RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

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

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



>gnl|CDD|182822 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
          Length = 427

 Score =  243 bits (622), Expect = 8e-65
 Identities = 137/402 (34%), Positives = 212/402 (52%), Gaps = 38/402 (9%)

Query: 4   GMNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFLPRI 63
            MN R +++  +  V+ +  SL+  L      +  + +S +D+ L++ +    LR LPR+
Sbjct: 1   SMNLRALAAAAILQVVDQGQSLSAALP-----ALQQKVSDKDRALLQELCYGVLRRLPRL 55

Query: 64  DAVLDFVLISSLPRKKYSLQQLLRVSVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKL 123
           + ++  +L   L  K+  +  LL V + Q+LY  +  +A VD  VE AK  K       L
Sbjct: 56  EWLIAQLLAKPLKGKQRIVHALLLVGLYQLLYTRIPAHAAVDETVEAAKALK-RPWAKGL 114

Query: 124 VNSILRRVSREKIELLQRIAGISII----PEWFKERLENFYGK--ERVLAISDACISPL- 176
           VN++LRR  RE+ ELL  +    +     P W  +RL+  Y +  + +LA ++    P+ 
Sbjct: 115 VNAVLRRFQREQEELLAELQADPVARYNHPSWLIKRLKKAYPEQWQAILAANNQ-RPPMW 173

Query: 177 ------------YIDLTVKFDIETWAHKLNAVMLPTGGIRLKELPESIVSLPGFAEGVWW 224
                       Y+ L  +  IE + H +         IRL E P  +  LPGFAEG   
Sbjct: 174 LRVNRRHHSRDAYLALLAEAGIEAFPHAVGP-----DAIRL-ETPVPVHQLPGFAEGWVS 227

Query: 225 VQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQL--IVSGAKVTALDVSKRRLEKLRCN 282
           VQDA+A +   L    N   VLD CAAPGGKTA +  +   A+V ALD+  +RLE++R N
Sbjct: 228 VQDAAAQLAATLLAPQNGERVLDACAAPGGKTAHILELAPQAQVVALDIDAQRLERVREN 287

Query: 283 LDRLHLYAEDIIEMDAFD---YCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVK 339
           L RL L A  +I  DA D   +   + FD +L+DAPCS+TG IRRHPD+ W R  +DI  
Sbjct: 288 LQRLGLKAT-VIVGDARDPAQWWDGQPFDRILLDAPCSATGVIRRHPDIKWLRRPEDIAA 346

Query: 340 SACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVL 381
            A  Q ++L      +KPGG ++++ CS+  +++E+ ++  L
Sbjct: 347 LAALQSEILDALWPLLKPGGTLLYATCSILPEENEQQIKAFL 388


>gnl|CDD|184895 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
          Length = 444

 Score =  225 bits (575), Expect = 3e-59
 Identities = 135/429 (31%), Positives = 212/429 (49%), Gaps = 51/429 (11%)

Query: 41  LSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQLLRVSVAQILYLD-VA 99
           LS +D+ L+  +V  T++    +D  L   +        +    LLR+S+ Q+LYLD V 
Sbjct: 36  LSDKDKALLTELVYGTIQRKLTLDYYLAPFIKKRKKLDPWVRN-LLRMSLYQLLYLDKVP 94

Query: 100 DYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREKIELLQRIAG----ISI---IPEWF 152
           D+A V+ AVE AK+ + ++  AK VN +LR + RE +  +  I      +SI    P W 
Sbjct: 95  DHAAVNEAVEIAKK-RGHKGIAKFVNGVLRNILREGLPDIDEIKDPVKRLSIKYSHPVWL 153

Query: 153 KERLENFYGKERVLAISDACISPLYIDL---TVKFDIETWAHKLNAVMLPTGGIRLKE-- 207
            +R  + YG+E+   I ++   P    +   T+K  +E    KL        G  ++E  
Sbjct: 154 VKRWIDQYGEEKAEKILESLNEPPKASIRVNTLKISVEELIEKLEE-----EGYEVEESL 208

Query: 208 -LPE-------SIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKT--- 256
             PE       +I     F +G+  +QD S+ +           +VLD CAAPGGKT   
Sbjct: 209 LSPEALVIEKGNIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHI 268

