RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780608|ref|YP_003065021.1| ribosomal large subunit
pseudouridine synthase C [Candidatus Liberibacter asiaticus str.
psy62]
         (346 letters)



>gnl|CDD|30910 COG0564, RluA, Pseudouridylate synthases, 23S RNA-specific
           [Translation, ribosomal structure and biogenesis].
          Length = 289

 Score =  226 bits (576), Expect = 1e-59
 Identities = 100/308 (32%), Positives = 154/308 (50%), Gaps = 22/308 (7%)

Query: 7   VQYVVVENDEENMRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNNRIQSGQVVR 66
           +    V  +E   RLD++     P I+   +QK++R G+VRV+ K+VK + +++ G VVR
Sbjct: 1   MLEFEVPEEEAGQRLDKFLAKLLP-ISRSRIQKLIRKGRVRVNGKKVKPSYKLKPGDVVR 59

Query: 67  IPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSKIYVFNKPAGISVQGGSGIA 126
           IP         +  + I                 +LYED  + V NKPAG+ V  G G  
Sbjct: 60  IPLPEEPEEEKLVPEDIPLD--------------ILYEDEDLLVVNKPAGLVVHPGGGHH 105

Query: 127 YHID-GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWS 185
                  L        ++P + HRLD++TSG+L+VA+ R AA+ L+E F+ R+++K Y +
Sbjct: 106 EGTLVNALLRHCQDGVERPGIVHRLDKDTSGLLLVAKNREAARELSEQFKQRKVKKTYLA 165

Query: 186 LVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEM 245
           LV G     +  I   + +          V + + K    AI+H++V++ F   +  +E+
Sbjct: 166 LVRGHLPEDEGTIDAPIGRDPKNRKKMAVVKEGSGK---PAITHYEVLERFGDNYTLVEL 222

Query: 246 QPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPIQNKLYLHARYMDLPHPEGGR- 304
           +P TGRTHQ+RVH  H+G PIVGD  Y    K         +  LHA  +   HP  G  
Sbjct: 223 KPETGRTHQIRVHLAHLGHPIVGDPLYGGKDK--SAGAGLKRQALHAYKLSFTHPLTGEE 280

Query: 305 LQITAPLP 312
           L+  APLP
Sbjct: 281 LEFEAPLP 288


>gnl|CDD|30029 cd02869, PseudoU_synth_RluCD_like, PseudoU_synth_RsuA/RluD:
           Pseudouridine synthase, RsuA/RluD family. This group is
           comprised of eukaryotic, bacterial and archeal proteins
           similar to eight site specific Escherichia coli
           pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD,
           RluE, RluF and TruA.  Pseudouridine synthases catalyze
           the isomerization of specific uridines in a n RNA
           molecule to pseudouridines (5-ribosyluracil, psi)
           requiring no cofactors.  E. coli RluC for example makes
           psi955, 2504 and 2580 in 23S RNA.  Some psi sites such
           as psi1917 in 23S RNA made by RluD are universally
           conserved.  Other psi sites occur in a more restricted
           fashion, for example psi2819 in 21S mitochondrial
           ribosomal RNA made by S. cerevisiae Pus5p is only found
           in mitochondrial large subunit rRNAs from some other
           species and in gram negative bacteria. The E. coli
           counterpart of this psi residue is psi2580 in 23S rRNA. 
           psi2604in 23S RNA made by RluF has only been detected in
           E.coli. .
          Length = 185

 Score =  166 bits (421), Expect = 9e-42
 Identities = 68/193 (35%), Positives = 99/193 (51%), Gaps = 11/193 (5%)

Query: 108 IYVFNKPAGISVQGGSGIAYHID---GFLKSWVDSKGQKPRLTHRLDQETSGILVVARTR 164
           + V NKPAG+ V  G G               +  +  +P L HRLD++TSG+L+VA+ +
Sbjct: 1   LLVVNKPAGLPVHPGPGHLTGTLVNALLKLLLLLGEEFRPGLVHRLDKDTSGLLLVAKNK 60

Query: 165 AAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGAN 224
            AA  L++ F+ R+++K Y +LV G P   +  I   L +K       V V     +   
Sbjct: 61  KAAAKLSKQFKERKVKKTYLALVDGKPPEDEGTIDAPLGRKKRKKRARVVV----SEDGK 116

