RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780666|ref|YP_003065079.1| Fmu (Sun) domain protein
[Candidatus Liberibacter asiaticus str. psy62]
         (445 letters)



>gnl|CDD|30493 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
           ribosomal structure and biogenesis].
          Length = 355

 Score =  254 bits (650), Expect = 3e-68
 Identities = 128/364 (35%), Positives = 183/364 (50%), Gaps = 32/364 (8%)

Query: 98  VADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREKIELLQRIAGISI---IPEWFKE 154
           V  +A VD  VE AK        AK VN++LRR+ R +  LL+ I   +     PEW  E
Sbjct: 1   VPPHAAVDETVEAAKERLGKDRAAKFVNAVLRRLERSEEALLEEILRPAFRYSHPEWLVE 60

Query: 155 RLENFYGKERVLAISDACISPLYIDL---TVKFDIETWAHKLNAV-------MLPTGGIR 204
           +L +  G++   AI+ A + P    L   T+K D+E     L           +    +R
Sbjct: 61  KLPDALGEDEAEAIAAALLRPPPRSLRVNTLKADVEELLEALEEAGVLDEKPWVLDEVLR 120

Query: 205 LKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLI---- 260
           ++     I  LP FAEG+ +VQD ++ +P  +        VLDLCAAPGGKT  L     
Sbjct: 121 IEA-SGPIGRLPEFAEGLIYVQDEASQLPALVLDPKPGERVLDLCAAPGGKTTHLAELME 179

Query: 261 VSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAF----DYCPKKLFDAVLVDAPC 316
             GA V A+DVS +RL++LR NL RL +    ++  DA          + FD +L+DAPC
Sbjct: 180 NEGAIVVAVDVSPKRLKRLRENLKRLGVRNVIVVNKDARRLAELLPGGEKFDRILLDAPC 239

Query: 317 SSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEV 376
           S TG IRR PDV W R  +DI + A  Q+++L   +  +KPGG++V+S CSL  +++EEV
Sbjct: 240 SGTGVIRRDPDVKWRRTPEDIAELAKLQKEILAAALKLLKPGGVLVYSTCSLTPEENEEV 299

Query: 377 VQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFFAV 436
           V++ L   P   EL P+    W  +   +        R+ P           G DGFF  
Sbjct: 300 VERFLERHPD-FELEPVRLP-WGPLFEGLGSELGKTRRLYPH--------VHGTDGFFIA 349

Query: 437 ALRR 440
            LR+
Sbjct: 350 KLRK 353


>gnl|CDD|144689 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family. 
          Length = 277

 Score =  165 bits (420), Expect = 2e-41
 Identities = 89/244 (36%), Positives = 129/244 (52%), Gaps = 17/244 (6%)

Query: 202 GIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKT---AQ 258
            + + +LP SI SLP F  G   VQDAS+ +         +  +LD+CAAPGGKT   A+
Sbjct: 45  ALPVGDLPYSIGSLPPFENGAVTVQDASSQLDAIALNPQEDEFILDMCAAPGGKTTHIAE 104

Query: 259 LIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDA---FDYCPKKLFDAVLVDAP 315
           L+ +   V A+D +K+RL+++  N+ RL ++   + E DA           FD +L+DAP
Sbjct: 105 LMKNEGTVVAVDRNKQRLKRVYANIQRLGVFNIIVQEGDARQIDQKLLGGEFDRILLDAP 164

Query: 316 CSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEE 375
           CS TG IRR PD+ W R   DI + A  Q++LL      VKPGG++V+S CS+  +++E 
Sbjct: 165 CSGTGVIRRDPDIKWLRREADIAQLAELQKELLKAAWDLVKPGGVLVYSTCSVLPEENEA 224

Query: 376 VVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFFA 435
           V++  L+  P  VELVP   +  K              RI    L+ +       DGFF 
Sbjct: 225 VIKYFLQKRPD-VELVPTGLSEGKIA---------LAKRIVKGGLQSLPH-ELNRDGFFF 273

Query: 436 VALR 439
             LR
Sbjct: 274 AKLR 277



 Score = 34.7 bits (80), Expect = 0.053
 Identities = 23/102 (22%), Positives = 40/102 (39%), Gaps = 5/102 (4%)

Query: 310 VLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLD 369
           +L    CS  GT+R++            ++ A  Q + L +    + P G + +S  SL 
Sbjct: 1   ILEANNCSPPGTLRKNVLKTKRWSLLQALELAGVQLEPLGRYPHAL-PVGDLPYSIGSLP 59

Query: 370 KQDSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEG 411
             ++  V  +   S    + L P    +   +DM  A  P G
Sbjct: 60  PFENGAVTVQDASSQLDAIALNPQEDEFI--LDMCAA--PGG 97


>gnl|CDD|36338 KOG1122, KOG1122, KOG1122, tRNA and rRNA cytosine-C5-methylase
           (nucleolar protein NOL1/NOP2) [RNA processing and
           modification].
          Length = 460

 Score =  137 bits (347), Expect = 5e-33
 Identities = 78/246 (31%), Positives = 122/246 (49%), Gaps = 12/246 (4%)

Query: 202 GIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKT---AQ 258
           G+ + +    I + P +  G + +Q+AS+ +PV          +LD+CAAPGGKT   A 
Sbjct: 202 GLVVFDSVVPIGATPEYLAGHYMLQNASSFLPVMALDPQPGERILDMCAAPGGKTTHIAA 261

Query: 259 LIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYCPKKL---FDAVLVDAP 315
           L+ +   + A D ++ RL+ L+ NL RL +    +   D  ++  K+    FD VL+DAP
Sbjct: 262 LMKNTGVIFANDSNENRLKSLKANLHRLGVTNTIVSNYDGREFPEKEFPGSFDRVLLDAP 321

Query: 316 CSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEE 375
           CS TG I +   V   +   DI++ A  QR+LLL  I  VK GG++V+S CS+  +++E 
Sbjct: 322 CSGTGVISKDQSVKTNKTVKDILRYAHLQRELLLSAIDLVKAGGVLVYSTCSITVEENEA 381