Query: 257 AQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYC--PKKL---FDAVL 311
           A+L+ +  KV ALD+ + +L+ +  N  RL L     IE  A D     +K    FD +L
Sbjct: 269 AELLKNTGKVVALDIHEHKLKLIEENAKRLGL---TNIETKALDARKVHEKFAEKFDKIL 325

Query: 312 VDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQ 371
           VDAPCS  G IRR PD+ + +  +DI      Q ++L     ++K GGI+V+S C+++K+
Sbjct: 326 VDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKE 385

Query: 372 DSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMD 431
           ++EEV++  L   P   ELVPL       +   +    +G+++I P+          G D
Sbjct: 386 ENEEVIEAFLEEHP-EFELVPLQHEKPDELVYEVK---DGYLQILPND--------YGTD 433

Query: 432 GFFAVALRR 440
           GFF   LR+
Sbjct: 434 GFFIAKLRK 442


>gnl|CDD|161931 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
           RsmB.  The seed alignment is built from bacterial
           sequences only. Eukaryotic homologs include Nop2, a
           protein required for processing pre-rRNA, that is likely
           also a rRNA methyltransferase, although the fine
           specificity may differ. Cutoff scores are set to avoid
           treating archaeal and eukaroytic homologs automatically
           as functionally equivalent, although they may have very
           similar roles.
          Length = 426

 Score =  208 bits (531), Expect = 3e-54
 Identities = 124/393 (31%), Positives = 195/393 (49%), Gaps = 33/393 (8%)

Query: 21  KRISLTCLLDLEYGDSAFRLL-------SQRDQILVRAIVNVTLRFLPRIDAVLDFVLIS 73
           + I+   L  LE G S   LL       S +D+ L++ +    LR L ++D ++  ++  
Sbjct: 1   RSIAAQALEQLEQGQSLSNLLPPLQQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDR 60

Query: 74  SLPRKKYSLQQLLRVSVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSR 133
            +  K  ++  L+ V + Q+LY  +  +A V   VE AK  K  +    LVN +LRR  R
Sbjct: 61  PMKGKPRTVHYLILVGLYQLLYTRIPAHAAVAETVEGAKAIK-RKGLKGLVNGVLRRFQR 119

Query: 134 EKIELLQ---RIAGISIIPEWFKERL-ENFYGKERVLAISDACISPLYIDLTV---KFDI 186
           E+ ELL     +    + PEW  +RL + + G+ +  +I +A      + L +   K   
Sbjct: 120 EQEELLAEFNALDARYLHPEWLVKRLQKAYPGQWQ--SICEANNQRPPMWLRINRTKHSR 177

Query: 187 ETWAHKLNAV-------MLPTGGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGT 239
           + W   L           L    +RL E P ++ +LPGF EG   VQDASA         
Sbjct: 178 DEWLALLAEAGMKGFPHDLAPDAVRL-ETPAAVHALPGFEEGWVTVQDASAQWVATWLAP 236

Query: 240 LNNLSVLDLCAAPGGKTAQL--IVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMD 297
            N  ++LD CAAPGGKT  +  +   A+V ALD+ + RL+++  NL RL L  +     D
Sbjct: 237 QNEETILDACAAPGGKTTHILELAPQAQVVALDIHEHRLKRVYENLKRLGLTIK-AETKD 295

Query: 298 A-----FDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGI 352
                   +   + FD +L+DAPCS+TG IRRHPD+ W R   DI + A  Q ++L    
Sbjct: 296 GDGRGPSQWAENEQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIW 355

Query: 353 SFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSP 385
             +K GG +V++ CS+  +++ E ++  L+  P
Sbjct: 356 PLLKTGGTLVYATCSVLPEENSEQIKAFLQEHP 388


>gnl|CDD|184894 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
          Length = 434

 Score =  193 bits (492), Expect = 9e-50
 Identities = 118/387 (30%), Positives = 176/387 (45%), Gaps = 56/387 (14%)

Query: 82  LQQLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSR--EKIEL 138
           L+ LL + + Q+ Y+D +   A V+  VE AK++      A +VN ILR+  R  E  + 
Sbjct: 74  LRWLLHLGLYQLRYMDRIPASAAVNTTVELAKQNGLGG-LAGVVNGILRQYLRAREAGDP 132