Query: 225 YAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYCANFKGNFTSPI 284
            AI+H+KV++ F      +E+Q  TGRTHQ+RVH   +G PIVGD KY         SP 
Sbjct: 117 PAITHYKVLERFG-NVTLVELQLETGRTHQIRVHLASIGHPIVGDPKYGGKAS---DSPG 172

Query: 285 QNKLYLHARYMDL 297
             +L LHA  +  
Sbjct: 173 LKRLALHAYRLSF 185


>gnl|CDD|144443 pfam00849, PseudoU_synth_2, RNA pseudouridylate synthase.  Members
           of this family are involved in modifying bases in RNA
           molecules. They carry out the conversion of uracil bases
           to pseudouridine. This family includes RluD, a
           pseudouridylate synthase that converts specific uracils
           to pseudouridine in 23S rRNA. RluA from E. coli converts
           bases in both rRNA and tRNA.
          Length = 151

 Score =  115 bits (291), Expect = 1e-26
 Identities = 42/158 (26%), Positives = 71/158 (44%), Gaps = 11/158 (6%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAA 167
             V NKPAG+ V             L    +    +    HRLD++TSG+L++A+   AA
Sbjct: 1   YIVVNKPAGVPVHPTDLSDLLSLTELLLVAELGKFRLYPVHRLDRDTSGLLLLAKDGEAA 60

Query: 168 QHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNE--KGANY 225
             L + F  R+++K Y +LV G  + +          K+ I  D   V ++ +       
Sbjct: 61  NKLNKLFPERKVEKEYLALVDGPEEEEGTI-------KAPIKKDKNKVPRRKKEELDGKK 113

Query: 226 AISHFKVIDCF--AQKFCWLEMQPHTGRTHQLRVHALH 261
           A++H +V+      +    +E++  TGR HQ+R H   
Sbjct: 114 AVTHLRVLRSGSKIEDVSLVELELVTGRKHQIRAHLAA 151


>gnl|CDD|37130 KOG1919, KOG1919, KOG1919, RNA pseudouridylate synthases [RNA
           processing and modification].
          Length = 371

 Score =  115 bits (290), Expect = 1e-26
 Identities = 66/237 (27%), Positives = 105/237 (44%), Gaps = 25/237 (10%)

Query: 41  LRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
           ++ G+V V+ ++V+ +  +++G V  +   ++     +    I                 
Sbjct: 66  IKLGRVTVNGEQVRVSLIVKNGDV--LCHTVHRHEPPVAYLPIR---------------- 107

Query: 101 LLYEDSKIYVFNKPAGISVQ-GGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED    V NKP GI V   G      I   L +    +G   R  HRLD+ TSG+LV
Sbjct: 108 IVFEDKDYVVVNKPHGIPVHPTGRYRENTITKILAALHKVEG--LRPCHRLDRLTSGLLV 165

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKK---ECIANWLLKKSHIGGDYVHVV 216
           +A+T+ AA    E  R R ++K Y       P       E       ++  +      V 
Sbjct: 166 LAKTKEAADKFHEVLRKRTVKKEYVVARVEGPFPVVGEVEIKEPIGEEERPLRMGLNAVG 225

Query: 217 KQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            ++E  A  A + FKV+         +E +P TGRTHQ+RVH  ++G PI GD KY 
Sbjct: 226 VRDEVAAKDAKTLFKVLSYDGGSS-LVECRPLTGRTHQIRVHLQYLGHPIAGDPKYG 281


>gnl|CDD|30016 cd02563, PseudoU_synth_TruC, tRNA pseudouridine isomerase C:
           Pseudouridine synthases catalyze the isomerization of
           specific uridines in an tRNA molecule to pseudouridines
           (5-ribosyluracil, psi).  No cofactors are required. TruC
           makes psi65 in tRNAs.  This psi residue is not
           universally conserved..
          Length = 223

 Score =  107 bits (269), Expect = 5e-24
 Identities = 67/229 (29%), Positives = 105/229 (45%), Gaps = 25/229 (10%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGF-LKSWVDSKGQKPRLTHRLDQETSGILV 159
           +LY+D  +   NKP+G+ V   S +  H   F L++  D  GQ     HRLD+ TSG+L+
Sbjct: 3   ILYQDEHLVAINKPSGLLVHR-SELDRHETRFALQTLRDQLGQHVYPVHRLDRPTSGVLL 61

