RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

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



>gnl|CDD|144239 pfam00572, Ribosomal_L13, Ribosomal protein L13. 
          Length = 128

 Score =  188 bits (479), Expect = 7e-49
 Identities = 72/129 (55%), Positives = 92/129 (71%), Gaps = 1/129 (0%)

Query: 16  WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75
           W ++DAKG I+GRLAS++A  LRGK+KPTYTP  D GD+VV++NA K+  +GKK DQK Y
Sbjct: 1   WHVIDAKGQILGRLASKVAKLLRGKHKPTYTPHVDCGDYVVVVNAEKIVLTGKKRDQKKY 60

Query: 76  YRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDHHPHE 135
           YRHTGYPGG+K  TAK  L    P  IL++A+  MLP+  L R  +K L +YA   HPH 
Sbjct: 61  YRHTGYPGGLKNPTAKGPLE-RKPERILERAVRGMLPKNKLGRAALKRLKVYAGSPHPHA 119

Query: 136 AQKPVFMDI 144
           AQKP  ++I
Sbjct: 120 AQKPEVLEI 128


>gnl|CDD|30451 COG0102, RplM, Ribosomal protein L13 [Translation, ribosomal
           structure and biogenesis].
          Length = 148

 Score =  184 bits (468), Expect = 9e-48
 Identities = 77/146 (52%), Positives = 102/146 (69%)

Query: 4   TFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKV 63
           TF  K SEVE+KW ++DA+G ++GRLAS++A RLRGK+KPTYTP  D GD+V++INA KV
Sbjct: 3   TFTAKPSEVERKWYVIDAEGKVLGRLASEVAKRLRGKHKPTYTPHVDTGDYVIVINAEKV 62

Query: 64  AFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKN 123
             +GKK   K YYRH+GYPGG+K  T    LA   P  IL++A+  MLP+ PL R  +K 
Sbjct: 63  VITGKKLTDKKYYRHSGYPGGLKNPTRGGPLAPRRPERILERAVRGMLPKNPLGRAALKR 122

Query: 124 LHIYAEDHHPHEAQKPVFMDIAKMNP 149
           L +YA   HPHEAQKP  +++  +  
Sbjct: 123 LKVYAGIPHPHEAQKPEALELKLLKG 148


>gnl|CDD|177072 CHL00159, rpl13, ribosomal protein L13; Validated.
          Length = 143

 Score =  158 bits (402), Expect = 5e-40
 Identities = 69/144 (47%), Positives = 93/144 (64%), Gaps = 1/144 (0%)

Query: 1   MIPTFFQKSSEVEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINA 60
           M  TF        +KW ++DAK   +GRLA++IA  LRGKNKP+Y PS D GD+V++INA
Sbjct: 1   MNKTFIPSKDYKNRKWYIIDAKDQTLGRLATKIASLLRGKNKPSYHPSVDTGDYVIVINA 60

Query: 61  SKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQ 120
            K+  +G K  QK Y RH+G PGG+K  T +E L    P  I++KA+  MLP+GPL RK 
Sbjct: 61  EKIKVTGNKTSQKFYVRHSGRPGGLKIETFEE-LQNRLPNRIIEKAVKGMLPKGPLGRKL 119

Query: 121 MKNLHIYAEDHHPHEAQKPVFMDI 144
              L +Y  + HPH AQKP+ ++I
Sbjct: 120 FTKLKVYKGESHPHVAQKPIKINI 143


>gnl|CDD|88313 cd00392, Ribosomal_L13, Ribosomal protein L13.  Protein L13, a
           large ribosomal subunit protein, is one of five proteins
           required for an early folding intermediate of 23S rRNA
           in the assembly of the large subunit. L13 is situated on
           the bottom of the large subunit, near the polypeptide
           exit site.  It interacts with proteins L3 and L6, and
           forms an extensive network of interactions with 23S
           rRNA. L13 has been identified as a homolog of the human
           breast basic conserved protein 1 (BBC1), a protein
           identified through its increased expression in breast
           cancer.  L13 expression is also upregulated in a variety
           of human gastrointestinal cancers, suggesting it may
           play a role in the etiology of a variety of human
           malignancies..
          Length = 114

 Score =  150 bits (381), Expect = 1e-37
 Identities = 59/113 (52%), Positives = 80/113 (70%), Gaps = 1/113 (0%)

Query: 16  WILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTY 75
           W ++DAKG ++GRLAS++A  L GK+KPTYTP  D GD+VV++NA K+  +GKK+ QK Y
Sbjct: 1   WHVIDAKGQVLGRLASKVAKLLLGKHKPTYTPHVDCGDYVVVVNAEKIVITGKKWRQKVY 60

Query: 76  YRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYA 128
           YRHTGYPGG+K  TA  +    +P  ILK+A+  MLP+  L R  +K L +Y 
Sbjct: 61  YRHTGYPGGLKNPTAGPLHP-RAPERILKRAVRGMLPKNKLGRAALKRLKVYE 112