Query: 139 L-------QRIAGISIIPEWFKERLENFYGKERVLAISDACISPLYIDLTV---KFDIET 188
           L       +R+A +   P+W  +    + G E    +      P  +DL +   +  +E 
Sbjct: 133 LPLPEDPIERLAILHSFPDWLVKLWLEWLGLEEAEQLCKWFNQPPSLDLRINPLRTSLEE 192

Query: 189 WAHKLNAVMLPT-------GGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLN 241
               L    +          G+RL   P SI  LPG+ EG W VQD SA +   L     
Sbjct: 193 VQAALAEAGITATPIPGLPQGLRLTGNPGSIRQLPGYEEGWWTVQDRSAQLVAPLLDPQP 252

Query: 242 NLSVLDLCAAPGGKT---AQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDA 298
              +LD CAAPGGKT   A+L+    ++ A+D S  RL+KL+ N  RL L +  I+  D+
Sbjct: 253 GEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADS 312

Query: 299 FDYCPKK-----LFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGIS 353
            +    K      FD +L+DAPCS  GT+ RHPD  W +  + I + A  Q +LL     
Sbjct: 313 RNLLELKPQWRGYFDRILLDAPCSGLGTLHRHPDARWRQTPEKIQELAPLQAELLESLAP 372

Query: 354 FVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWI 413
            +KPGG +V++ C+L   ++E  +++ L   P            WK       L P    
Sbjct: 373 LLKPGGTLVYATCTLHPAENEAQIEQFLARHP-----------DWK-------LEPPKQ- 413

Query: 414 RITPDMLEKIDGVSSGMDGFFAVALRR 440
           +I P             DGFF   LR+
Sbjct: 414 KIWPH--------RQDGDGFFMAVLRK 432


>gnl|CDD|184897 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
          Length = 445

 Score =  172 bits (438), Expect = 1e-43
 Identities = 132/453 (29%), Positives = 217/453 (47%), Gaps = 52/453 (11%)

Query: 23  ISLTCLLDLEYG----DSAF-RLLS-----QRDQILVRAIVNVTLRFLPRIDAVLDFVLI 72
           ++L  L +LE G    D+   R+L      + D+ L   +VN  LR+  ++D +     I
Sbjct: 7   LALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFI-----I 61

Query: 73  SSLPRKKYS-----LQQLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKENRHFAKLVNS 126
           S             L+ +LR+ V Q+L+LD V  +A V+  V+ A++ K   H AKLVN 
Sbjct: 62  SRFYHHDLEKAAPVLKNILRLGVYQLLFLDRVPRWAAVNECVKLARKYK-GEHMAKLVNG 120

Query: 127 ILRRVSREKI---------ELLQRIAGISIIPEWFKERLENFYGKERVLAI-SDACISPL 176
           +LR +S E I            +R++ +   PEW  ER    YG+ER  A+ S    +PL
Sbjct: 121 VLRNISPETISLDEWLKGMPEAERLSLLYSHPEWLLERWIARYGEERTEAMLSYNNQAPL 180

Query: 177 Y---IDLTVKFDIETWAHKLN--AVMLPTGGIRLKELPESIVSL-PGFAEGVWWVQDASA 230
           +   I+  +K   E +       +V     G+    L +      P    G+  VQ+ + 
Sbjct: 181 FGFRIN-RLKTTPEKFLAAPADASVTFEKSGLPNFFLSKDFSLFEPFLKLGLVSVQNPTQ 239

Query: 231 SIPVQLFGTLNNLSVLDLCAAPGGKT---AQLIVSGAKVTALDVSKRRLEKLRCNLDRLH 287
           ++   L       +VLDLCAAPGGK+   A+L+ +  ++TA+D   ++LEK+R +   L 
Sbjct: 240 ALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALG 299

Query: 288 LYAEDIIEMDAFDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKL 347
           +   + IE DA  + P++  DA+L+DAPC+ TG + R  ++ W    + + +    Q +L
Sbjct: 300 ITIIETIEGDARSFSPEEQPDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAEL 359