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQN 219
            A +   A+ L E F   R+ K Y ++V G              +   +   +      +
Sbjct: 62  FALSSEVARKLGEQFTEHRVHKTYLAVVRGYVPESGTIDYPLSEELDKLADKFA----SD 117

Query: 220 EKGANYAISHFK---------VIDCFAQ-KFCWLEMQPHTGRTHQLRVHALHMGCPIVGD 269
           +K    A +H++         V+  +   ++  +E+ PHTGR HQLR H  H+  PI+GD
Sbjct: 118 DKAPQAATTHYRLLAVEELPVVVGKYPTSRYSLVELTPHTGRKHQLRRHLAHIRHPIIGD 177

Query: 270 HKYCAN-----FKGNFTSPIQNKLYLHARYMDLPHPEGG-RLQITAPLP 312
             +        F+ +F      +L L A  ++  HP  G RL I APL 
Sbjct: 178 TTHGDGRHNRFFREHFGCH---RLLLAATRLEFTHPVTGERLLIEAPLD 223


>gnl|CDD|73313 cd02557, PseudoU_synth_ScRIB2, PseudoU_synth_ScRIB2_like:
           Pseudouridine synthase, Saccharomyces cerevisiae
           RIB2_like. This group is comprised of eukaryotic and
           bacterial proteins similar to Saccharomyces cerevisiae
           RIB2, S. cerevisiae Pus6p and human hRPUDSD2. S.
           cerevisiae RIB2 displays two distinct catalytic
           activities. The N-terminal domain of RIB2 is
           RNA:psi-synthase which makes psi32 on cytoplasmic tRNAs.
           Psi32 is highly phylogenetically conserved.   The
           C-terminal domain of RIB2 has a DRAP deaminase activity
           which catalyses the formation of
           5-amino-6-ribitylamino-2,4(1H,3H)-pyrimidinedione
           5'-phosphate from
           2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone
           5'-phosphate during riboflavin biosynthesis. S.
           cerevisiae Pus6p makes the psi31 of cytoplasmic and
           mitochondrial tRNAs..
          Length = 213

 Score = 89.5 bits (222), Expect = 1e-18
 Identities = 60/202 (29%), Positives = 88/202 (43%), Gaps = 30/202 (14%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYH-IDGFLKSWVDSKGQKPRLTHRLDQETSGILV 159
           +++ED  + V +KP+GI V       Y+ +   LKS       +P   HRLD+ TSG+L+
Sbjct: 18  IVHEDDDLLVVDKPSGIPVHPTGRYRYNTVTEILKSEYGLTELRP--CHRLDRLTSGLLL 75

Query: 160 VARTRAAAQHLTESFRMRRIQKIYWSLVWG-IPKNKKECIANWLLKKSHIGGDYVHVVKQ 218
            A+T   A  L +  R R ++K Y + V G  P  +        L     G     +   
Sbjct: 76  FAKTSQTASRLQQQIRSREVKKEYLARVKGEFPDGEVVVDQPIGLVSPKGG-----LRND 130

Query: 219 NEKGANYAISHFKVIDCFAQK-----FCWLEMQPHTGRTHQLRVHALHMGCPIVGDHKYC 273
            ++    A + FK +            C    +P TGRTHQ+RVH  ++G PIV D  Y 
Sbjct: 131 VDEKGKDARTIFKRLSYNGDLNTSVVLC----KPITGRTHQIRVHLQYLGHPIVNDPIYN 186

Query: 274 ANFKGNFTSPIQNKLYLHA-RY 294
                         +YLHA RY
Sbjct: 187 -----------NLGIYLHALRY 197


>gnl|CDD|30015 cd02558, PSRA_1, PSRA_1: Pseudouridine synthase, a subgroup of the
           RluA family. This group is comprised of bacterial
           proteins assigned to the RluA family of pseudouridine
           synthases. Pseudouridine synthases catalyze the
           isomerization of specific uridines in an RNA molecule to
           pseudouridines (5-ribosyluracil, psi).  No cofactors are
           required. The RluA family is comprised of proteins
           related to Escherichia coli RluA. .
          Length = 246

 Score = 74.9 bits (184), Expect = 3e-14
 Identities = 56/219 (25%), Positives = 94/219 (42%), Gaps = 38/219 (17%)