>gnl|CDD|38413 KOG3203, KOG3203, KOG3203, Mitochondrial/chloroplast ribosomal
           protein L13 [Translation, ribosomal structure and
           biogenesis].
          Length = 165

 Score =  142 bits (359), Expect = 4e-35
 Identities = 65/134 (48%), Positives = 89/134 (66%), Gaps = 7/134 (5%)

Query: 12  VEKKWILVDAKGLIVGRLASQIALRLRGKNKPTYTPSADDGDHVVIINASKVAFSGKKYD 71
             + W +VDAK   +GRLASQIA  L+GK+KP Y PS D GDHVV+ N  K+AFSGKK++
Sbjct: 19  FARVWHVVDAKQQPLGRLASQIATTLQGKHKPIYHPSTDCGDHVVVTNCKKIAFSGKKWE 78

Query: 72  QKTYYRHTGYPGGIKKTTAKEILAGASPTNILKKAIARMLPRGPLARKQMKNLHIYAEDH 131
           QK Y  H+GYPGG+K+TTA + LA   P  I++ A+  MLP+  L R++M+ LH++  + 
Sbjct: 79  QKIYRSHSGYPGGLKQTTADQ-LADRDPCRIVRLAVYGMLPKNLLRRRRMQRLHLFPGEE 137

Query: 132 HP------HEAQKP 139
           HP       E  +P
Sbjct: 138 HPEKVNIGSELHQP 151


>gnl|CDD|73075 cd02669, Peptidase_C19M, A subfamily of Peptidase C19. Peptidase
           C19 contains ubiquitinyl hydrolases. They are
           intracellular peptidases that remove ubiquitin molecules
           from polyubiquinated peptides by cleavage of isopeptide
           bonds. They hydrolyze bonds involving the carboxyl group
           of the C-terminal Gly residue of ubiquitin. The purpose
           of the de-ubiquitination is thought to be editing of the
           ubiquitin conjugates, which could rescue them from
           degradation, as well as recycling of the ubiquitin. The
           ubiquitin/proteasome system is responsible for most
           protein turnover in the mammalian cell, and with over 50
           members, family C19 is one of the largest families of
           peptidases in the human genome..
          Length = 440

 Score = 26.0 bits (57), Expect = 5.2
 Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 12/63 (19%)

Query: 38  RGKNKPTYTPSADDGDHVVIINASKVAFSGKKYDQKTYYRHTGYPGGIKKTTAKEILAGA 97
           RGK    YT S +D  HV +   +           K Y     Y   I  ++  +I    
Sbjct: 41  RGKGSHAYTHSLEDNHHVFLNLET----------LKFYCLPDNYE--IIDSSLDDIKYVL 88

Query: 98  SPT 100
           +PT
Sbjct: 89  NPT 91


>gnl|CDD|34498 COG4889, COG4889, Predicted helicase [General function prediction
            only].
          Length = 1518

 Score = 25.3 bits (55), Expect = 6.8
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 9/54 (16%)

Query: 104  KKAIARMLPRGPL---------ARKQMKNLHIYAEDHHPHEAQKPVFMDIAKMN 148
            K  +A+  PR  L           K++ +LH+  E     ++ K   ++ A+M+
Sbjct: 1371 KNDLAKEAPRIALSEDFKELSMLGKELADLHLNYESGEMWDSIKHNKLEAAEMD 1424


>gnl|CDD|37314 KOG2103, KOG2103, KOG2103, Uncharacterized conserved protein
           [Function unknown].
          Length = 910

 Score = 25.3 bits (55), Expect = 7.1
 Identities = 20/77 (25%), Positives = 25/77 (32%), Gaps = 12/77 (15%)

Query: 59  NASKVAFSGKKYDQKTYYRHTG---YPGGIK-----KT----TAKEILAGASPTNILKKA 106
           N     F             T    +P  IK      T    T+K IL G     IL+  
Sbjct: 732 NKLSNVFDSLSAPPLPGQVQTQSYIFPQIIKTMSVTITEQGITSKHILIGLPSGQILEIP 791

Query: 107 IARMLPRGPLARKQMKN 123
            A + PR P A  + K 
Sbjct: 792 KALLDPRRPPAPTEKKR 808


  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
   0.317    0.133    0.386 

Gapped
Lambda     K      H
   0.267   0.0756    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,872,910
Number of extensions: 91150
Number of successful extensions: 207
Number of sequences better than 10.0: 1
Number of HSP's gapped: 203
Number of HSP's successfully gapped: 11
Length of query: 155
Length of database: 6,263,737
Length adjustment: 86
Effective length of query: 69
Effective length of database: 4,405,363
Effective search space: 303970047
Effective search space used: 303970047
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)