RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780776|ref|YP_003065189.1| ribosome recycling factor
[Candidatus Liberibacter asiaticus str. psy62]
         (186 letters)



>gnl|CDD|145100 pfam01765, RRF, Ribosome recycling factor.  The ribosome recycling
           factor (RRF / ribosome release factor) dissociates the
           ribosome from the mRNA after termination of translation,
           and is essential bacterial growth. Thus ribosomes are
           "recycled" and ready for another round of protein
           synthesis.
          Length = 165

 Score =  228 bits (583), Expect = 8e-61
 Identities = 83/164 (50%), Positives = 119/164 (72%)

Query: 21  LKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRMLVVSVWDKEMVASVE 80
           LKK++  +RTGR +PS+LD ++V+ YGS  PLNQ+A+++V E R L+++ WDK ++ ++E
Sbjct: 2   LKKELSKIRTGRANPSLLDNIRVDYYGSPTPLNQLASISVPEARTLLITPWDKSLIKAIE 61

Query: 81  RGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDHL 140
           + I  S+LGLNP  +GQV+RIP+P  TEERR  LVK A   AE++K+++RNIRRD  D L
Sbjct: 62  KAILASDLGLNPQNDGQVIRIPIPPLTEERRKELVKQAKKLAEEAKVAIRNIRRDANDKL 121

Query: 141 KKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
           KK  K  + SED V   E +IQK+TD  IK ID   ++K+KE+M
Sbjct: 122 KKLEKDKEISEDEVKKAEKEIQKLTDKYIKKIDELLKKKEKELM 165


>gnl|CDD|30582 COG0233, Frr, Ribosome recycling factor [Translation, ribosomal
           structure and biogenesis].
          Length = 187

 Score =  215 bits (548), Expect = 8e-57
 Identities = 90/186 (48%), Positives = 126/186 (67%)

Query: 1   MNQVIDLQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTV 60
           M     L++ +++M   +  LK ++  +RTGR +PS+LD + VE YGS  PLNQ+A+++V
Sbjct: 2   MMINEILKDAEEKMEKALEALKNELSKIRTGRANPSLLDRITVEYYGSPTPLNQLASISV 61

Query: 61  LEPRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHA 120
            E R LV+  +DK MV ++E+ I  SNLGLNP  +G V+R+P+P  TEERR  LVKVA  
Sbjct: 62  PEARTLVIKPFDKSMVKAIEKAILASNLGLNPNNDGNVIRVPLPPLTEERRKELVKVAKK 121

Query: 121 YAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKK 180
           YAE++K++VRNIRRD  D +KK  K  + SED V   E +IQK+TD  IK ID   ++K+
Sbjct: 122 YAEEAKVAVRNIRRDANDKIKKLEKDKEISEDEVKKAEEEIQKLTDEYIKKIDELLKDKE 181

Query: 181 KEIMHF 186
           KEIM  
Sbjct: 182 KEIMEV 187


>gnl|CDD|29621 cd00520, RRF, Ribosome recycling factor (RRF). Ribosome recycling
           factor dissociates the posttermination complex, composed
           of the ribosome, deacylated tRNA, and mRNA, after
           termination of translation.  Thus ribosomes are
           "recycled" and ready for another round of protein
           synthesis.  RRF is believed to bind the ribosome at the
           A-site in a manner that mimics tRNA, but the specific
           mechanisms remain unclear.  RRF is essential for
           bacterial growth.  It is not necessary for cell growth
           in archaea or eukaryotes, but is found in mitochondria
           or chloroplasts of some eukaryotic species..
          Length = 179

 Score =  186 bits (475), Expect = 2e-48
 Identities = 79/178 (44%), Positives = 123/178 (69%)

Query: 7   LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
           L+  K++M  ++  LK+++  +RTGR +P++LD + VE YG+  PLNQ+A+++V EPR +
Sbjct: 2   LKEAKEKMEKSLEALKEELNKIRTGRANPALLDSITVEYYGAPTPLNQLASISVPEPRTI 61

Query: 67  VVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSK 126
           V++ +DK  + ++E+ I  S+LGLNP  +G V+R+ +P  TEERR  LVK A   AE++K
Sbjct: 62  VINPFDKSAIKAIEKAILNSDLGLNPNNDGAVIRVNLPPLTEERRKELVKDAKKIAEEAK 121