Query: 101 LLYEDSKIYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGIL 158
           +L++D  + V +KP  + V        ++   L   +  +   P LT  HRLD+ T+G++
Sbjct: 41  ILHQDEHLLVADKPHFLPVTPRGR---YVTETLLVRLRRQTGNPDLTPAHRLDRLTAGLV 97

Query: 159 VVAR---TRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANW-------LLKKSHI 208
           + ++   TR A Q L   F  R + K Y            E +A +       L  +S I
Sbjct: 98  LFSKRPETRGAYQTL---FARREVSKTY------------EAVAPYVPALTFPLTVRSRI 142

Query: 209 GGDYVHVVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIVG 268
                    +  +G   A +  +++      +    + PHTG+THQLRVH   +G PI+ 
Sbjct: 143 VKGRGFFQAREVEGEPNAETRIELLARR-GGWGLYRLSPHTGKTHQLRVHMAALGVPILN 201

Query: 269 DHKY---CANFKGNFTSPIQNKLYLHARYMDLPHPEGGR 304
           D  Y         +F+ P+Q    L A+ ++   P  GR
Sbjct: 202 DPFYPVLLDKDPDDFSRPLQ----LLAKELEFTDPLTGR 236


>gnl|CDD|30008 cd02550, PseudoU_synth_Rsu_Rlu_like, PseudoU_synth_Rsu_Rlu:
           Pseudouridine synthase, Rsu/Rlu family. This group is
           comprised of eukaryotic, bacterial and archeal proteins
           similar to eight site specific Escherichia coli
           pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD,
           RluE, RluF and TruA. Pseudouridine synthases catalyze
           the isomerization of specific uridines in a n RNA
           molecule to pseudouridines (5-ribosyluracil, psi)
           requiring no cofactors.  E. coli RluC for example makes
           psi955, 2504 and 2580 in 23S RNA.  Some psi sites such
           as psi1917 in 23S RNA made by RluD are universally
           conserved.  Other psi sites occur in a more restricted
           fashion, for example psi2819 in 21S mitochondrial
           ribosomal RNA made by S. cerevisiae Pus5p is only found
           in mitochondrial large subunit rRNAs from some other
           species and in gram negative bacteria. The E. coli
           counterpart of this psi residue is psi2580 in 23S rRNA. 
           psi2604in 23S RNA made by RluF has only been detected in
           E.coli..
          Length = 154

 Score = 72.2 bits (177), Expect = 2e-13
 Identities = 42/162 (25%), Positives = 63/162 (38%), Gaps = 17/162 (10%)

Query: 108 IYVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLT--HRLDQETSGILVVARTRA 165
           I V NKP+G+                   +      PR+    RLD++TSG+L++     
Sbjct: 1   ILVLNKPSGLVCHPTDRDRDPTVVVRLDKLHG----PRVHAAGRLDKDTSGLLLLTNDGR 56

Query: 166 AAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANY 225
             + LTE    R I+K Y   V G    +        L     G     V +    G   
Sbjct: 57  LQRRLTEP--RREIEKEYLVTVRGELDEEGIED----LATVRRGRLSGLVDE----GVPL 106

Query: 226 AISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
           A++  +VI         L +   TGRTHQ+R H   +G P++
Sbjct: 107 AVTKVRVIGEHGGTG-RLRLTLKTGRTHQIRRHCAAVGFPVL 147


>gnl|CDD|30030 cd02870, PseudoU_synth_RsuA_like, Pseudouridine synthases  are
           responsible for the synthesis of pseudouridine from
           uracil in ribosomal RNA. The RsuA subfamily includes
           Pseudouridine Synthase similar to Ribosomal small
           subunit pseudouridine 516 synthase. Most of the proteins
           in this family are bacterial proteins..
          Length = 146

 Score = 38.2 bits (89), Expect = 0.004
 Identities = 36/161 (22%), Positives = 58/161 (36%), Gaps = 25/161 (15%)

Query: 109 YVFNKPAGISVQGGSGIAYHIDGFLKSWVDSKGQKPRLTH--RLDQETSGILVVARTRAA 166
            + NKP G+            +G        K    RL    RLD +T G+L++      
Sbjct: 2   LLLNKPRGVVST-----VRDPEGRPTVLDLLKDVGERLFPVGRLDYDTEGLLLLTNDGEL 56