Query: 376 VVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFFA 435
           VV   L+  P  V+LVP                  G    +  +  +       MDGFF 
Sbjct: 382 VVDYALKKRP-EVKLVPTGLDIGGE-----GRFRGGRFHPSLKLTRRFYPHVHNMDGFFV 435

Query: 436 VALRRL 441
             L++ 
Sbjct: 436 AKLKKA 441


>gnl|CDD|37409 KOG2198, KOG2198, KOG2198, tRNA cytosine-5-methylases and related
           enzymes of the NOL1/NOP2/sun superfamily [Translation,
           ribosomal structure and biogenesis].
          Length = 375

 Score =  112 bits (280), Expect = 3e-25
 Identities = 68/190 (35%), Positives = 96/190 (50%), Gaps = 21/190 (11%)

Query: 221 GVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLI------VSGAKVTALDVSKR 274
           G  + Q+A + +PV   G      VLD+CAAPGGKTAQL+       +   V A DV  +
Sbjct: 135 GNIYRQEAVSMLPVLALGVKPGDKVLDMCAAPGGKTAQLLEALHKDPTRGYVVANDVDPK 194

Query: 275 RLEKLRCNLDRLHLYAEDIIEMDA--FDYCPKK--------LFDAVLVDAPCSSTGTIRR 324
           RL  L   L RL      +   DA  F     K         FD VLVD PCS  GT+R+
Sbjct: 195 RLNMLVHQLKRLPSPNLLVTNHDASLFPNIYLKDGNDKEQLKFDRVLVDVPCSGDGTLRK 254

Query: 325 HPDVL---WTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVL 381
           +P++    W       + +   Q ++L +G+  +K GG +V+S CSL+  ++E VVQ+ L
Sbjct: 255 NPNIWKEGWKTQRALGLHA--LQLRILRRGLRLLKVGGRLVYSTCSLNPIENEAVVQEAL 312

Query: 382 RSSPIPVELV 391
           +     VELV
Sbjct: 313 QKVGGAVELV 322


>gnl|CDD|37571 KOG2360, KOG2360, KOG2360, Proliferation-associated nucleolar
           protein (NOL1) [Cell cycle control, cell division,
           chromosome partitioning].
          Length = 413

 Score = 93.1 bits (231), Expect = 1e-19
 Identities = 95/453 (20%), Positives = 173/453 (38%), Gaps = 69/453 (15%)

Query: 12  SHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRIDAVLDFVL 71
           + +L  V +K  S+     L Y        S+++     A+V  TL++ P +D +L+   
Sbjct: 5   AEILRDVEKKEGSIK---MLVYE------SSKQNPKRTLALVCETLKYRPVLDEILED-- 53

Query: 72  ISSLPRKKYSLQQLLRVSVAQILY---------------LDVADYAVVDLAVEQAKRDKE 116
                 K  +    + V V  +L                  +    ++ L +E     K+
Sbjct: 54  SELKDAKMLARLVHMVVLVHDLLLSKIKRSGLMIDKRELKVIRLRLILRLKIETVMLKKK 113

Query: 117 NRHFAKLVNSILRRVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACISPL 176
                + V S LR +       L R   I+ + +   +   ++   E+   I++      
Sbjct: 114 -----RKVKS-LRELKLTMKIPLPRYVRINTL-KGTTDEALDYLDYEKWKMITELKPDEF 166

Query: 177 YIDLTVKFDIETWAHKLNAVMLPTGGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQL 236
           Y+D  V+                   + +      IV    +  G + +QD ++ +P  L
Sbjct: 167 YVDPHVE------------------NLIIFPPSNFIVEHELYKNGKFILQDKASCLPAHL 208

Query: 237 FGTLNNLSVLDLCAAPGGKTAQL---IVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDI 293
                   V+D CAAPG KT+ L   + +  K+ A +   +R   LR  L    +   + 
Sbjct: 209 LDPRPGSRVIDTCAAPGNKTSHLAAIMRNQGKIYAFERDAKRAATLRKLLKIAGVSIVES 268

Query: 294 IEMDAFDYCPKKLFDAV---LVDAPCSSTGTIRRHPDVLW--TRDTDDIVKSACFQRKLL 348
           +E D  +    + F  V   LVD  CS +G + R  +     T   + +     FQ ++L
Sbjct: 269 VEGDFLNTATPEKFRDVTYILVDPSCSGSGMVSRQDEDPGAETESPERLENLQSFQIRIL 328

Query: 349 LQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELVPLN-SAYWKSIDMAMAL 407
              ++F     + V+S CSL ++++E+VVQ+VL+ +P    L P      W    ++   
Sbjct: 329 KHALTFPNLKRL-VYSTCSLHREENEQVVQEVLQQNPDAKRLAPKKVLPAWPHRGLSTFS 387

Query: 408 SPEGWIRITPDMLEKIDGVSSGMDGFFAVALRR 440
             E  +R +P         S+   GFF     R
Sbjct: 388 GAEHCLRASPK--------STLTIGFFVALFER 412


>gnl|CDD|144570 pfam01029, NusB, NusB family.  The NusB protein is involved in the
           regulation of rRNA biosynthesis by transcriptional
           antitermination.
          Length = 126

 Score = 76.5 bits (189), Expect = 1e-14
 Identities = 38/131 (29%), Positives = 63/131 (48%), Gaps = 7/131 (5%)

Query: 5   MNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRID 64
            NAR ++   L  V  +  SL  LLD          L +RD+     +V   LR L  +D
Sbjct: 1   RNARELALQALYAVEERGASLNELLDKL----LEADLDERDRAFATELVYGVLRNLEELD 56

Query: 65  AVLD-FVLISSLPRKKYSLQQLLRVSVAQILYL-DVADYAVVDLAVEQAKRDKENRHFAK 122
           A++   +    L R     + +LR++  ++LYL D+  +  ++ AVE AK+       A 
Sbjct: 57  ALIAKLLENWPLERLDPVDRAILRLAAYELLYLDDIPPHVAINEAVELAKK-FGGEKSAG 115