Query: 127 ISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
           +++RNIRRD  D +KK  K  + SED V   E D+QK+TD  IK ID   + K+KE++
Sbjct: 122 VAIRNIRRDANDKIKKLEKEKEISEDEVKKAEEDLQKLTDEYIKKIDELLKSKEKELL 179


>gnl|CDD|39956 KOG4759, KOG4759, KOG4759, Ribosome recycling factor [Translation,
           ribosomal structure and biogenesis].
          Length = 263

 Score =  123 bits (310), Expect = 3e-29
 Identities = 61/179 (34%), Positives = 100/179 (55%), Gaps = 3/179 (1%)

Query: 7   LQNIKDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVPLNQVANVTVLEPRML 66
                 +M  TI  LK+D   +R GR +P MLD + V+A G   PLN++A V++  P+ +
Sbjct: 85  EAKANSQMEKTIEALKEDFNKIRQGRFNPGMLDKIVVKANGPKRPLNEIAQVSLKGPQTI 144

Query: 67  VVSVWDK-EMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKS 125
           +++ +D    + ++ + I  S L L P ++G VLR+ +P  T+E R  L KV   Y E+ 
Sbjct: 145 LINPFDFPVDIKAILKAIEASGLNLTPNLDGTVLRVSIPPVTKESREKLAKVLKRYFEEY 204

Query: 126 KISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
           K S+R IR   +   KK++KS   SED V   E ++QK+    +  +D   + K+KE++
Sbjct: 205 KQSLRKIRTKSIKKSKKNKKS--LSEDEVKKAEAELQKLAKDAVNKLDDLLKSKEKELL 261


>gnl|CDD|145770 pfam02789, Peptidase_M17_N, Cytosol aminopeptidase family,
           N-terminal domain. 
          Length = 126

 Score = 27.8 bits (62), Expect = 1.7
 Identities = 14/77 (18%), Positives = 36/77 (46%), Gaps = 13/77 (16%)

Query: 67  VVSVWDKEMVASVERGIHESNLG-LNPIVE--------GQVLRIPVPETTEERRLALVKV 117
           VV V++   ++     + E+  G L+ +++        G+ L +P     + +R+ LV +
Sbjct: 1   VVGVFEDGKLSPAAEKLDEALDGLLSELLKEGDFSGKAGETLLLPSLPGVKAKRVLLVGL 60

Query: 118 AHAYAEKSKISVRNIRR 134
                ++ ++S   +R+
Sbjct: 61  ----GKEEELSAEALRK 73


>gnl|CDD|146948 pfam04556, DpnII, DpnII restriction endonuclease.  Members of this
           family are type II restriction enzymes (EC:3.1.21.4).
           They recognize the double-stranded unmethylated sequence
           GATC and cleave before G-1.
           http://rebase.neb.com/rebase/enz/DpnII.html.
          Length = 284

 Score = 27.6 bits (62), Expect = 2.3
 Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 7/49 (14%)

Query: 136 GMD-HLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEI 183
           G+D + +K+R SGKA E +V   E  ++KI D   K I    +    EI
Sbjct: 138 GLDSNARKNR-SGKAMELLV---ERLLKKICD--KKGITYKKQATIDEI 180


>gnl|CDD|35900 KOG0681, KOG0681, KOG0681, Actin-related protein - Arp5p
           [Cytoskeleton].
          Length = 645

 Score = 27.3 bits (60), Expect = 2.7
 Identities = 22/105 (20%), Positives = 38/105 (36%), Gaps = 5/105 (4%)

Query: 80  ERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYAEKSKISVRNIRRDGMDH 139
           +   +   L    ++    L +   E  +E+RL       A     KI+ R  RR+    
Sbjct: 257 DENRNYFQLPYTEVLAEVELALTA-EKKQEKRLQ---EQAALKRVEKINARENRREDEQQ 312

Query: 140 LKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIM 184
           L+   K+    E     LE     +      + D   E+KK+ I+
Sbjct: 313 LESYNKAQGEQESN-LDLEQKFPLLNVPAELDEDQLKEKKKQRIL 356


