RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780318|ref|YP_003064731.1| ribosomal protein L20
[Candidatus Liberibacter asiaticus str. psy62]
         (123 letters)



>gnl|CDD|179959 PRK05185, rplT, 50S ribosomal protein L20; Provisional.
          Length = 114

 Score =  177 bits (451), Expect = 8e-46
 Identities = 68/113 (60%), Positives = 84/113 (74%)

Query: 3   RVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWI 62
           RVKRGVV+ A+ KK+LK AKG+ G R    R AK AV ++ QYAYRDRR KKRDFR LWI
Sbjct: 2   RVKRGVVARARRKKILKLAKGYRGARSRLYRVAKQAVMKALQYAYRDRRQKKRDFRKLWI 61

Query: 63  QRINAAVRVYDLNYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRS 115
            RINAA R   L+YS+FINGL KAGI +DRKVL+DLA+    +F  +VE +++
Sbjct: 62  ARINAAARQNGLSYSRFINGLKKAGIEIDRKVLADLAVNDPAAFAALVEKAKA 114


>gnl|CDD|130104 TIGR01032, rplT_bact, ribosomal protein L20.  This protein binds
           directly to 23s ribosomal RNA and is necessary for the
           in vitro assembly process of the 50s ribosomal subunit.
           It is not involved in the protein synthesizing functions
           of that subunit. GO process changed accordingly.
          Length = 113

 Score =  134 bits (339), Expect = 6e-33
 Identities = 66/113 (58%), Positives = 83/113 (73%)

Query: 2   TRVKRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLW 61
            RVK GVV+  + KK+LK AKGF G RK   R AK  V ++  YAYRDRR +KRDFRSLW
Sbjct: 1   MRVKGGVVARRRRKKILKQAKGFRGTRKRHYRVAKQTVIKAMAYAYRDRRQRKRDFRSLW 60

Query: 62  IQRINAAVRVYDLNYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSR 114
           I RINAA R + L+YS+FINGL KA I ++RKVLS+LAI   ++F +IVE ++
Sbjct: 61  ITRINAAARQHGLSYSRFINGLKKANIEINRKVLSELAINDPEAFAEIVEQAK 113


>gnl|CDD|185406 PTZ00030, PTZ00030, 60S ribosomal protein L20; Provisional.
          Length = 121

 Score =  108 bits (273), Expect = 3e-25
 Identities = 50/103 (48%), Positives = 71/103 (68%)

Query: 15  KKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDL 74
            KV K AKGF GR KN  + A+  V ++  Y+Y  RR +KR  R  WIQ INAA R +++
Sbjct: 6   DKVFKLAKGFRGRSKNCFKLARNRVMKALLYSYISRRKRKRILRVHWIQTINAATREHNM 65

Query: 75  NYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRSRL 117
            YS+FINGL+ + I L+RK+L++LAIT+  SFK +V+ S+ +L
Sbjct: 66  TYSRFINGLNNSNIQLNRKILANLAITEPFSFKALVDESKYQL 108


>gnl|CDD|173003 PRK14537, PRK14537, 50S ribosomal protein L20/unknown domain fusion
           protein; Provisional.
          Length = 230

 Score = 99.7 bits (248), Expect = 2e-22
 Identities = 51/105 (48%), Positives = 70/105 (66%)

Query: 13  KHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVY 72
           + KKVLK AKG++G +    + A   V RS QYAYRDR+ +KRDFR LWI RINA   + 
Sbjct: 13  RRKKVLKMAKGYFGSKSTLYKTAHEQVMRSLQYAYRDRKQRKRDFRKLWISRINAGAMLC 72

Query: 73  DLNYSQFINGLHKAGIVLDRKVLSDLAITQLDSFKKIVELSRSRL 117
            + YS+ ++GL  A + ++RKVLSDLA  Q + F + VEL++  L
Sbjct: 73  GIKYSRLMHGLALAKVDINRKVLSDLAHLQPEVFVQYVELAKKFL 117