Query: 123 LVNSILRRVSR 133
            VN +LR+++R
Sbjct: 116 FVNGVLRKIAR 126


>gnl|CDD|29566 cd00620, Methyltransferase_Sun, N-terminal RNA binding domain of
           the methyltransferase Sun. The rRNA-specific
           5-methylcytidine transferase Sun, also known as RrmB or
           Fmu shares the RNA-binding non-catalytic domain with the
           transcription termination factor NusB. The precise
           biological role of this domain in Sun is unknown,
           although it is likely to be involved in
           sequence-specific RNA binding. The C-terminal
           methyltransferase domain of Sun has been shown to
           catalyze formation of m5C at position 967 of 16S rRNA in
           Escherichia coli..
          Length = 126

 Score = 73.0 bits (179), Expect = 1e-13
 Identities = 47/131 (35%), Positives = 71/131 (54%), Gaps = 5/131 (3%)

Query: 5   MNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRID 64
           MNAR  ++ +L  V+++  SL  +L            S RD+ L   +V  TLR+L  +D
Sbjct: 1   MNARSTAAEVLRDVLQRGASLNAVLSALQKKD----KSDRDRGLATELVYGTLRWLALLD 56

Query: 65  AVLDFVLISSLPRKKYSLQQLLRVSVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKLV 124
            +++ +L      K   ++ LLR+ + Q+LYLDV  +A VD  VE AK  K+    A LV
Sbjct: 57  WIINPLLKKPDVGKDPDVRNLLRLGLYQLLYLDVPPHAAVDETVEIAKIRKD-LGRAGLV 115

Query: 125 NSILRRVSREK 135
           N++LRR  RE 
Sbjct: 116 NAVLRRFERED 126


>gnl|CDD|31289 COG1092, COG1092, Predicted SAM-dependent methyltransferases
           [General function prediction only].
          Length = 393

 Score = 59.9 bits (145), Expect = 1e-09
 Identities = 37/132 (28%), Positives = 58/132 (43%), Gaps = 21/132 (15%)

Query: 244 SVLDLCAAPGGKTAQLIVSGAK-VTALDVSKRRLEKLRCN--LDRLHLYAEDIIEMDAFD 300
            VL+L +  GG +    + GA  VT++D+SKR LE  R N  L+ L       I  D F 
Sbjct: 220 RVLNLFSYTGGFSVHAALGGASEVTSVDLSKRALEWARENAELNGLDGDRHRFIVGDVFK 279

Query: 301 YCPK-----KLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFV 355
           +  K     + FD +++D P     +  R     ++   D         + L    +  +
Sbjct: 280 WLRKAERRGEKFDLIILDPP-----SFARSKKQEFSAQRD--------YKDLNDLALRLL 326

Query: 356 KPGGIVVFSNCS 367
            PGG +V S+CS
Sbjct: 327 APGGTLVTSSCS 338


>gnl|CDD|29564 cd00447, NusB_Sun, RNA binding domain of NusB (N
           protein-Utilization Substance B) and Sun (also known as
           RrmB or Fmu) proteins. This family includes two
           orthologous groups exemplified by the transcription
           termination factor NusB and the N-terminal domain of the
           rRNA-specific 5-methylcytidine transferase
           (m5C-methyltransferase) Sun. The NusB protein plays a
           key role in the regulation of ribosomal RNA biosynthesis
           in eubacteria by modulating the efficiency of
           transcriptional antitermination. NusB along with other
           Nus factors (NusA, NusE/S10 and NusG) forms the core
           complex with the boxA element of the nut site of the
           rRNA operons. These interactions help RNA polymerase to
           counteract polarity during transcription of rRNA operons
           and allow stable antitermination. The transcription
           antitermination system can be appropriated by some
           bacteriophages such as lambda, which use the system to
           switch between the lysogenic and lytic modes of phage
           propagation. The m5C-methyltransferase Sun shares the
           N-terminal non-catalytic RNA-binding domain with NusB..
          Length = 129

 Score = 47.3 bits (112), Expect = 8e-06
 Identities = 31/99 (31%), Positives = 54/99 (54%), Gaps = 6/99 (6%)

Query: 41  LSQRDQILVRAIVNVTLRFLPRIDAVLDFVL----ISSLPRKKYSLQQLLRVSVAQILYL 96
           L+++D+     +V   LR LP +D ++  +L    +  L +   ++ +LL   + Q+LY 
Sbjct: 33  LAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDRLDKVDRAILRLLLYELYQLLY- 91

Query: 97  DVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREK 135
           DV     ++ AVE AKR  +    AK VN +LRR+++E 
Sbjct: 92  DVPPPVAINEAVELAKRFGD-DDSAKFVNGVLRRIAKES 129


>gnl|CDD|100107 cd02440, AdoMet_MTases, S-adenosylmethionine-dependent
           methyltransferases (SAM or AdoMet-MTase), class I;
           AdoMet-MTases are enzymes that use
           S-adenosyl-L-methionine (SAM or AdoMet) as a substrate
           for methyltransfer, creating the product
           S-adenosyl-L-homocysteine (AdoHcy). There are at least
           five structurally distinct families of AdoMet-MTases,
           class I being the largest and most diverse. Within this
           class enzymes can be classified by different substrate
           specificities (small molecules, lipids, nucleic acids,
           etc.) and different target atoms for methylation
           (nitrogen, oxygen, carbon, sulfur, etc.)..
          Length = 107

 Score = 45.1 bits (107), Expect = 4e-05
 Identities = 32/123 (26%), Positives = 49/123 (39%), Gaps = 24/123 (19%)

Query: 245 VLDLCAAPGGKTAQLIVS-GAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFD--Y 301
           VLDL    G     L    GA+VT +D+S   LE  R     L     ++++ DA +   
Sbjct: 2   VLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPP 61