Query: 348 LLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELVPLNSAYWKSIDMAMAL 407
           L    S +KPGG++V++ CS++ +++E  ++  L+  P   E     S            
Sbjct: 360 LDHAASLLKPGGVLVYATCSIEPEENELQIEAFLQRHP---EFSAEPSPGSLPEPFHEVA 416

Query: 408 SPEGWIRITPDMLEKIDGVSSGMDGFFAVALRR 440
            P+G I   P       G   G DG FA  LR+
Sbjct: 417 HPKGAILTLP-------GEHEGFDGGFAQRLRK 442


>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
          Length = 431

 Score =  147 bits (372), Expect = 7e-36
 Identities = 113/404 (27%), Positives = 195/404 (48%), Gaps = 37/404 (9%)

Query: 1   MKSGMNARLVSSHLLSCVMRKRISLTCLLDLEYGDSAFRLLSQRDQILVRAIVNVTLRFL 60
           MK+  N RL++  LL    RK      +   +  DS    L  +D+   + +V   +R  
Sbjct: 1   MKT--NVRLLAYRLL----RKYEKEKFIFREDV-DSVLSFLDDKDRRFFKELVWGVVR-- 51

Query: 61  PRIDAVLDFVLISSLPRKK---YSLQQLLRVSVAQILYLD-VADYAVVDLAVEQAKRDKE 116
              + +LD+  I+ L +KK    +++  LR+   Q+L+++ V DYA V   V+      +
Sbjct: 52  --KEELLDWY-INQLLKKKDIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLV----K 104

Query: 117 NRHFAKLVNSILRRVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACISPL 176
           N +F KLVN++LRR+    +   + +      P+W      +F  +E VL I +    PL
Sbjct: 105 NENFKKLVNAVLRRLR--TVPEPKELHLKYSHPKWLVNYWRSFLPEEAVLRIMEWNQEPL 162

Query: 177 YIDLTV--------KFDIETWAHKLNAVMLPTG--GIRLKELPESIVSLPGFAEGVWWVQ 226
              L V        +           AV        + +++L  ++       +G+  VQ
Sbjct: 163 PTMLRVNSLAITREEVIKILAEEGTEAVPGKHSPFSLIVRKLGVNMNDSRVIKDGLATVQ 222

Query: 227 DASASIPVQLFGTLNNLSVLDLCAAPGGKT---AQLIVSGAKVTALDVSKRRLEKLRCNL 283
             S+ I   L      L VLD CAAPGGKT   A+L+    K+ A+D+S+ +++ +  + 
Sbjct: 223 GESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHA 282

Query: 284 DRLHLYAEDIIEMDA--FDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSA 341
            RL L + +I   DA       +  FD +LVDAPC+S GT R HP+VL   + +D  K +
Sbjct: 283 KRLKLSSIEIKIADAERLTEYVQDTFDRILVDAPCTSLGTARNHPEVLRRVNKEDFKKLS 342

Query: 342 CFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSP 385
             Q +++ Q    ++ GGI+++S C++ K+++ EVV++ +    
Sbjct: 343 EIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKRFVYEQK 386


>gnl|CDD|129538 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase. 
          Length = 264

 Score =  136 bits (343), Expect = 2e-32
 Identities = 75/246 (30%), Positives = 121/246 (49%), Gaps = 18/246 (7%)

Query: 201 GGIRLKELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKT---A 257
           G   + E P  I S P +  G++++Q+AS+ IP           VLD+ AAPGGKT   +
Sbjct: 31  GFFEVNESPLPIGSTPEYLSGLYYIQEASSMIPPLALEPDPPERVLDMAAAPGGKTTQIS 90

Query: 258 QLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAF---DYCPKKLFDAVLVDA 314
            L+ +   + A + SK R + L  N++R  +    +   D        PK  FDA+L+DA
Sbjct: 91  ALMKNEGAIVANEFSKSRTKVLIANINRCGVLNVAVTNFDGRVFGAAVPK--FDAILLDA 148

Query: 315 PCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSE 374
           PCS  G IR+ P        +DI + +  Q++L+      +KPGG++V+S CSL+ +++E
Sbjct: 149 PCSGEGVIRKDPSRKKNWSEEDIQEISALQKELIDSAFDALKPGGVLVYSTCSLEPEENE 208

