RPS-BLAST 2.2.16 [Mar-25-2007]

Database: 40scop73nmM 
           9549 sequences; 1,678,726 total letters

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

Query= AAZ21934.1 pubi0 AAZ21934.1 GIB00256CH01 "SpoU rRNA Methylase
family"
         (247 letters)



                                                                 Score    E
Sequences producing significant alignments:                      (bits) Value

1gz0A1 [c.116.1.1] HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH...   138   7e-36
1v2xA [c.116.1.1] TRNA (GM18) METHYLTRANSFERASE                       134   1e-34
1j85A [c.116.1.1] YIBK                                                131   6e-34
1ipaA1 [c.116.1.1] RNA 2'-O-RIBOSE METHYLTRANSFERASE A:106 -- 263     120   2e-30
1gqiA2 [d.92.2.2] ALPHA-GLUCURONIDASE A:5 -- 151                      104   1e-25
1z67A1 [a.259.1.1] HYPOTHETICAL PROTEIN S4005 A:3 -- 131               87   2e-20
1gz0A2 [d.79.3.3] HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH ...    38   1e-05
1vhkA2 [c.116.1.5] HYPOTHETICAL PROTEIN YQEU A:74 -- 253               34   2e-04

>1gz0A1 [c.116.1.1] HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
           A:78 -- 243
          Length = 166

 Score =  138 bits (349), Expect = 7e-36
 Identities = 44/154 (28%), Positives = 76/154 (49%)

Query: 86  DLKEFIKGKNELTFVCIDEVTDPRNIGSLIRSASSFHIDGLIVKERQFPSDSKLMYKAAS 145
           DL + I   ++   + +D VTDP N+G+ +RSA +  +  +IV + +    +    K A 
Sbjct: 7   DLPDLIASLDQPFLLILDGVTDPHNLGACLRSADAAGVHAVIVPKDRSAQLNATAKKVAC 66

Query: 146 GCMEHINIFEVSNINSTLKNLREKNFWVYGFDARGEKDFTEIKWEGKNVLLFGSEGFGMR 205
           G  E + +  V+N+  T + L+E+N W+ G     +    + K  G+  L+ G+EG G R
Sbjct: 67  GAAESVPLIRVTNLARTXRXLQEENIWIVGTAGEADHTLYQSKXTGRLALVXGAEGEGXR 126

Query: 206 EHTGKYTDFFVKIDINKDVESLNISNSAAIVFHH 239
             T ++ D  + I     V SLN+S +  I    
Sbjct: 127 RLTREHCDELISIPXAGSVSSLNVSVATGICLFE 160


>1v2xA [c.116.1.1] TRNA (GM18) METHYLTRANSFERASE
          Length = 192

 Score =  134 bits (339), Expect = 1e-34
 Identities = 38/164 (23%), Positives = 73/164 (44%), Gaps = 14/164 (8%)

Query: 76  IAEVEHIDQPDLKEFIKGKNELTFVCIDEVTDPRNIGSLIRSASSFHIDGLIVKERQFPS 135
           I EV    QPDL            V ++ V  P N+ +++R+  +  +            
Sbjct: 12  IEEVLRRRQPDL-----------TVLLENVHKPHNLSAILRTCDAVGVLEAHAVNPT--G 58

Query: 136 DSKLMYKAASGCMEHINIFEVSNINSTLKNLREKNFWVYGFDARGE-KDFTEIKWEGKNV 194
                 + + G  + + +    +++   + L+E+ F VY    R + +DF E+ +     
Sbjct: 59  GVPTFNETSGGSHKWVYLRVHPDLHEAFRFLKERGFTVYATALREDARDFREVDYTKPTA 118

Query: 195 LLFGSEGFGMREHTGKYTDFFVKIDINKDVESLNISNSAAIVFH 238
           +LFG+E +G+ E      D  +KI +   V+SLN+S +AA++  
Sbjct: 119 VLFGAEKWGVSEEALALADGAIKIPMLGMVQSLNVSVAAAVILF 162