Query: 302 CPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIV 361
              + FD ++ D P                 D    ++ A   R+LL       KPGG++
Sbjct: 62  EADESFDVIISDPPLHH-----------LVEDLARFLEEA---RRLL-------KPGGVL 100

Query: 362 VFS 364
           V +
Sbjct: 101 VLT 103


>gnl|CDD|31243 COG1041, COG1041, Predicted DNA modification methylase [DNA
           replication, recombination, and repair].
          Length = 347

 Score = 36.5 bits (84), Expect = 0.014
 Identities = 36/156 (23%), Positives = 59/156 (37%), Gaps = 19/156 (12%)

Query: 230 ASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLY 289
           A   V L        VLD     GG   +  + GA+V   D+ +R +   + NL+   + 
Sbjct: 186 ARAMVNLARVKRGELVLDPFCGTGGILIEAGLMGARVIGSDIDERMVRGAKINLEYYGI- 244

Query: 290 AEDIIEMDAFDYC----PKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQR 345
            ED   +   D           DA+  D P   +  I+           ++ ++SA    
Sbjct: 245 -EDYPVLKVLDATNLPLRDNSVDAIATDPPYGRSTKIKGEG---LDELYEEALESA---- 296

Query: 346 KLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVL 381
                    +KPGG +VF+     + + EE+  KVL
Sbjct: 297 ------SEVLKPGGRIVFAAPRDPRHELEELGFKVL 326


>gnl|CDD|29565 cd00619, Terminator_NusB, Transcription termination factor NusB (N
           protein-Utilization Substance B). NusB plays a key role
           in the regulation of ribosomal RNA biosynthesis in
           eubacteria by modulating the efficiency of
           transcriptional antitermination. NusB along with other
           Nus factors (NusA, NusE/S10 and NusG) forms the core
           complex with the boxA element of the nut site of the
           rRNA operons. These interactions help RNA polymerase to
           counteract polarity during transcription of rRNA operons
           and allow stable antitermination. The transcription
           antitermination system can be appropriated by some
           bacteriophages such as lambda, which use the system to
           switch between the lysogenic and lytic modes of phage
           propagation..
          Length = 130

 Score = 36.4 bits (84), Expect = 0.016
 Identities = 26/89 (29%), Positives = 50/89 (56%), Gaps = 5/89 (5%)

Query: 50  RAIVNVTLRFLPRIDAVLDFVLIS-SLPRKKYSLQQLLRVSVAQILYL-DVADYAVVDLA 107
             +V   L  +  ID +++  L + SL R     + +LR++V ++L+L DV    V++ A
Sbjct: 44  LKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVINEA 103

Query: 108 VEQAKR-DKENRHFAKLVNSILRRVSREK 135
           +E AKR   ++ H  K VN +L +++++ 
Sbjct: 104 IELAKRFGGDDSH--KFVNGVLDKIAKDL 130


>gnl|CDD|31124 COG0781, NusB, Transcription termination factor [Transcription].
          Length = 151

 Score = 36.1 bits (83), Expect = 0.022
 Identities = 23/91 (25%), Positives = 45/91 (49%), Gaps = 3/91 (3%)

Query: 50  RAIVNVTLRFLPRIDAVLDFVLIS-SLPRKKYSLQQLLRVSVAQILYLDVADYAVV-DLA 107
           R++V   L     +D ++   L   SL R     + +LR+++ ++L+ D   Y VV + A
Sbjct: 59  RSLVKGVLENQEELDELISPHLKKWSLERLDLVERAILRLALYELLFRDDVPYKVVINEA 118

Query: 108 VEQAKRDKENRHFAKLVNSILRRVSREKIEL 138
           +E AK+        K VN +L +++++    
Sbjct: 119 IELAKKFSGEDSH-KFVNGVLDKIAKKLRPK 148


>gnl|CDD|145073 pfam01728, FtsJ, FtsJ-like methyltransferase.  This family consists
           of FtsJ from various bacterial and archaeal sources FtsJ
           is a methyltransferase, but actually has no effect on
           cell division. FtsJ's substrate is the 23S rRNA. The 1.5
           A crystal structure of FtsJ in complex with its cofactor
           S-adenosylmethionine revealed that FtsJ has a
           methyltransferase fold. This family also includes the N
           terminus of flaviviral NS5 protein. It has been
           hypothesized that the N-terminal domain of NS5 is a
           methyltransferase involved in viral RNA capping.
          Length = 176

 Score = 34.9 bits (81), Expect = 0.041
 Identities = 37/149 (24%), Positives = 59/149 (39%), Gaps = 31/149 (20%)

Query: 241 NNLSVLDLCAAPGGKTAQLI--VSGAKVTALDV----SKRRLEKLRCNLDRLHLYAEDII 294
              +VLDL AAPGG +  L+   +  +V A+D+      + +  LR +        E ++
Sbjct: 21  GGKTVLDLGAAPGGFSQVLLERGAKGRVVAVDLGPMKPIQGVTFLRGD-ITDPETLEKLL 79

Query: 295 EMDAFDYCPKKLFDAVLVD-APCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGIS 353
           E+           D VL D AP  S          L       +V +A     L L+   
Sbjct: 80  EL------LPGKVDLVLCDGAPNVSGLENTDSFISL------RLVLAAL---LLALE--- 121

Query: 354 FVKPGGIVVFSNCSL--DKQDSEEVVQKV 380
            ++PGG  V     L    + S E++ K+
Sbjct: 122 VLRPGGNFV---VKLFKGFEFSVELLYKL 147


>gnl|CDD|32446 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA
           (uracil-5-)-methyltransferase [Translation, ribosomal
           structure and biogenesis].
          Length = 432

 Score = 33.4 bits (76), Expect = 0.15
 Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 4/75 (5%)

Query: 245 VLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYCPK 304
           VLDL    G     L     KV  +++S   +E  + N     +   + I  DA ++ P 
Sbjct: 297 VLDLYCGVGTFGLPLAKRVKKVHGVEISPEAVEAAQENAAANGIDNVEFIAGDAEEFTPA 356