Query: 375 EVVQKVLRSSPIPVELVPLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFF 434
            VV  +L   P  VE +P    ++ +         +G +R+ P             +GFF
Sbjct: 209 AVVDYLLEKRPDVVEELPKGDEFFGANKGKE--EVKGALRVFPQ--------IYDCEGFF 258

Query: 435 AVALRR 440
              LR+
Sbjct: 259 VAKLRK 264


>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
           Reviewed.
          Length = 470

 Score = 99.2 bits (248), Expect = 2e-21
 Identities = 74/230 (32%), Positives = 120/230 (52%), Gaps = 22/230 (9%)

Query: 221 GVWWVQDASASIPVQ-LFGTLN-NLSVLDLCAAPGGKTAQLIV----SGAKVTALDVSKR 274
           G++++Q+AS+ +PV  LF   N    VLD+ AAPG KT Q+       GA V A + S  
Sbjct: 91  GLFYIQEASSMLPVAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIV-ANEYSAS 149

Query: 275 RLEKLRCNLDRLHLYAEDIIEMDA--F-DYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWT 331
           R++ L  N+ R  +    +   D   F    P+  FDA+L+DAPCS  GT+R+ PD L  
Sbjct: 150 RVKVLHANISRCGVSNVALTHFDGRVFGAALPET-FDAILLDAPCSGEGTVRKDPDALKN 208

Query: 332 RDTDDIVKSACFQRKLLLQGISFVKPGGIVVFSNCSLDKQDSEEVVQKVLRSSPIPVELV 391
              +  ++ A  QR+L+      +KPGG +V+S C+L++++++ V   +  + P  VE  
Sbjct: 209 WSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNREENQAVCLWLKETYPDAVEFE 268

Query: 392 PLNSAYWKSIDMAMALSPEGWIRITPDMLEKIDGVSSGMDGFFAVALRRL 441
           PL   +        AL+ EG++ + P + +         +GFF   LR+ 
Sbjct: 269 PLGDLF---PGAEKALTEEGFLHVFPQIYDS--------EGFFVARLRKT 307


>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
           Provisional.
          Length = 207

 Score = 48.7 bits (117), Expect = 3e-06
 Identities = 34/107 (31%), Positives = 53/107 (49%), Gaps = 16/107 (14%)

Query: 39  RLLSQRDQILVRA----IVNVTLRFLPRIDAVLDFVL----ISSLPRKKYSLQQLLRVSV 90
            LL   DQ  VR      +   +R    ID +LD V+    +  LPR     + +LR++V
Sbjct: 102 ELLQLADQEEVREYALERIGAVIRNRKEIDQLLDTVMVGWQLKRLPRID---RDILRLAV 158

Query: 91  AQILYLDVADYAVVDLAVEQAKR--DKENRHFAKLVNSILRRVSREK 135
            +IL+L+      ++ AVE AKR  D++ R F   +N +LRR+    
Sbjct: 159 VEILFLNTPAAVAINEAVELAKRYSDEQGRRF---INGVLRRLQDAL 202


>gnl|CDD|162621 TIGR01951, nusB, transcription antitermination factor NusB.  A
           transcription antitermination complex active in many
           bacteria was designated N-utilization substance (Nus) in
           E. coli because of its interaction with phage lambda
           protein N. This model represents NusB. Other components
           are NusA and NusG. NusE is, in fact, ribosomal protein
           S10.
          Length = 129

 Score = 38.6 bits (91), Expect = 0.003
 Identities = 29/109 (26%), Positives = 49/109 (44%), Gaps = 21/109 (19%)

Query: 37  AFRLLSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQL-------LRVS 89
             R L + D+     +V   L     ID ++   L      K +SL++L       LR++
Sbjct: 31  EERELDEEDREYFLELVRGVLENQEEIDELISPHL------KDWSLERLDPVDRAILRLA 84

Query: 90  VAQILYLDVADYAVV-DLAVEQAKR---DKENRHFAKLVNSILRRVSRE 134
             ++LY     Y VV + AVE AK+   +       K VN +L ++++E
Sbjct: 85  AYELLYRPDVPYKVVINEAVELAKKFGDEDS----HKFVNGVLDKIAKE 129