Query: 167 AQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVHVVKQNEKGANYA 226
           A  LT       ++K Y   V G+P   +E +                   + + G   A
Sbjct: 57  ANRLTHP--RYGVEKTYLVKVRGVPS--EEELRRLR------------AGVELDDGKT-A 99

Query: 227 ISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
            +  KV+    +    LE+  H GR  Q+R     +G P++
Sbjct: 100 PAKVKVLSRDPKN-TLLEVTLHEGRNRQVRRMFEAVGHPVL 139


>gnl|CDD|31380 COG1187, RsuA, 16S rRNA uridine-516 pseudouridylate synthase and
           related pseudouridylate synthases [Translation,
           ribosomal structure and biogenesis].
          Length = 248

 Score = 35.6 bits (82), Expect = 0.019
 Identities = 40/233 (17%), Positives = 76/233 (32%), Gaps = 48/233 (20%)

Query: 38  QKILRSGQVRVDKKRVKFNNRIQSGQVVRIPPVINALNHIIKEQKILDSSVNLTKHSDFL 97
           +K++  G+V V+            G+V  +  V+   +  + E                 
Sbjct: 21  EKLIEEGRVTVN------------GKVATLGGVVVDPDDDVVE---------------VD 53

Query: 98  KSILLYEDSKIYV-FNKPAGI--SVQGGSGIAYHIDGFLKSWVDSKGQKPRLTHRLDQET 154
              +  ++ ++Y+  NKP G   S +   G     D  L   +  K ++     RLD++T
Sbjct: 54  GKRIELKEERVYLLLNKPRGYVSSTEDDEGRPTVFD-LLPERLPRK-KRLFPVGRLDKDT 111

Query: 155 SGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWGIPKNKKECIANWLLKKSHIGGDYVH 214
            G+L++      A  L        ++K Y   V G    +       L K   +      
Sbjct: 112 EGLLLLTNDGELAHRLMHP--SSEVEKEYLVRVEGPVTEED---LEKLRKGVTLDD---- 162

Query: 215 VVKQNEKGANYAISHFKVIDCFAQKFCWLEMQPHTGRTHQLRVHALHMGCPIV 267
                  G         +     +   WL +    GR  Q+R     +G  ++
Sbjct: 163 -------GETKPAKPASLEKEPGKNNSWLRITLTEGRNRQVRRMFEAVGLEVL 208


>gnl|CDD|31381 COG1188, COG1188, Ribosome-associated heat shock protein implicated
           in the recycling of the 50S subunit (S4 paralog)
           [Translation, ribosomal structure and biogenesis].
          Length = 100

 Score = 34.9 bits (80), Expect = 0.035
 Identities = 19/102 (18%), Positives = 42/102 (41%), Gaps = 22/102 (21%)

Query: 13  ENDEENMRLDRWFKNHYPHINFVNL-------QKILRSGQVRVDKKRVKFNNRIQSGQVV 65
           + D + MRLD+W                    ++++  G+V+V+ +R K +  ++ G ++
Sbjct: 3   DKDADRMRLDKWLW-------AARFIKRRSLAKEMIEGGRVKVNGQRAKPSKEVKVGDIL 55

Query: 66  RIPPVINALNHIIKEQKILDSSVNLTKHSDFLKSILLYEDSK 107
            I        +     K+L             ++ LLYE+++
Sbjct: 56  TI-----RFGNKEFTVKVLALGEQRRPAE---EARLLYEETE 89


>gnl|CDD|147225 pfam04947, Pox_VLTF3, Poxvirus Late Transcription Factor VLTF3
           like.  Members of this family are approximately 26 KDa,
           and are involved in trans-activator of late
           transcription.
          Length = 171

 Score = 33.0 bits (76), Expect = 0.11
 Identities = 18/55 (32%), Positives = 24/55 (43%), Gaps = 4/55 (7%)

Query: 50  KKRVKFNN---RIQSGQVVRIPP-VINALNHIIKEQKILDSSVNLTKHSDFLKSI 100
            + + F N   R+Q  Q   IP  V   L   +K+  I    V  TK  DFLK +
Sbjct: 12  NRLIHFRNCLRRLQGKQTTTIPDKVYEELRKKLKKYNIDTDDVTTTKVLDFLKKL 66