Query: 305 ----KLFDAVLVDAP 315
                  D V+VD P
Sbjct: 357 WWEGYKPDVVVVDPP 371


>gnl|CDD|32408 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
           biosynthesis [Coenzyme metabolism].
          Length = 238

 Score = 32.6 bits (74), Expect = 0.25
 Identities = 23/82 (28%), Positives = 34/82 (41%), Gaps = 3/82 (3%)

Query: 234 VQLFGTLNNLSVLDLCAAPGGKTAQL--IVSGAKVTALDVSKRRLEKLRCNLDRLHLYAE 291
           + L G      VLD+    G     L   V   +V  LD+S+  LE  R  L +  +   
Sbjct: 44  ISLLGIKPGDKVLDVACGTGDMALLLAKSVGTGEVVGLDISESMLEVAREKLKKKGVQNV 103

Query: 292 DIIEMDAFDY-CPKKLFDAVLV 312
           + +  DA +   P   FDAV +
Sbjct: 104 EFVVGDAENLPFPDNSFDAVTI 125


>gnl|CDD|145225 pfam01936, DUF88, Protein of unknown function DUF88.  This highly
           conserved bacterial protein has no known function. The
           alignment contains many conserved aspartates, suggesting
           an enzymatic function such as an endonuclease or
           glycosyl hydrolase (Bateman A pers. obs).
          Length = 140

 Score = 32.2 bits (74), Expect = 0.29
 Identities = 30/125 (24%), Positives = 46/125 (36%), Gaps = 30/125 (24%)

Query: 328 VLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVV---FSNCSLDKQDSEEVVQKVLRSS 384
           V    D ++    A    + +L+       G +V    + + S  K          L S+
Sbjct: 4   VFI--DGENCPVPAGIDYRKVLE--EIKSGGEVVRARAYGDWSDPKLRK---FPDALSST 56

Query: 385 PIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLE-----KIDG---VSSGMDGFFAV 436
            IPV+  PL  +   ++D+ +A+          D LE       D    VS   DG FA 
Sbjct: 57  GIPVQHKPLTKSGKNAVDVGLAV----------DALELAYDNNPDTFVLVSG--DGDFAP 104

Query: 437 ALRRL 441
            L RL
Sbjct: 105 LLERL 109


>gnl|CDD|32423 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
          Length = 187

 Score = 32.1 bits (73), Expect = 0.33
 Identities = 21/91 (23%), Positives = 39/91 (42%), Gaps = 7/91 (7%)

Query: 245 VLDLCAAPGGKTAQLIVSG--AKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYC 302
           + D+ A  G  T +  ++G   +V A++  +  LE +  N  R  +   +++E DA +  
Sbjct: 38  LWDIGAGTGSITIEWALAGPSGRVIAIERDEEALELIERNAARFGVDNLEVVEGDAPEAL 97

Query: 303 PK-KLFDAVLVDAPCSSTGTIRRHPDVLWTR 332
           P     DA+ +       G I    +  W R
Sbjct: 98  PDLPSPDAIFI----GGGGNIEEILEAAWER 124


>gnl|CDD|35693 KOG0472, KOG0472, KOG0472, Leucine-rich repeat protein [Function
           unknown].
          Length = 565

 Score = 31.5 bits (71), Expect = 0.51
 Identities = 34/131 (25%), Positives = 53/131 (40%), Gaps = 37/131 (28%)

Query: 204 RLKELPESIVSLPGFAEGVWWVQDASASIPVQL---FGTLNNLSVLD-----LCAAPGG- 254
           +L ELPE I SL    +      D S++   +L    G L +L  LD     + + P   
Sbjct: 102 KLSELPEQIGSLISLVK-----LDCSSNELKELPDSIGRLLDLEDLDATNNQISSLPEDM 156

Query: 255 ----KTAQLIVSGAKVTALD---VSKRRLEKLRCN----------------LDRLHLYAE 291
               K ++L + G K+ AL    ++ +RL+ L CN                L+ L+L   
Sbjct: 157 VNLSKLSKLDLEGNKLKALPENHIAMKRLKHLDCNSNLLETLPPELGGLESLELLYLRRN 216

Query: 292 DIIEMDAFDYC 302
            I  +  F  C
Sbjct: 217 KIRFLPEFPGC 227


>gnl|CDD|30409 COG0060, IleS, Isoleucyl-tRNA synthetase [Translation, ribosomal
           structure and biogenesis].
          Length = 933

 Score = 31.3 bits (71), Expect = 0.55
 Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 5/45 (11%)

Query: 130 RVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACIS 174
            V + + ++L+ I  ++ +P+W K R  N           D CIS
Sbjct: 421 SVDKLRDKMLKEINKVNWVPDWGKNRFGNMVENRP-----DWCIS 460


>gnl|CDD|30641 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
           and biogenesis].
          Length = 205

 Score = 31.3 bits (71), Expect = 0.56
 Identities = 33/145 (22%), Positives = 57/145 (39%), Gaps = 26/145 (17%)

Query: 245 VLDLCAAPGGKT---AQLIVSGAKVTALDV----SKRRLEKLRCNLDRLHLYAEDIIEMD 297
           V+DL AAPGG +   A+ + +G K+ A+D+        +  L+ ++       E ++E  
Sbjct: 49  VVDLGAAPGGWSQVAAKKLGAGGKIVAVDILPMKPIPGVIFLQGDI-TDEDTLEKLLEAL 107

Query: 298 AFDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKP 357
                     D VL D            P+    R  D   +S       L   +  +KP
Sbjct: 108 -----GGAPVDVVLSDM----------APNTSGNRSVDHA-RSMYLCELALEFALEVLKP 151

Query: 358 GGIVVFSNCSLDKQDSEEVVQKVLR 382
           GG  V        +D E++++ + R
Sbjct: 152 GGSFVAK--VFQGEDFEDLLKALRR 174


>gnl|CDD|32757 COG2933, COG2933, Predicted SAM-dependent methyltransferase
           [General function prediction only].
          Length = 358

