177795 PLN00205, PLN00205, ribisomal protein L13 family protein;
           Provisional.
          Length = 191

 Score =  121 bits (305), Expect = 9e-29
 Identities = 53/119 (44%), Positives = 80/119 (67%), Gaps = 1/119 (0%)

Query: 15  KWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKT 74
           +W + DAKG ++GRLASQI+  L+GK+KPTY P+ DDGD  +++NA  ++ +G+K   K 
Sbjct: 16  RWRVFDAKGQVLGRLASQISTVLQGKDKPTYAPNRDDGDICIVLNAKDISVTGRKLTDKF 75

Query: 75  YYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHP 133
           Y  HTGY G +K+ + K+ +A   PT +++KA+ RMLPR  L   + + L I+A   HP
Sbjct: 76  YRWHTGYIGHLKERSLKDQMA-KDPTEVIRKAVLRMLPRNRLRDDRDRKLRIFAGSEHP 133


>gnl|CDD|180552 PRK06394, rpl13p, 50S ribosomal protein L13P; Reviewed.
          Length = 146

 Score = 59.5 bits (145), Expect = 3e-10
 Identities = 38/124 (30%), Positives = 56/124 (45%), Gaps = 29/124 (23%)

Query: 13  EKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSG----- 67
            +  +++DA+G I+GRLAS +A RL             +G+ VVI+NA K   +G     
Sbjct: 1   FEAMVVIDAEGQILGRLASYVAKRLL------------EGEEVVIVNAEKAVITGNRERV 48

Query: 68  -KKYDQKTYYRHTGYP--GGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKN 123
            +KY Q+        P   G K            P  I K+ I  MLP + P  R+ +K 
Sbjct: 49  IEKYKQRRERGSHYNPYRNGPKYPR--------RPDRIFKRTIRGMLPYKKPRGREALKR 100

Query: 124 LHIY 127
           L +Y
Sbjct: 101 LKVY 104


>gnl|CDD|162192 TIGR01077, L13_A_E, ribosomal protein L13, archaeal/eukaryotic.
           This model represents ribosomal protein of L13 from the
           Archaea and from the eukaryotic cytosol. Bacterial and
           organellar forms are represented by TIGR01066.
          Length = 142

 Score = 49.7 bits (119), Expect = 3e-07
 Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 16/129 (12%)

Query: 17  ILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYY 76
            ++D  G I+GRLAS +A +L             +G+ VV++NA K+  SG  Y  K  Y
Sbjct: 1   TVIDGSGHILGRLASVVAKQLL------------NGEKVVVVNAEKIVISGNFYRNKLKY 48

Query: 77  RHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLP-RGPLARKQMKNLHIYAEDHHPHE 135
           +             +      +P+ I ++ +  MLP +    R  ++ L +Y     P E
Sbjct: 49  KEF-LRKRTLTNPRRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVY--VGIPPE 105

Query: 136 AQKPVFMDI 144
             K   + +
Sbjct: 106 LDKKKRVVV 114


>gnl|CDD|185423 PTZ00068, PTZ00068, 60S ribosomal protein L13a; Provisional.
          Length = 202

 Score = 34.6 bits (80), Expect = 0.010
 Identities = 31/117 (26%), Positives = 50/117 (42%), Gaps = 25/117 (21%)

Query: 14  KKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQK 73
           KK I++D KG ++GRLAS +A  L              G  +V++    +  SG  +  K
Sbjct: 3   KKVIVIDCKGHLLGRLASVVAKELL------------LGQKIVVVRCEDLNISGSLFRNK 50

Query: 74  TYYRHTGYPGGIKKTTAKEILAGA----SPTNILKKAIARMLP----RGPLARKQMK 122
             Y        ++K        G     +P++I  + +  MLP    RG  A K++K
Sbjct: 51  VKYEEF-----LRKRMNTNPRRGPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLK 102


>gnl|CDD|178796 PRK00016, PRK00016, metal-binding heat shock protein; Provisional.
          Length = 159

 Score = 29.8 bits (68), Expect = 0.27
 Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 20/64 (31%)

Query: 35  LRLRGKNKPT---------YTPSADD--------GDHVVIINASKVAFSGKKYDQKTYYR 77
           L  RGK+KPT              DD        GD  ++I         ++    +  R
Sbjct: 55  LEYRGKDKPTDVLSFPMDELPLLEDDGEEGPAYLGD--IVICPEVAEEQAEEQ-GHSLER 111