>gnl|CDD|163311 TIGR03534, RF_mod_PrmC, protein-(glutamine-N5) methyltransferase,
           release factor-specific.  Members of this protein family
           are HemK (PrmC), a protein once thought to be involved
           in heme biosynthesis but now recognized to be a
           protein-glutamine methyltransferase that modifies the
           peptide chain release factors. All members of the seed
           alignment are encoded next to the release factor 1 gene
           (prfA) and confirmed by phylogenetic analysis. SIMBAL
           analysis (manuscript in prep.) shows the motif
           [LIV]PRx[DE]TE (in Escherichia coli, IPRPDTE) confers
           specificity for the release factors rather than for
           ribosomal protein L3.
          Length = 251

 Score = 35.5 bits (83), Expect = 0.031
 Identities = 23/72 (31%), Positives = 30/72 (41%), Gaps = 2/72 (2%)

Query: 241 NNLSVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDA 298
             L VLDL    G            A+VTA+D+S   L   R N  RL L     ++ D 
Sbjct: 87  GPLRVLDLGTGSGAIALALAKERPDARVTAVDISPEALAVARKNAARLGLDNVTFLQSDW 146

Query: 299 FDYCPKKLFDAV 310
           F+  P   FD +
Sbjct: 147 FEPLPGGKFDLI 158


>gnl|CDD|178926 PRK00202, nusB, transcription antitermination protein NusB;
           Reviewed.
          Length = 137

 Score = 33.6 bits (78), Expect = 0.11
 Identities = 24/106 (22%), Positives = 50/106 (47%), Gaps = 21/106 (19%)

Query: 41  LSQRDQILVRAIVNVTLRFLPRIDAVLDFVLISSLPRKKYSLQQL-------LRVSVAQI 93
             + D    R++V   +     +D ++   L      K ++L++L       LR+++ ++
Sbjct: 37  YDKADPAYFRSLVRGVVENQAELDELISPYL------KDWTLERLDPVERAILRLALYEL 90

Query: 94  LYLDVADYAVV-DLAVEQAKR---DKENRHFAKLVNSILRRVSREK 135
           L+ D   Y VV + A+E AK+   +       K VN +L ++++E 
Sbjct: 91  LFRDDVPYKVVINEAIELAKKFGDEDS----HKFVNGVLDKIAKEL 132


>gnl|CDD|162639 TIGR01983, UbiG, ubiquinone biosynthesis O-methyltransferase.  This
           model represents an O-methyltransferase believed to act
           at two points in the ubiquinone biosynthetic pathway in
           bacteria (UbiG) and fungi (COQ3). A separate methylase
           (MenG/UbiE) catalyzes the single C-methylation step. The
           most commonly used names for genes in this family do not
           indicate whether this gene is an O-methyl, or C-methyl
           transferase.
          Length = 224

 Score = 33.0 bits (76), Expect = 0.17
 Identities = 33/143 (23%), Positives = 51/143 (35%), Gaps = 28/143 (19%)

Query: 224 WVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNL 283
           +++D        LFG    L VLD+    G  +  L   GA VT +D S+  +E  + + 
Sbjct: 32  YIRDTIRKNKKPLFG----LRVLDVGCGGGLLSEPLARLGANVTGIDASEENIEVAKLHA 87

Query: 284 DRLHLYAEDIIEMDAFDYC--PKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSA 341
            +  L   +       D      K FD V     C     +  H       D    +++ 
Sbjct: 88  KKDPLLKIEYRCTSVEDLAEKGAKSFDVVT----CME---VLEHVP-----DPQAFIRAC 135

Query: 342 CFQRKLLLQGISFVKPGGIVVFS 364
                        +KPGGI+ FS
Sbjct: 136 A----------QLLKPGGILFFS 148


>gnl|CDD|183301 PRK11760, PRK11760, putative 23S rRNA C2498 ribose 2'-O-ribose
           methyltransferase; Provisional.
          Length = 357

 Score = 32.1 bits (74), Expect = 0.29
 Identities = 15/24 (62%), Positives = 17/24 (70%)