 Score = 31.1 bits (70), Expect = 0.66
 Identities = 12/30 (40%), Positives = 17/30 (56%)

Query: 241 NNLSVLDLCAAPGGKTAQLIVSGAKVTALD 270
             +  +DL A PGG T QL+    +V A+D
Sbjct: 211 PGMWAVDLGACPGGWTYQLVKRNMRVYAVD 240


>gnl|CDD|37941 KOG2730, KOG2730, KOG2730, Methylase [General function prediction
           only].
          Length = 263

 Score = 30.4 bits (68), Expect = 1.2
 Identities = 18/77 (23%), Positives = 32/77 (41%), Gaps = 6/77 (7%)

Query: 245 VLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNL------DRLHLYAEDIIEMDA 298
           ++D     GG T Q  + G  V A+D+   ++   R N       DR+     D +++ +
Sbjct: 98  IVDAFCGVGGNTIQFALQGPYVIAIDIDPVKIACARHNAEVYGVPDRITFICGDFLDLAS 157

Query: 299 FDYCPKKLFDAVLVDAP 315
                K  +D V +  P
Sbjct: 158 KLKADKIKYDCVFLSPP 174


>gnl|CDD|38127 KOG2916, KOG2916, KOG2916, Translation initiation factor 2, alpha
           subunit (eIF-2alpha) [Translation, ribosomal structure
           and biogenesis].
          Length = 304

 Score = 30.3 bits (68), Expect = 1.3
 Identities = 28/89 (31%), Positives = 45/89 (50%), Gaps = 18/89 (20%)

Query: 70  VLISSLPRKKY-SLQQLLRVSVAQIL----------YLDVADYAVVDLAVEQAKRDKENR 118
           +L+S L R++  S+Q+L+RV   + +          Y+D++   V     E  ++ +E  
Sbjct: 46  ILLSELSRRRIRSIQKLIRVGRNEPVVVLRVDKEKGYIDLSKRRVSP---EDKEKCEERF 102

Query: 119 HFAKLVNSILRRVSR----EKIELLQRIA 143
             +KLV SILR V+     E  EL QRI 
Sbjct: 103 AKSKLVYSILRHVAEKLGYELEELYQRIG 131


>gnl|CDD|36314 KOG1098, KOG1098, KOG1098, Putative SAM-dependent rRNA
           methyltransferase SPB1 [RNA processing and modification,
           General function prediction only].
          Length = 780

 Score = 29.6 bits (66), Expect = 1.6
 Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 3/33 (9%)

Query: 244 SVLDLCAAPGG---KTAQLIVSGAKVTALDVSK 273
            VLDLCAAPGG     +Q +  G+ +  +D+  
Sbjct: 47  VVLDLCAAPGGWLQVASQSMPVGSLIVGVDLVP 79


>gnl|CDD|32715 COG2890, HemK, Methylase of polypeptide chain release factors
           [Translation, ribosomal structure and biogenesis].
          Length = 280

 Score = 29.6 bits (66), Expect = 1.6
 Identities = 30/125 (24%), Positives = 53/125 (42%), Gaps = 6/125 (4%)

Query: 244 SVLDLCAAPGGKTAQLIVSG--AKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDY 301
            +LDL    G     L   G  A+V A+D+S   L   R N +R  L    +++ D F+ 
Sbjct: 113 RILDLGTGSGAIAIALAKEGPDAEVIAVDISPDALALARENAERNGLVRVLVVQSDLFE- 171

Query: 302 CPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSAC---FQRKLLLQGISFVKPG 358
             +  FD ++ + P          P+V+       +V         R++L +    +KPG
Sbjct: 172 PLRGKFDLIVSNPPYIPAEDPELLPEVVRYEPLLALVGGGDGLEVYRRILGEAPDILKPG 231

Query: 359 GIVVF 363
           G+++ 
Sbjct: 232 GVLIL 236


>gnl|CDD|31264 COG1064, AdhP, Zn-dependent alcohol dehydrogenases [General
           function prediction only].
          Length = 339

 Score = 29.4 bits (66), Expect = 2.1
 Identities = 31/142 (21%), Positives = 51/142 (35%), Gaps = 17/142 (11%)

Query: 263 GAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYCP--KKLFDAVLVDAPCSSTG 320
           GA+V A+  S+ +LE  +       L A+ +I     D     K++ DA++         
Sbjct: 190 GAEVIAITRSEEKLELAK------KLGADHVINSSDSDALEAVKEIADAIID---TVGPA 240

Query: 321 TIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKV 380
           T+      L    T  +V         LL     +    I +  +    + D EE +   
Sbjct: 241 TLEPSLKALRRGGTLVLVGLPGGGPIPLLPAFLLI-LKEISIVGSLVGTRADLEEALDFA 299

Query: 381 LRSS--PIPVELVPL---NSAY 397
                 P  +E +PL   N AY
Sbjct: 300 AEGKIKPEILETIPLDEINEAY 321


>gnl|CDD|73191 cd00315, Cyt_C5_DNA_methylase, Cytosine-C5 specific DNA methylases;
           Methyl transfer reactions play an important role in many
           aspects of biology. Cytosine-specific DNA methylases are
           found both in prokaryotes and eukaryotes. DNA
           methylation, or the covalent addition of a methyl group
           to cytosine within the context of the CpG dinucleotide,
           has profound effects on the mammalian genome. These
           effects include transcriptional repression via
           inhibition of transcription factor binding or the
           recruitment of methyl-binding proteins and their
           associated chromatin remodeling factors, X chromosome
           inactivation, imprinting and the suppression of
           parasitic DNA sequences. DNA methylation is also
           essential for proper embryonic development and is an
           important player in both DNA repair and genome
           stability..
          Length = 275

 Score = 29.1 bits (65), Expect = 2.4
 Identities = 23/75 (30%), Positives = 32/75 (42%), Gaps = 4/75 (5%)