>gnl|CDD|147905 pfam05997, Nop52, Nucleolar protein,Nop52.  Nop52 believed to be
           involved in the generation of 28S rRNA.
          Length = 212

 Score = 26.1 bits (58), Expect = 2.2
 Identities = 21/84 (25%), Positives = 38/84 (45%), Gaps = 13/84 (15%)

Query: 50  RRVKKRDFRSLWIQRINAAVRVYDLNYSQFINGL--HKAGIVLD--RKVLSDLAITQLDS 105
           R +K+  +    ++ +N  +    LN     NGL  H   I LD   KVL   +  ++ +
Sbjct: 119 RLLKENKWDLDLVEELNEILLEKILNPEDDPNGLKYHFIDIFLDELAKVLEGESEDEVSA 178

Query: 106 ---------FKKIVELSRSRLLVD 120
                    F KI++ ++ ++LVD
Sbjct: 179 VQVLLLLEPFLKILKKTKDKVLVD 202


>gnl|CDD|162876 TIGR02478, 6PF1K_euk, 6-phosphofructokinase, eukaryotic type.
           Members of this family are eukaryotic (with one
           exception) ATP-dependent 6-phosphofructokinases (EC
           2.7.1.11) in which two tandem copies of the
           phosphofructokinase are found. Members are found, often
           including several isozymes, in animals and fungi and in
           the bacterium Propionibacterium acnes KPA171202 (a human
           skin commensal).
          Length = 745

 Score = 25.8 bits (57), Expect = 3.1
 Identities = 13/53 (24%), Positives = 25/53 (47%), Gaps = 6/53 (11%)

Query: 26  GRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQRINAAVRVYDLNYSQ 78
           G+RKN +  A+ A+DR          +   D + + ++R+    R+  L + Q
Sbjct: 239 GKRKNIVIVAEGAIDRDLN------PITSEDVKDVLVERLGLDTRITVLGHVQ 285


>gnl|CDD|184717 PRK14508, PRK14508, 4-alpha-glucanotransferase; Provisional.
          Length = 497

 Score = 25.5 bits (57), Expect = 3.6
 Identities = 8/28 (28%), Positives = 17/28 (60%), Gaps = 1/28 (3%)

Query: 47  YRDRRVKKRDFRSLWIQRINAAVRVYDL 74
           Y    ++K  +R  WI+R+  + ++YD+
Sbjct: 267 YNWDALRKDGYRW-WIERLRRSFKLYDI 293


>gnl|CDD|135648 PRK05898, dnaE, DNA polymerase III DnaE; Validated.
          Length = 971

 Score = 25.6 bits (56), Expect = 3.6
 Identities = 9/22 (40%), Positives = 14/22 (63%)

Query: 82  GLHKAGIVLDRKVLSDLAITQL 103
           G H AG+VL   +L+++   QL
Sbjct: 439 GTHAAGVVLSNSLLTNIIPIQL 460


>gnl|CDD|130711 TIGR01650, PD_CobS, cobaltochelatase, CobS subunit.  This model
           describes the aerobic cobalamin pathway Pseudomonas
           denitrificans CobS gene product, which is a cobalt
           chelatase subunit, with a MW ~37 kDa. The aerobic
           pathway cobalt chelatase is a heterotrimeric,
           ATP-dependent enzyme that catalyzes cobalt insertion
           during cobalamin biosynthesis. The other two subunits
           are the P. denitrificans CobT (TIGR01651) and CobN
           (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid
           potential confusion with the nonhomologous Salmonella
           typhimurium/E.coli cobS gene product, the P.
           denitrificans gene symbol is not used in the name of
           this model.
          Length = 327

 Score = 25.4 bits (55), Expect = 4.0
 Identities = 13/31 (41%), Positives = 17/31 (54%), Gaps = 1/31 (3%)

Query: 53  KKRDFRSLWIQR-INAAVRVYDLNYSQFING 82
           K + F     +  INA VRV D+  + FING
Sbjct: 232 KAKGFDDTEGKDIINAMVRVADMTRNAFING 262