Query: 78  HTGY 81
              +
Sbjct: 112 ELAH 115


>gnl|CDD|162131 TIGR00956, 3a01205, Pleiotropic Drug Resistance (PDR) Family
           protein. 
          Length = 1394

 Score = 28.9 bits (65), Expect = 0.58
 Identities = 24/114 (21%), Positives = 43/114 (37%), Gaps = 13/114 (11%)

Query: 53  DHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPT-NILKKAIARML 111
           D V+++      + G     K Y+   G+    ++TTA  + +  SP    +K    + +
Sbjct: 279 DKVIVLYEGYQIYFGPADKAKQYFEKMGFKCPDRQTTADFLTSLTSPAERQIKPGYEKKV 338

Query: 112 PRGPLARKQM-KNLHIYAE---------DHHPHEAQKPVFMDIAKMNPKNSRRT 155
           PR P   +   +N   YA+         D       K  + +      K S+RT
Sbjct: 339 PRTPQEFETYWRNSPEYAQLMKEIDEYLDRCSESDTKEAYRE--SHVAKQSKRT 390


>gnl|CDD|177788 PLN00194, PLN00194, aldose 1-epimerase; Provisional.
          Length = 337

 Score = 27.0 bits (60), Expect = 2.4
 Identities = 24/89 (26%), Positives = 36/89 (40%), Gaps = 19/89 (21%)

Query: 23  GLIVGRLASQIA---LRLRGKNKPTYTPSADDGD---HVVIINASKVAFSGKKYDQK--- 73
           G IVGR+A++I      L G    TY    ++G    H      SKV +   KY +    
Sbjct: 63  GAIVGRVANRIKGAKFTLNGV---TYKLPPNNGPNSLHGGPKGFSKVVWEVAKYKKGEKP 119

Query: 74  ----TYYRH---TGYPGGIKKTTAKEILA 95
                Y+      G+PG +  T    +L+
Sbjct: 120 SITFKYHSFDGEEGFPGDLSVTVTYTLLS 148


>gnl|CDD|178689 PLN03144, PLN03144, Carbon catabolite repressor protein 4 homolog;
           Provisional.
          Length = 606

 Score = 26.6 bits (59), Expect = 3.0
 Identities = 11/24 (45%), Positives = 15/24 (62%), Gaps = 5/24 (20%)

Query: 44  TYTPSADDGDHV-----VIINASK 62
           TYTP+ADD  HV     V+++A  
Sbjct: 182 TYTPTADDVGHVLKFECVVVDAET 205


>gnl|CDD|185632 PTZ00453, PTZ00453, cyclin-dependent kinase; Provisional.
          Length = 96

 Score = 26.1 bits (57), Expect = 3.8
 Identities = 17/70 (24%), Positives = 25/70 (35%), Gaps = 22/70 (31%)

Query: 47  PSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKA 106
               +   ++    SK+ +S K YD +  YRH                       IL K 
Sbjct: 12  NGQREALIMISKLQSKILYSDKYYDDEYEYRHV----------------------ILPKD 49

Query: 107 IARMLPRGPL 116
            AR++PR  L
Sbjct: 50  FARLVPRSRL 59


>gnl|CDD|182731 PRK10788, PRK10788, periplasmic folding chaperone; Provisional.
          Length = 623

 Score = 26.1 bits (58), Expect = 4.4
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 34  ALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           AL L  K+KP+Y  + D   +VV+I   +V
Sbjct: 549 ALPLPAKDKPSYGMAQDMQGNVVLIALDEV 578


>gnl|CDD|114555 pfam05834, Lycopene_cycl, Lycopene cyclase protein.  This family
           consists of lycopene beta and epsilon cyclase proteins.
           Carotenoids with cyclic end groups are essential
           components of the photosynthetic membranes in all
           plants, algae, and cyanobacteria. These lipid-soluble
           compounds protect against photo-oxidation, harvest light
           for photosynthesis, and dissipate excess light energy
           absorbed by the antenna pigments. The cyclisation of
           lycopene (psi, psi-carotene) is a key branch point in
           the pathway of carotenoid biosynthesis. Two types of
           cyclic end groups are found in higher plant carotenoids:
           the beta and epsilon rings. Carotenoids with two beta
           rings are ubiquitous, and those with one beta and one
           epsilon ring are common; however, carotenoids with two
           epsilon rings are rare.
          Length = 374

 Score = 25.3 bits (56), Expect = 6.8
 Identities = 7/14 (50%), Positives = 9/14 (64%)