Query: 243 LSVLDLCAAPGGKTAQLIVSGAK-VTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDY 301
           L V+DL A  GG    L  +G + V A ++ K   E    N     L   DI ++D  D+
Sbjct: 1   LRVIDLFAGIGGFRLGLEKAGFEIVAANEIDKSAAETYEANF-PNKLIEGDITKIDEKDF 59

Query: 302 CPKKLFDAVLVDAPC 316
            P    D +    PC
Sbjct: 60  IPD--IDLLTGGFPC 72


>gnl|CDD|173909 cd00818, IleRS_core, catalytic core domain of isoleucyl-tRNA
           synthetases.  Isoleucine amino-acyl tRNA synthetases
           (IleRS) catalytic core domain . This class I enzyme is a
           monomer which aminoacylates the 2'-OH of the nucleotide
           at the 3' of the appropriate tRNA. The core domain is
           based on the Rossman fold and is responsible for the
           ATP-dependent formation of the enzyme bound
           aminoacyl-adenylate. It contains the characteristic
           class I HIGH and KMSKS motifs, which are involved in ATP
           binding.  IleRS has an insertion in the core domain,
           which is subject to both deletions and rearrangements.
           This editing region hydrolyzes mischarged cognate tRNAs
           and thus prevents the incorporation of chemically
           similar amino acids.
          Length = 338

 Score = 29.1 bits (66), Expect = 2.7
 Identities = 17/45 (37%), Positives = 24/45 (53%), Gaps = 5/45 (11%)

Query: 130 RVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACIS 174
           RV++ K  LL+    ++ IPEW K R  N+  + R     D CIS
Sbjct: 156 RVTKIKDRLLEANDKVNWIPEWVKNRFGNWL-ENR----RDWCIS 195


>gnl|CDD|147386 pfam05175, MTS, Methyltransferase small domain.  This domain is
           found in ribosomal RNA small subunit methyltransferase C
           as well as other methyltransferases .
          Length = 170

 Score = 29.1 bits (66), Expect = 2.8
 Identities = 19/70 (27%), Positives = 28/70 (40%), Gaps = 2/70 (2%)

Query: 244 SVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDY 301
            VLDL    G  G          +VT +D++ R LE  R NL    L   ++   D +  
Sbjct: 34  KVLDLGCGYGVLGAALAKRSPDLEVTMVDINARALESARANLAANGLENGEVFWSDLYSA 93

Query: 302 CPKKLFDAVL 311
                FD ++
Sbjct: 94  VEPGKFDLII 103


>gnl|CDD|36940 KOG1729, KOG1729, KOG1729, FYVE finger containing protein [General
           function prediction only].
          Length = 288

 Score = 28.9 bits (64), Expect = 3.3
 Identities = 17/72 (23%), Positives = 23/72 (31%), Gaps = 11/72 (15%)

Query: 323 RRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNC----SLDKQDSEEVVQ 378
           RRH      R+  DIV + C + + LL     +    I V   C        +   E   
Sbjct: 184 RRHH----CRNCGDIVCAPCSRNRFLLP---NLSTKPIRVCDICFEELEKGARGDREDSL 236

Query: 379 KVLRSSPIPVEL 390
            V      P  L
Sbjct: 237 PVFHGKCYPNWL 248


>gnl|CDD|30771 COG0422, ThiC, Thiamine biosynthesis protein ThiC [Coenzyme
           metabolism].
          Length = 432

 Score = 28.6 bits (64), Expect = 3.4
 Identities = 14/56 (25%), Positives = 25/56 (44%), Gaps = 2/56 (3%)

Query: 372 DSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVS 427
           D  E+ + ++R+SP+PV  VP+  A  +       L+ + +        E   GV 
Sbjct: 103 DLHEIREWIIRNSPVPVGTVPIYQALEEVNGKVEDLTEDDFFDTVEKQAE--QGVD 156


>gnl|CDD|38290 KOG3080, KOG3080, KOG3080, Nucleolar protein-like/EBNA1-binding
           protein [RNA processing and modification].
          Length = 328

 Score = 28.5 bits (63), Expect = 3.4
 Identities = 13/35 (37%), Positives = 22/35 (62%), Gaps = 1/35 (2%)

Query: 109 EQAKRDKENRHFAKLV-NSILRRVSREKIELLQRI 142
           E+A++ +E + F K V  + L+   REK E L++I
Sbjct: 200 EEARKQRELKKFGKQVQKAKLQERQREKKETLEKI 234


>gnl|CDD|143905 pfam00133, tRNA-synt_1, tRNA synthetases class I (I, L, M and V).
           Other tRNA synthetase sub-families are too dissimilar to
           be included.
          Length = 606

 Score = 28.5 bits (64), Expect = 3.6
 Identities = 19/108 (17%), Positives = 36/108 (33%), Gaps = 32/108 (29%)

Query: 130 RVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACIS---------PLYID- 179
           R+       L+ +  +  +P+W ++R  N+     +  I D CIS         P +   
Sbjct: 387 RMKNLAEAALKAVEKVQFVPKWGEKRYGNW-----LENIQDWCISRQRWWGHPIPAWYSK 441

Query: 180 -----------------LTVKFDIETWAHKLNAVMLPTGGIRLKELPE 210
                               +  IE W H+    +L  G   L++  +
Sbjct: 442 DTGEVYVRGSLKELVAGREEEEGIEAWLHRDAKDLLGKGAGTLEQDED 489


>gnl|CDD|36484 KOG1270, KOG1270, KOG1270, Methyltransferases [Coenzyme transport
           and metabolism].
          Length = 282

 Score = 28.0 bits (62), Expect = 5.1
 Identities = 20/82 (24%), Positives = 32/82 (39%), Gaps = 8/82 (9%)

Query: 237 FGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCN------LDRLHLYA 290
              L  + +LD+    G  +  L   GA+VT +D S   +E    +      L+    Y 
Sbjct: 85  SKPLLGMKILDVGCGGGLLSEPLARLGAQVTGIDASDDMVEVANEHKKMDPVLEGAIAYR 144