Query: 247 DLCAAPGGKTAQLIVSGAKVTALD 270
           DL AAPGG T QL+  G  VTA+D
Sbjct: 217 DLGAAPGGWTYQLVRRGMFVTAVD 240


>gnl|CDD|184931 PRK14967, PRK14967, putative methyltransferase; Provisional.
          Length = 223

 Score = 31.6 bits (72), Expect = 0.41
 Identities = 36/133 (27%), Positives = 51/133 (38%), Gaps = 19/133 (14%)

Query: 245 VLDLCAAPGGKTAQLIVSGA-KVTALDVSKRRLEKLRCN--LDRLHLYAEDIIEMDAFDY 301
           VLDLC   G        +GA  VTA+D+S+R +   R N  L  + +   D+   D    
Sbjct: 40  VLDLCTGSGALAVAAAAAGAGSVTAVDISRRAVRSARLNALLAGVDV---DVRRGDWARA 96

Query: 302 CPKKLFDAVLVD---APCSSTGTIRRHPDVLWT--RDTDDIVKSACFQRKLLLQGISFVK 356
              + FD V+ +    P        R P   W    D   ++   C     LL       
Sbjct: 97  VEFRPFDVVVSNPPYVPAPPDAPPSRGPARAWDAGPDGRAVLDRLCDAAPALL------A 150

Query: 357 PGG--IVVFSNCS 367
           PGG  ++V S  S
Sbjct: 151 PGGSLLLVQSELS 163


>gnl|CDD|177728 PLN00113, PLN00113, leucine-rich repeat receptor-like protein
           kinase; Provisional.
          Length = 968

 Score = 30.6 bits (69), Expect = 0.92
 Identities = 17/42 (40%), Positives = 22/42 (52%), Gaps = 1/42 (2%)

Query: 207 ELPESIVSLPGFAEGVWWVQDASASIPVQLFGTLNNLSVLDL 248
           ++P ++ SLP       W    S  IP  L G  NNL+VLDL
Sbjct: 323 KIPVALTSLPRLQVLQLWSNKFSGEIPKNL-GKHNNLTVLDL 363


>gnl|CDD|162239 TIGR01177, TIGR01177, conserved hypothetical protein TIGR01177.
           This family is found exclusively in the Archaea.
          Length = 329

 Score = 30.5 bits (69), Expect = 0.93
 Identities = 21/83 (25%), Positives = 31/83 (37%), Gaps = 1/83 (1%)

Query: 234 VQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDI 293
           V L        VLD     GG   +  + GAKV   D+  + +   R NL+   +    +
Sbjct: 175 VNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKVIGCDIDWKMVAGARINLEHYGIEDFFV 234

Query: 294 IEMDAFDY-CPKKLFDAVLVDAP 315
              DA       +  DA+  D P
Sbjct: 235 KRGDATKLPLSSESVDAIATDPP 257


>gnl|CDD|162871 TIGR02469, CbiT, precorrin-6Y C5,15-methyltransferase
           (decarboxylating), CbiT subunit.  This model recognizes
           the CbiT methylase which is responsible, in part (along
           with CbiE), for methylating precorrin-6y (or
           cobalt-precorrin-6y) at both the 5 and 15 positions as
           well as the concomitant decarbozylation at C-12. In many
           organisms, this protein is fused to the CbiE subunit.
           The fused protein, when found in organisms catalyzing
           the oxidative version of the cobalamin biosynthesis
           pathway, is called CobL.
          Length = 124

 Score = 30.0 bits (68), Expect = 1.4
 Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 4/72 (5%)

Query: 245 VLDLCAAPGGKT--AQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDYC 302
           + D+ A  G  T  A  +V   +V A++ +   L  +  N  R  +    I+E DA +  
Sbjct: 23  LWDIGAGSGSITIEAARLVPNGRVYAIERNPEALRLIERNARRFGVSNIVIVEGDAPEAL 82

Query: 303 PKKL--FDAVLV 312
              L   D V +
Sbjct: 83  EDSLPEPDRVFI 94


>gnl|CDD|183320 PRK11805, PRK11805, N5-glutamine S-adenosyl-L-methionine-dependent
           methyltransferase; Provisional.
          Length = 307