>1j85A [c.116.1.1] YIBK
          Length = 156

 Score =  131 bits (332), Expect = 6e-34
 Identities = 27/145 (18%), Positives = 63/145 (43%), Gaps = 4/145 (2%)

Query: 99  FVCIDEVTDPRNIGSLIRSASSFHIDGLIVKERQFPSDSKLMYKAASGCMEHINIFEVSN 158
            + + E   P+N G++IR  ++      +++   F  D K + ++     E   I     
Sbjct: 3   DIVLYEPEIPQNTGNIIRLCANTGFRLHLIEPLGFTWDDKRLRRSGLDYHEFAEIKRHKT 62

Query: 159 INSTLKNLREKNFWVYGFDARGEKDFTEIKWEGKNVLLFGSEGFGMREH--TGKYTDFFV 216
             + L++ + K  +      +G    +++K++  + L+FG E  G+          +  +
Sbjct: 63  FEAFLESEKPKRLFALT--TKGCPAHSQVKFKLGDYLMFGPETRGIPMSILNEMPMEQKI 120

Query: 217 KIDINKDVESLNISNSAAIVFHHLS 241
           +I +  +  S+N+SNS A+  +   
Sbjct: 121 RIPMTANSRSMNLSNSVAVTVYEAW 145


>1ipaA1 [c.116.1.1] RNA 2'-O-RIBOSE METHYLTRANSFERASE A:106 -- 263
          Length = 158

 Score =  120 bits (302), Expect = 2e-30
 Identities = 30/152 (19%), Positives = 64/152 (42%), Gaps = 3/152 (1%)

Query: 87  LKEFIKGKNELTFVCIDEVTDPRNIGSLIRSASSFHIDGLIVKERQFPSDSKLMYKAASG 146
           L+E+    + L  V    +  P N+G+++RSA +   + ++V         + + + ++G
Sbjct: 2   LEEYRPSPDALILVA-VGLEKPGNLGAVLRSADAAGAEAVLVAGGVDLYSPQ-VIRNSTG 59

Query: 147 CMEHINIFEVSNINSTLKNLREKNFWVYGFDARGEKDFTEIKWEGKNVLLFGSEGFGMRE 206
            +  +     S     L  +++ N  +       E  + E        +  G E  G+R 
Sbjct: 60  VVFSLRTLAASESE-VLDWIKQHNLPLVATTPHAEALYWEANLRPPVAIAVGPEHEGLRA 118

Query: 207 HTGKYTDFFVKIDINKDVESLNISNSAAIVFH 238
              +     V+I +    +SLN+S SAA++ +
Sbjct: 119 AWLEAAQTQVRIPMQGQADSLNVSVSAALLLY 150


>1gqiA2 [d.92.2.2] ALPHA-GLUCURONIDASE A:5 -- 151
          Length = 147

 Score =  104 bits (261), Expect = 1e-25
 Identities = 20/162 (12%), Positives = 48/162 (29%), Gaps = 22/162 (13%)

Query: 74  GYIAEVEHIDQPDLKEFIKGKNELTFVCIDEVTDPRNIGSLIRSASSFH---IDGLIVKE 130
           GY   + +    D               I  +    +    I +A++     + GL+ K 
Sbjct: 3   GYDMWLRYQPIADQTL----LKTYQ-KQIRHLHVAGD-SPTINAAAAELQRGLSGLLNKP 56

Query: 131 RQFPSDSKLMYKAASGCMEHINIFEVSNINSTLKNLREKNFWVYGFDARGEKDFTEIKWE 190
                +    Y    G  ++  +    N+   L+ L  + + +                 
Sbjct: 57  IVARDEKLKDYSLVIGTPDNSPLIASLNLGERLQALGAEGYLLEQTRINKRHV------- 109

Query: 191 GKNVLLFGSEGFGMREHTGKYTDFFVKIDINKDVESLNISNS 232
              V++  +   G+   +         I     +E L++S++
Sbjct: 110 ---VIVAANSDVGVLYGS---FHLLRLIQTQHALEKLSLSSA 145