Query: 291 EDIIEMDAFDYCPKKLFDAVLV 312
            +  + D      K  FDAV+ 
Sbjct: 145 LEYEDTDVEGLTGK--FDAVVC 164


>gnl|CDD|145244 pfam01964, ThiC, ThiC family.  ThiC is found within the thiamine
           biosynthesis operon. ThiC is involved in pyrimidine
           biosynthesis. The precise catalytic function of ThiC is
           still not known. ThiC participates in the formation of
           4-Amino-5-hydroxymethyl-2-methylpyrimidine from AIR, an
           intermediate in the de novo pyrimidine biosynthesis.
          Length = 421

 Score = 28.2 bits (64), Expect = 5.2
 Identities = 16/70 (22%), Positives = 31/70 (44%), Gaps = 17/70 (24%)

Query: 372 DSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKI-----DGV 426
           D +E+ + +L +SP+PV  VP+  A  +     + ++ +       D+ + I     DGV
Sbjct: 101 DLDEIRRAILENSPVPVGTVPIYQAAERKGGSVVDMTED-------DLFDVIEEQAKDGV 153

Query: 427 SSGMDGFFAV 436
                 F  +
Sbjct: 154 D-----FMTI 158


>gnl|CDD|32409 COG2227, UbiG,
           2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol
           methylase [Coenzyme metabolism].
          Length = 243

 Score = 27.5 bits (61), Expect = 7.3
 Identities = 33/125 (26%), Positives = 48/125 (38%), Gaps = 28/125 (22%)

Query: 243 LSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLE--KLRCNLDRLHL-YAEDIIEMDAF 299
           L VLD+    G  +  L   GA VT +D S++ +E  KL      +++ Y +  +E  A 
Sbjct: 61  LRVLDVGCGGGILSEPLARLGASVTGIDASEKPIEVAKLHALESGVNIDYRQATVEDLAS 120

Query: 300 DYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGG 359
                  FD V     C          +VL      +    AC +          VKPGG
Sbjct: 121 A---GGQFDVVT----CM---------EVLEHVPDPESFLRACAKL---------VKPGG 155

Query: 360 IVVFS 364
           I+  S
Sbjct: 156 ILFLS 160


>gnl|CDD|173970 cd08205, RuBisCO_IV_RLP, Ribulose bisphosphate carboxylase like
           proteins, Rubisco-Form IV.  Ribulose bisphosphate
           carboxylase (Rubisco) plays an important role in the
           Calvin reductive pentose phosphate pathway. It catalyzes
           the primary CO2 fixation step. Rubisco is activated by
           carbamylation of an active site lysine, stabilized by a
           divalent cation, which then catalyzes the proton
           abstraction from the substrate ribulose 1,5 bisphosphate
           (RuBP) and leads to the formation of two molecules of
           3-phosphoglycerate. Members of the Rubisco family can be
           divided into 4 subgroups, Form I-IV, which differ in
           their taxonomic distribution and subunit composition.
           Form I-III have Rubisco activity, while Form IV, also
           called Rubisco-like proteins (RLP), are missing critical
           active site residues and therefore do not catalyze CO2
           fixation. They are believed to utilize a related
           enzymatic mechanism, but have divergent functions, like
           for example 2,3-diketo-5-methylthiopentyl-1-phosphate
           enolase or 5-methylthio-d-ribulose 1-phosphate
           isomerase.
          Length = 367

 Score = 27.1 bits (61), Expect = 8.8
 Identities = 15/46 (32%), Positives = 18/46 (39%), Gaps = 15/46 (32%)

Query: 139 LQRIAG--ISIIPEWFKERLENFYGK-----ERVLAISDACISPLY 177
           L R+AG    I P           G+     E  LAI+ AC  PL 
Sbjct: 276 LMRLAGADAVIFP--------GPGGRFPFSREECLAIARACRRPLG 313


>gnl|CDD|147240 pfam04965, GPW_gp25, Gene 25-like lysozyme.  This family includes
          the phage protein Gene 25 from T4 which is a structural
          component of the outer wedge of the baseplate that has
          acidic lysozyme activity. The family also includes
          relatives from bacteria that are also presumably
          lysozymes.
          Length = 98

 Score = 27.2 bits (61), Expect = 8.9
 Identities = 20/76 (26%), Positives = 28/76 (36%), Gaps = 14/76 (18%)

Query: 7  ARLVSSHLLSCVMRKRISLTCLLDLEYG--DSAFRLLSQRD-QILVRAIVNVTLRFLPRI 63
            L+++     V R           +YG  D  F  LS      + RAI    LRF PR+
Sbjct: 14 EDLLNTRPGERVSR----------PDYGLPDLIFEPLSPALRLAIARAIREAILRFEPRL 63

Query: 64 DAV-LDFVLISSLPRK 78
            V ++ V     P  
Sbjct: 64 RLVSVEVVPDEDDPGT 79


>gnl|CDD|32588 COG2518, Pcm, Protein-L-isoaspartate carboxylmethyltransferase
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 209

 Score = 27.1 bits (60), Expect = 9.8
 Identities = 15/72 (20%), Positives = 31/72 (43%), Gaps = 1/72 (1%)

Query: 244 SVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFD-YC 302
            VL++    G + A L     +V +++  +   E+ R NL+ L      +   D    + 
Sbjct: 75  RVLEIGTGSGYQAAVLARLVGRVVSIERIEELAEQARRNLETLGYENVTVRHGDGSKGWP 134

Query: 303 PKKLFDAVLVDA 314
            +  +D ++V A
Sbjct: 135 EEAPYDRIIVTA 146


  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    0.406 

Gapped
Lambda     K      H
   0.267   0.0796    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 5,411,157
Number of extensions: 291317
Number of successful extensions: 803
Number of sequences better than 10.0: 1
Number of HSP's gapped: 779
Number of HSP's successfully gapped: 49
Length of query: 445
Length of database: 6,263,737
Length adjustment: 97
Effective length of query: 348
Effective length of database: 4,167,664
Effective search space: 1450347072
Effective search space used: 1450347072
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: 59 (26.4 bits)