RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy2824
         (242 letters)



>gnl|CDD|218337 pfam04939, RRS1, Ribosome biogenesis regulatory protein (RRS1).
           This family consists of several eukaryotic ribosome
           biogenesis regulatory (RRS1) proteins. RRS1 is a nuclear
           protein that is essential for the maturation of 25 S
           rRNA and the 60 S ribosomal subunit assembly in
           Saccharomyces cerevisiae.
          Length = 164

 Score =  180 bits (459), Expect = 1e-57
 Identities = 81/165 (49%), Positives = 108/165 (65%), Gaps = 2/165 (1%)

Query: 29  IELEIDPGTLLAFDKNDINLGELRQDKDKYLKDLTRDNTQLLINKIWELPTERRDEDIVA 88
              E D G LLAFD N ++L +   D+++ LK L RDN QLLIN++  LPTER  + ++ 
Sbjct: 1   SPYEFDLGNLLAFDPNPLDLSD-GTDREEDLKSLARDNVQLLINQLLSLPTERTTDGVLV 59

Query: 89  TLPDPTYILPREKPLPK-ITMTKWEEFALEKGIRKTKKVKKKWDDILKEWVPTYGFKRRL 147
            LP+PT  LPREKPLPK    TKWE+FA +KGI+K KK K  +D+   EWVP +G+KR  
Sbjct: 60  QLPEPTTRLPREKPLPKPKPPTKWEKFAKKKGIKKRKKSKLVYDEATGEWVPRWGYKRAN 119

Query: 148 AEKKHQWMLPVPANADPMEDQFAKKSAAQKERVARNEYQRLRNIA 192
            + +  W++ V  N DP ED FAKK   +KERVA+NE + L+N  
Sbjct: 120 KDLEKDWIIEVKPNDDPKEDPFAKKRREKKERVAKNEKRELKNKK 164


>gnl|CDD|227550 COG5225, RRS1, Uncharacterized protein involved in ribosome
           biogenesis [Translation, ribosomal structure and
           biogenesis].
          Length = 172

 Score = 94.4 bits (234), Expect = 4e-24
 Identities = 59/177 (33%), Positives = 87/177 (49%), Gaps = 11/177 (6%)

Query: 22  PTTVNKLIELEIDPGTLLAFDKNDINLGELR-QDKDKYLKDLTRDNTQLLINKIWELPTE 80
           P      I   +D G + AFD N ++  +L    ++  +K L RDN Q L N++  LP  
Sbjct: 2   PVMNELKIPTVVDLGNVAAFDLNVLDKNDLDSSQEESNIKSLKRDNVQELKNQLCSLPAR 61

Query: 81  RRDEDIVATLPDPTYILPREKPLPKI-TMTKWEEFALEKGIRKTKKVKKK-WDDILKEWV 138
           R  + ++  LP+ T  LPREKPLPK    TKWE FA  KGI   K+     +D+   EWV
Sbjct: 62  RTSDLVLLQLPESTTALPREKPLPKEKIETKWERFARTKGIEPKKRSGPLVYDEASGEWV 121

Query: 139 PTYGFKRRLAEKKHQWMLPVPANADPMEDQFAKKSAAQKER-VARNEYQRLRNIARS 194
           P +G+K +      QW++         E +       Q++  + +NE  R  NI+R 
Sbjct: 122 PKWGYKGKNKRLLKQWLVEG-------EVKLKTLLRRQRKNNIKKNEANRRGNISRR 171


>gnl|CDD|237046 PRK12297, obgE, GTPase CgtA; Reviewed.
          Length = 424

 Score = 29.7 bits (68), Expect = 1.3
 Identities = 10/52 (19%), Positives = 19/52 (36%)

Query: 62  LTRDNTQLLINKIWELPTERRDEDIVATLPDPTYILPREKPLPKITMTKWEE 113
           LT      L+  + EL  E  +  +     +       E+     T+T+ E+
Sbjct: 310 LTGQGLDELLYAVAELLEETPEFPLEEEEVEEEVYYKFEEEEKDFTITRDED 361


>gnl|CDD|233986 TIGR02729, Obg_CgtA, Obg family GTPase CgtA.  This model describes
           a univeral, mostly one-gene-per-genome GTP-binding
           protein that associates with ribosomal subunits and
           appears to play a role in ribosomal RNA maturation. This
           GTPase, related to the nucleolar protein Obg, is
           designated CgtA in bacteria. Mutations in this gene are
           pleiotropic, but it appears that effects on cellular
           functions such as chromosome partition may be secondary
           to the effect on ribosome structure. Recent work done in
           Vibrio cholerae shows an essential role in the stringent
           response, in which RelA-dependent ability to synthesize
           the alarmone ppGpp is required for deletion of this
           GTPase to be lethal [Protein synthesis, Other].
          Length = 329

 Score = 28.2 bits (64), Expect = 4.0
 Identities = 11/51 (21%), Positives = 21/51 (41%), Gaps = 11/51 (21%)

Query: 38  LLAFDKNDINLGELRQDKDKYLKD-----------LTRDNTQLLINKIWEL 77
           ++  +K D+   E  ++  K LK+           LT +    L+  + EL
Sbjct: 277 IVVLNKIDLLDEEELEELLKELKEALGKPVFPISALTGEGLDELLYALAEL 327


>gnl|CDD|185562 PTZ00335, PTZ00335, tubulin alpha chain; Provisional.
          Length = 448

 Score = 27.8 bits (62), Expect = 6.7
 Identities = 12/22 (54%), Positives = 15/22 (68%)

Query: 204 VMPHESVLSSRQLREAADVAVV 225
           V P+ SVLS+  L E  DVAV+
Sbjct: 182 VEPYNSVLSTHSLLEHTDVAVM 203


>gnl|CDD|215089 PLN00175, PLN00175, aminotransferase family protein; Provisional.
          Length = 413

 Score = 27.5 bits (61), Expect = 7.2
 Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 8/39 (20%)

Query: 12 EVARRNEQFKPTTVNKLIELEIDPGTLLAFDKNDINLGE 50
          +VA+R E+FK T   ++        + LA     INLG+
Sbjct: 31 QVAKRLEKFKTTIFTQM--------SSLAIKHGAINLGQ 61


>gnl|CDD|225547 COG3001, COG3001, Uncharacterized protein conserved in bacteria
           [Function unknown].
          Length = 286

 Score = 27.4 bits (61), Expect = 7.9
 Identities = 18/81 (22%), Positives = 32/81 (39%), Gaps = 14/81 (17%)

Query: 130 WDDILKEWVPTYGFKRRLAEKK-------HQ-WMLPVPANADPMEDQFAKKSAAQKERVA 181
           W  I ++     G +  + E++       ++ W L      D  +  F K +  ++  + 
Sbjct: 2   WQAISQQLSEQLG-EGEIKEREEVSGGDINEAWRL-----RDGTDPFFVKCNQREQLSMF 55

Query: 182 RNEYQRLRNIARSNKTKVPSV 202
             E   L  +ARSN   VP V
Sbjct: 56  TAEADGLELLARSNTITVPKV 76


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.314    0.131    0.378 

Gapped
Lambda     K      H
   0.267   0.0686    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,666,585
Number of extensions: 1216133
Number of successful extensions: 1003
Number of sequences better than 10.0: 1
Number of HSP's gapped: 999
Number of HSP's successfully gapped: 23
Length of query: 242
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 148
Effective length of database: 6,768,326
Effective search space: 1001712248
Effective search space used: 1001712248
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: 42 (22.0 bits)
S2: 58 (26.2 bits)