>gnl|CDD|145968 pfam03105, SPX, SPX domain.  We have named this region the SPX
           domain after (SYG1, Pho81 and XPR1). This 180 residue
           length domain is found at the amino terminus of a
           variety of proteins. In the yeast protein SYG1, the
           N-terminus directly binds to the G- protein beta subunit
           and inhibits transduction of the mating pheromone
           signal. This finding suggests that all the members of
           this family are involved in G-protein associated signal
           transduction. The N-termini of several proteins involved
           in the regulation of phosphate transport, including the
           putative phosphate level sensors PHO81 from
           Saccharomyces cerevisiae and NUC-2 from Neurospora
           crassa, are also members of this family. The SPX domain
           of S. cerevisiae low-affinity phosphate transporters
           Pho87 and Pho90 auto-regulates uptake and prevents
           efflux. This SPX dependent inhibition is mediated by the
           physical interaction with Spl2. NUC-2 contains several
           ankyrin repeats pfam00023. Several members of this
           family are annotated as XPR1 proteins: the xenotropic
           and polytropic retrovirus receptor confers
           susceptibility to infection with murine leukaemia
           viruses (MLV). The similarity between SYG1, phosphate
           regulators and XPR1 sequences has been previously noted,
           as has the additional similarity to several predicted
           proteins, of unknown function, from Drosophila
           melanogaster, Arabidopsis thaliana, Caenorhabditis
           elegans, Schizosaccharomyces pombe, and Saccharomyces
           cerevisiae. In addition, given the similarities between
           XPR1 and SYG1 and phosphate regulatory proteins, it has
           been proposed that XPR1 might be involved in G-protein
           associated signal transduction and may itself function
           as a phosphate sensor.
          Length = 178

 Score = 27.0 bits (60), Expect = 3.1
 Identities = 11/60 (18%), Positives = 30/60 (50%)

Query: 126 KISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFEEKKKEIMH 185
           K   R       +  ++   S   +E+ +   E++  +  D  ++ ++SF++EK++E++ 
Sbjct: 30  KELTRAKLSLTTEEDEEDESSNLLNEEELEEDESEFFEALDKELEKVNSFYKEKEEELLE 89


>gnl|CDD|176343 cd01267, CED6_AIDA1b, Phosphotyrosine-binding (PTB) domain,
           phosphotyrosine-interaction (PI) domain.
           Phosphotyrosine-binding (PTB) domain,
           phosphotyrosine-interaction (PI) domain.  PTB domains
           have a PH-like fold and are found in various eukaryotic
           signaling molecules. They were initially identified
           based upon their ability to recognize phosphorylated
           tyrosine residues. In contrast to SH2 domains, which
           recognize phosphotyrosine and adjacent carboxy-terminal
           residues, PTB-domain binding specificity is conferred by
           residues amino-terminal to the phosphotyrosine. More
           recent studies have found that some types of PTB domains
           can bind to peptides which are not tyrosine
           phosphorylated or lack tyrosine residues altogether.
          Length = 132

 Score = 26.6 bits (59), Expect = 4.2
 Identities = 11/51 (21%), Positives = 24/51 (47%), Gaps = 2/51 (3%)

Query: 136 GMDHLKKSRKSGKASEDMVASLENDIQKIT-DSTIKNIDSFFEEKKKEIMH 185
           G +  +++ +  K S  +  +    I K+  D +IK +    + K K ++H
Sbjct: 19  GTEVAREAIRKLKFSRILKTAEWEKIPKVELDISIKGV-KIIDPKTKTVLH 68


>gnl|CDD|36394 KOG1179, KOG1179, KOG1179, Very long-chain acyl-CoA
           synthetase/fatty acid transporter [Lipid transport and
           metabolism].
          Length = 649

 Score = 26.4 bits (58), Expect = 5.4
 Identities = 14/41 (34%), Positives = 20/41 (48%)

Query: 11  KDRMGDTISFLKKDMMTLRTGRVSPSMLDLVKVEAYGSHVP 51
           KDR GDT  +  +++ T     V  ++  L  V  YG  VP
Sbjct: 507 KDRTGDTFRWKGENVSTTEVEDVLSALDFLQDVNVYGVTVP 547