>gnl|CDD|29105 cd00165, S4, S4/Hsp/ tRNA synthetase RNA-binding domain; The
          domain surface is populated by conserved, charged
          residues that define a likely RNA-binding site;  Found
          in stress proteins, ribosomal proteins and tRNA
          synthetases; This may imply a hitherto unrecognized
          functional similarity between these three protein
          classes..
          Length = 70

 Score = 32.2 bits (73), Expect = 0.21
 Identities = 13/68 (19%), Positives = 33/68 (48%), Gaps = 1/68 (1%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVVRIPPVINALNHI 77
          MRLD+         +    +++++ G V V+ K V   + +++ G V+ +       + +
Sbjct: 1  MRLDKILARLGLAPSRSEARQLIKHGHVLVNGKVVTKPSYKVKPGDVIEVDGKSIEEDIV 60

Query: 78 IKEQKILD 85
           +++K+L 
Sbjct: 61 YEDKKLLV 68


>gnl|CDD|144902 pfam01479, S4, S4 domain.  The S4 domain is a small domain
          consisting of 60-65 amino acid residues that was
          detected in the bacterial ribosomal protein S4,
          eukaryotic ribosomal S9, two families of pseudouridine
          synthases, a novel family of predicted RNA methylases,
          a yeast protein containing a pseudouridine synthetase
          and a deaminase domain, bacterial tyrosyl-tRNA
          synthetases, and a number of uncharacterized, small
          proteins that may be involved in translation
          regulation. The S4 domain probably mediates binding to
          RNA.
          Length = 48

 Score = 29.8 bits (68), Expect = 1.2
 Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 1/48 (2%)

Query: 19 MRLDRWFKNHYPHINFVNLQKILRSGQVRVDKKRVKFNN-RIQSGQVV 65
          MRLD+         +    ++++R G VRV+ K VK  + R++ G V+
Sbjct: 1  MRLDKVLARLGLASSRSEARQLIRHGHVRVNGKVVKDPSYRVKPGDVI 48


>gnl|CDD|145350 pfam02145, Rap_GAP, Rap/ran-GAP. 
          Length = 187

 Score = 29.5 bits (67), Expect = 1.2
 Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)

Query: 202 LLKKSHIGGDYVHVVKQ-NEKGANYAI--SHF 230
           L KK HIG D V+++   + K  N     S F
Sbjct: 73  LEKKRHIGNDIVNIIFNESGKPFNPDTIKSQF 104


>gnl|CDD|38891 KOG3687, KOG3687, KOG3687, Tuberin - Rap/ran-GTPase-activating
            protein [Cell cycle control, cell division, chromosome
            partitioning, Signal transduction mechanisms].
          Length = 1697

 Score = 28.2 bits (62), Expect = 3.5
 Identities = 11/23 (47%), Positives = 14/23 (60%), Gaps = 1/23 (4%)

Query: 203  LKKSHIGGDYVHVVKQNEKGANY 225
             KK HIG D+V ++  NE G  Y
Sbjct: 1539 KKKRHIGNDFVSII-YNESGEEY 1560


>gnl|CDD|35589 KOG0368, KOG0368, KOG0368, Acetyl-CoA carboxylase [Lipid transport
            and metabolism].
          Length = 2196

 Score = 27.6 bits (61), Expect = 4.6
 Identities = 11/79 (13%), Positives = 30/79 (37%)

Query: 130  DGFLKSWVDSKGQKPRLTHRLDQETSGILVVARTRAAAQHLTESFRMRRIQKIYWSLVWG 189
             G +   ++    +     RL +  +   ++    +A+  LT   +   +QK +      
Sbjct: 2067 KGVISKVLEWTESRRFFYWRLRRRLAEDQLLKEILSASPDLTYKEKQAMLQKWFEESEGA 2126

Query: 190  IPKNKKECIANWLLKKSHI 208
            +     + +  W+ ++S I
Sbjct: 2127 VKWEDDQQVVTWIEEQSTI 2145


  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
   0.323    0.138    0.430 

Gapped
Lambda     K      H
   0.267   0.0742    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,352,088
Number of extensions: 227304
Number of successful extensions: 471
Number of sequences better than 10.0: 1
Number of HSP's gapped: 447
Number of HSP's successfully gapped: 19
Length of query: 346
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 251
Effective length of database: 4,210,882
Effective search space: 1056931382
Effective search space used: 1056931382
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: 41 (22.0 bits)
S2: 58 (26.1 bits)