>gnl|CDD|163467 TIGR03755, conj_TIGR03755, integrating conjugative element protein,
           PFL_4711 family.  Members of this protein family are
           found in genomic regions associated with conjugative
           transfer and integrated TOL-like plasmids. The specific
           function is unknown.
          Length = 418

 Score = 25.4 bits (56), Expect = 4.2
 Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 6/35 (17%)

Query: 62  IQRINAAVRVYDLNYSQFINGLHKAGIVLDRKVLS 96
           IQR N  +  Y+L      NG+ +A +  DR   +
Sbjct: 82  IQRANPGL--YNL----LTNGVLQARLDFDRSKKT 110


>gnl|CDD|182098 PRK09828, PRK09828, putative fimbrial outer membrane usher protein;
           Provisional.
          Length = 865

 Score = 25.1 bits (55), Expect = 4.8
 Identities = 10/17 (58%), Positives = 12/17 (70%)

Query: 59  SLWIQRINAAVRVYDLN 75
           SLW   INAA+  Y+LN
Sbjct: 168 SLWENGINAAMLSYNLN 184


>gnl|CDD|161866 TIGR00413, rlpA, rare lipoprotein A.  This is a family of
           prokaryotic proteins with unknown function. Lipoprotein
           annotation based on the presence of consensus
           lipoprotein signal sequence. Included in this family is
           the E. coli putative lipoprotein rlpA.
          Length = 208

 Score = 24.6 bits (53), Expect = 6.5
 Identities = 15/76 (19%), Positives = 24/76 (31%)

Query: 5   KRGVVSSAKHKKVLKSAKGFYGRRKNTIRAAKAAVDRSQQYAYRDRRVKKRDFRSLWIQR 64
           K+     AK + VL+S   F   +K+            Q    R R    +    L +  
Sbjct: 109 KQAKKQEAKDRLVLESNTLFDNTKKSINALKGTEFFCLQMGELRSRSQANKLITQLALAN 168

Query: 65  INAAVRVYDLNYSQFI 80
           +   V      Y  +I
Sbjct: 169 LQTEVNRSGPKYEVYI 184


>gnl|CDD|162706 TIGR02104, pulA_typeI, pullulanase, type I.  Pullulan is an
           unusual, industrially important polysaccharide in which
           short alpha-1,4 chains (maltotriose) are connected in
           alpha-1,6 linkages. Enzymes that cleave alpha-1,6
           linkages in pullulan and release maltotriose are called
           pullulanases although pullulan itself may not be the
           natural substrate. This family consists of pullulanases
           related to the subfamilies described in TIGR02102 and
           TIGR02103 but having a different domain architecture
           with shorter sequences. Members are called type I
           pullulanases.
          Length = 605

 Score = 24.6 bits (54), Expect = 7.3
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 5/48 (10%)

Query: 65  INAAVRVYDLNYSQFINGLHKAGI--VLDRKVLSDLAITQLDSFKKIV 110
            + A R+ +L   Q I  LH+ GI  ++D  V +     +   F+K V
Sbjct: 222 YDPATRIRELK--QMIQALHENGIRVIMD-VVYNHTYSREESPFEKTV 266


>gnl|CDD|177661 PLN00023, PLN00023, GTP-binding protein; Provisional.
          Length = 334

 Score = 24.4 bits (53), Expect = 8.4
 Identities = 9/20 (45%), Positives = 14/20 (70%)

Query: 55  RDFRSLWIQRINAAVRVYDL 74
           +D RSL+  +IN  + V+DL
Sbjct: 97  KDCRSLFYSQINGVIFVHDL 116


  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    0.134    0.366 

Gapped
Lambda     K      H
   0.267   0.0727    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,918,929
Number of extensions: 111436
Number of successful extensions: 308
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 33
Length of query: 123
Length of database: 5,994,473
Length adjustment: 82
Effective length of query: 41
Effective length of database: 4,222,617
Effective search space: 173127297
Effective search space used: 173127297
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 (21.6 bits)
S2: 51 (23.4 bits)