>1z67A1 [a.259.1.1] HYPOTHETICAL PROTEIN S4005 A:3 -- 131
          Length = 127

 Score = 87.3 bits (216), Expect = 2e-20
 Identities = 17/120 (14%), Positives = 39/120 (32%), Gaps = 9/120 (7%)

Query: 87  LKEFIKGKNELTFVCIDEVTDPRNIGSLIRSASSFHIDGLIV-----KERQFPSDSKLMY 141
           +  F+KG        +  V +   I  L+    S  +  ++      ++R      + + 
Sbjct: 6   VGAFLKGDAGKYQAILSWVEEQGGIQVLLEKLQSGGLGAILSTWLSNQQRNQSVSGEQL- 64

Query: 142 KAASGC--MEHINIFEVSNINSTLKNLREKNFWVYG-FDARGEKDFTEIKWEGKNVLLFG 198
           ++A G   +  +      + ++    L E+   +      +GE             LL G
Sbjct: 65  ESALGTNAVSDLGQKLGVDTSTASSLLAEQLPKIIDALSPQGEVQANNDLLSAGXELLKG 124


>1gz0A2 [d.79.3.3] HYPOTHETICAL TRNA/RRNA METHYLTRANSFERASE YJFH
          A:2 -- 77
          Length = 76

 Score = 38.1 bits (89), Expect = 1e-05
 Identities = 18/79 (22%), Positives = 32/79 (40%), Gaps = 14/79 (17%)

Query: 8  IVGQHAVIEALRNPKRKVLKVFLTEESKKNIHRKNPKKNVLED------VKVYFKSKKEL 61
          I G HAV   L     +  +VF+ +       R++ +   L        V +   +++ L
Sbjct: 4  IYGIHAVQALLERAPERFQEVFILK------GREDKRLLPLIHALESQGVVIQLANRQYL 57

Query: 62 DKYTSKDQIMHGGYIAEVE 80
          D+ +      H G IA V+
Sbjct: 58 DEKSDGAV--HQGIIARVK 74


>1vhkA2 [c.116.1.5] HYPOTHETICAL PROTEIN YQEU A:74 -- 253
          Length = 163

 Score = 34.0 bits (78), Expect = 2e-04
 Identities = 19/154 (12%), Positives = 44/154 (28%), Gaps = 14/154 (9%)

Query: 100 VCIDEVTDPRNIGSLIRSASSFHIDG--LIVKERQFPSDSKL--MYKAASGCMEHIN--- 152
                +     +  +I+  +             R   S  K     K A    E      
Sbjct: 9   YIASGLPKGDKLEWIIQKGTELGAHAFIPFQAAR---SVVKRERWTKIAKEAAEQSYRNE 65

Query: 153 ---IFEVSNINSTLKNLREKNFWVYGFDARGEKDFTEIKWEGKNVLLFGSEGFGMREHTG 209
              + +V +    L+  ++ +  V  +++      + +      +++FG EG G+ E   
Sbjct: 66  VPRVXDVHSFQQLLQRXQDFDKCVVAYESAFSAIVSSLPKGSSLLIVFGPEG-GLTEAEV 124

Query: 210 KYTDFFVKIDINKDVESLNISNSAAIVFHHLSYL 243
           +       +        L    +       +SY 
Sbjct: 125 ERLTEQDGVTCGLGPRILRTETAPLYALSAISYQ 158


  Database: 40scop73nmM
    Posted date:  Nov 2, 2009 11:39 AM
  Number of letters in database: 1,678,726
  Number of sequences in database:  9549
  
Lambda     K      H
   0.317    0.136    0.393 

Gapped
Lambda     K      H
   0.267   0.0739    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 9549
Number of Hits to DB: 11,503,293
Number of extensions: 809613
Number of successful extensions: 3202
Number of sequences better than 1.0e-03: 10
Number of HSP's gapped: 2990
Number of HSP's successfully gapped: 137
Length of database: 100,000
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)