>gnl|CDD|99907 cd05565, PTS_IIB_lactose, PTS_IIB_lactose: subunit IIB of enzyme
          II (EII) of the lactose-specific
          phosphoenolpyruvate:carbohydrate phosphotransferase
          system (PTS) found in Firmicutes as well as
          Actinobacteria. In this system, EII is a
          lactose-specific permease with two cytoplasmic domains
          (IIA and IIB) and a transmembrane channel IIC domain.
          The IIC and IIB domains are expressed as a single
          protein from the lac operon. The IIB domain fold
          includes a central four-stranded parallel open twisted
          beta-sheet flanked by alpha-helices on both sides. The
          seven major PTS systems with this IIB fold include
          lactose, chitobiose/lichenan, ascorbate, galactitol,
          mannitol, fructose, and a sensory system with
          similarity to the bacterial bgl system..
          Length = 99

 Score = 26.2 bits (58), Expect = 5.8
 Identities = 8/22 (36%), Positives = 13/22 (59%)

Query: 44 EAYGSHVPLNQVANVTVLEPRM 65
           AYGSH  +    ++ +L P+M
Sbjct: 36 GAYGSHYDMIPDYDLVILAPQM 57


>gnl|CDD|112900 pfam04104, DNA_primase_lrg, Eukaryotic and archaeal DNA primase,
           large subunit.  DNA primase is the polymerase that
           synthesizes small RNA primers for the Okazaki fragments
           made during discontinuous DNA replication. DNA primase
           is a heterodimer of two subunits, the small subunit Pri1
           (48 kDa in yeast), and the large subunit Pri2 (58 kDa in
           the yeast S. cerevisiae). The large subunit of DNA
           primase forms interactions with the small subunit and
           the structure implicates that it is not directly
           involved in catalysis, but plays roles in correctly
           positioning the primase/DNA complex, and in the transfer
           of RNA to DNA polymerase.
          Length = 217

 Score = 25.8 bits (57), Expect = 7.1
 Identities = 24/147 (16%), Positives = 52/147 (35%), Gaps = 35/147 (23%)

Query: 63  PRMLVVSVWDKEMVASVERGIHESNLGLNPIVEGQVLRIPVPETTEERRLALVKVAHAYA 122
           P+  ++ +  +   + +E+ ++ +   L  ++E         E   E+   L++     A
Sbjct: 29  PKEELLRLLVEAFRSRLEKALNLTYESLPELLEEYE------EDIREKLEPLLEHLSKEA 82

Query: 123 EKSKISVRNIR-----------RDGMDHLKK--SRK-----------SGKASEDMVASLE 158
           E  KIS  NI            R+ ++ L+     K            G        SL+
Sbjct: 83  EDGKISAENIDKLSPEHFPPCMRNLLEGLRAGGHLKHEGRFQLTLFLKGIGL-----SLD 137

Query: 159 NDIQKITDSTIKNIDSFFEEKKKEIMH 185
             ++   ++  +    F +E +  I H
Sbjct: 138 EILEFWREAFTRTSPDFDKEYRYNIRH 164


>gnl|CDD|35775 KOG0555, KOG0555, KOG0555, Asparaginyl-tRNA synthetase
           [Translation, ribosomal structure and biogenesis].
          Length = 545

 Score = 25.7 bits (56), Expect = 7.1
 Identities = 15/66 (22%), Positives = 30/66 (45%)

Query: 118 AHAYAEKSKISVRNIRRDGMDHLKKSRKSGKASEDMVASLENDIQKITDSTIKNIDSFFE 177
           +  Y   SK +++ I++  +   KKS K+ +   +     E ++++    TI    S   
Sbjct: 50  SEEYEPISKSALKKIKKGWVRECKKSAKASQKEAEASEKREKNLEEAKKITISEDKSLPA 109

Query: 178 EKKKEI 183
            KK +I
Sbjct: 110 AKKIKI 115


  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
   0.316    0.131    0.355 

Gapped
Lambda     K      H
   0.267   0.0793    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 2,067,434
Number of extensions: 99482
Number of successful extensions: 302
Number of sequences better than 10.0: 1
Number of HSP's gapped: 298
Number of HSP's successfully gapped: 27
Length of query: 186
Length of database: 6,263,737
Length adjustment: 88
Effective length of query: 98
Effective length of database: 4,362,145
Effective search space: 427490210
Effective search space used: 427490210
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 (21.6 bits)
S2: 54 (24.5 bits)