Query: 130 DHHPHEAQKPVFMD 143
           D+ PH+   PV MD
Sbjct: 161 DNPPHDPDVPVIMD 174


>gnl|CDD|130850 TIGR01790, carotene-cycl, lycopene cyclase family protein.  This
           family includes lycopene beta and epsilion cyclases
           (which form beta and delta carotene, respectively) from
           bacteria and plants as well as the plant
           capsanthin/capsorubin and neoxanthin cyclases which
           appear to have evolved from the plant lycopene cyclases.
           The plant lycopene epsilon cyclases also transform
           neurosporene to alpha zeacarotene.
          Length = 388

 Score = 25.5 bits (56), Expect = 7.0
 Identities = 5/14 (35%), Positives = 5/14 (35%)

Query: 130 DHHPHEAQKPVFMD 143
              PH     V MD
Sbjct: 165 SRPPHGPSSMVIMD 178


>gnl|CDD|180885 PRK07208, PRK07208, hypothetical protein; Provisional.
          Length = 479

 Score = 25.2 bits (56), Expect = 7.1
 Identities = 18/38 (47%), Positives = 20/38 (52%), Gaps = 5/38 (13%)

Query: 5  FFQKSSEVEKKW--ILVDAKGLIVGRLASQIALRLRGK 40
          FF KS EV   W  IL D   L+  RL S+I    RGK
Sbjct: 60 FFSKSPEVMDLWNEILPDDDFLLRPRL-SRI--YYRGK 94


>gnl|CDD|166612 PLN02971, PLN02971, tryptophan N-hydroxylase.
          Length = 543

 Score = 25.0 bits (54), Expect = 8.0
 Identities = 12/40 (30%), Positives = 24/40 (60%), Gaps = 2/40 (5%)

Query: 87  KTTAKEILAGA--SPTNILKKAIARMLPRGPLARKQMKNL 124
           K T KE++  A  +P+N ++ A+A M+ +  +  K M+ +
Sbjct: 329 KPTIKELVMAAPDNPSNAVEWAMAEMINKPEILHKAMEEI 368


>gnl|CDD|178437 PLN02844, PLN02844, oxidoreductase/ferric-chelate reductase.
          Length = 722

 Score = 24.8 bits (54), Expect = 8.9
 Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 11/57 (19%)

Query: 97  ASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMNPKNSR 153
            S    +K     M  RGP+            E+H  H   +P F DI    PK +R
Sbjct: 627 VSQKQGIKPEEGSMEKRGPVL-----------EEHEIHFGGRPNFQDIFSKFPKETR 672


>gnl|CDD|163145 TIGR03124, ctirate_citX, holo-ACP synthase CitX.  Members of this
           protein family are the CitX protein, or CitX domain of
           the CitXG bifunctional protein, of the citrate lyase
           system. CitX transfers the prosthetic group
           2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the
           citrate lyase gamma chain, an acyl carrier protein. This
           enzyme may be designated holo-ACP synthase, holo-citrate
           lyase synthase, or apo-citrate lyase
           phosphoribosyl-dephospho-CoA transferase. In a few
           genera, including Haemophilus, this protein occurs as a
           fusion protein with CitG (2.7.8.25), an enzyme involved
           in prosthetic group biosynthesis. This CitX family is
           easily separated from the holo-ACP synthases of other
           enzyme systems.
          Length = 165

 Score = 24.9 bits (55), Expect = 9.3
 Identities = 16/70 (22%), Positives = 21/70 (30%), Gaps = 17/70 (24%)

Query: 81  YPGGIKKTTA---------KEILAGASPTNI-LKKAIARMLPRGP-------LARKQMKN 123
            PG IK             K I A  +     +    A     GP           ++K 
Sbjct: 35  IPGPIKNNELLRRVFDIGIKAIEALLAKNGWTILVQQALNEATGPEAFLVVDAPALELKR 94

Query: 124 LHIYAEDHHP 133
           L I  E+ HP
Sbjct: 95  LMIKLEESHP 104


  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
   0.317    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0757    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,581,732
Number of extensions: 155694
Number of successful extensions: 288
Number of sequences better than 10.0: 1
Number of HSP's gapped: 279
Number of HSP's successfully gapped: 24
Length of query: 155
Length of database: 5,994,473
Length adjustment: 85
Effective length of query: 70
Effective length of database: 4,157,793
Effective search space: 291045510
Effective search space used: 291045510
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 (24.1 bits)