 Score = 29.4 bits (67), Expect = 2.0
 Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 12/81 (14%)

Query: 244 SVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAED---IIEMDA 298
            +LDLC   G            A+V A+D+S   L     N++R  L  ED   +IE D 
Sbjct: 136 RILDLCTGSGCIAIACAYAFPDAEVDAVDISPDALAVAEINIERHGL--EDRVTLIESDL 193

Query: 299 FDYCPKKLFDAVL-----VDA 314
           F   P + +D ++     VDA
Sbjct: 194 FAALPGRRYDLIVSNPPYVDA 214


>gnl|CDD|163564 TIGR03852, sucrose_gtfA, sucrose phosphorylase.  In the forward
           direction, this enzyme uses phosphate to cleave sucrose
           into D-fructose + alpha-D-glucose 1-phosphate.
           Characterized representatives from Streptococcus mutans
           and Bifidobacterium adolescentis represent
           well-separated branches of a molecular phylogenetic
           tree. In S. mutans, the region including this gene has
           been associated with neighboring transporter genes and
           multiple sugar metabolism.
          Length = 470

 Score = 29.3 bits (66), Expect = 2.1
 Identities = 16/39 (41%), Positives = 23/39 (58%), Gaps = 1/39 (2%)

Query: 269 LDVSKRRLEK-LRCNLDRLHLYAEDIIEMDAFDYCPKKL 306
           LDV+    ++ +R NL+ L  +   II +DAF Y  KKL
Sbjct: 160 LDVTSETTKRFIRDNLENLAEHGASIIRLDAFAYAVKKL 198


>gnl|CDD|182340 PRK10258, PRK10258, biotin biosynthesis protein BioC; Provisional.
          Length = 251

 Score = 29.0 bits (65), Expect = 2.3
 Identities = 21/70 (30%), Positives = 28/70 (40%), Gaps = 1/70 (1%)

Query: 226 QDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDR 285
           Q  SA   + +        VLD    PG  +      G++VTALD+S   L + R   D 
Sbjct: 27  QRQSADALLAMLPQRKFTHVLDAGCGPGWMSRYWRERGSQVTALDLSPPMLAQARQK-DA 85

Query: 286 LHLYAEDIIE 295
              Y    IE
Sbjct: 86  ADHYLAGDIE 95


>gnl|CDD|185285 PRK15387, PRK15387, E3 ubiquitin-protein ligase SspH2; Provisional.
          Length = 788

 Score = 29.0 bits (64), Expect = 2.6
 Identities = 32/103 (31%), Positives = 48/103 (46%), Gaps = 21/103 (20%)

Query: 189 WAHKLNAVMLPTGGIRLKELPES---IVSLPGFAEGVWWVQDASASIPVQLFG--TLNNL 243
           WA+      LPT    L+EL  S   + SLP              ++P +L+     NN 
Sbjct: 328 WAYNNQLTSLPTLPSGLQELSVSDNQLASLP--------------TLPSELYKLWAYNN- 372

Query: 244 SVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRL 286
            +  L A P G   +LIVSG ++T+L V    L++L  + +RL
Sbjct: 373 RLTSLPALPSG-LKELIVSGNRLTSLPVLPSELKELMVSGNRL 414


>gnl|CDD|162684 TIGR02072, BioC, biotin biosynthesis protein BioC.  This enzyme,
           which is found in biotin biosynthetic gene clusters in
           proteobacteria, firmicutes, green-sulfur bacteria,
           fusobacterium and bacteroides, is believed to carry out
           an enzymatic step prior to the formation of pimeloyl-CoA
           (although attribution of this annotation is not
           traceable). The enzyme appears related to
           methyltransferases by homology.
          Length = 240

 Score = 28.8 bits (65), Expect = 2.6
 Identities = 28/146 (19%), Positives = 48/146 (32%), Gaps = 32/146 (21%)

Query: 225 VQDASASIPVQLFGTLNNL---SVLDLCAAPGGKTAQLIVSGAKV--TALDVSKRRLEKL 279
           +Q   A   + L          SVLD+    G  T  L+    +    ALD+S   L + 
Sbjct: 15  IQREMAKRLLALLKEKGIFIPASVLDIGCGTGYLTRALLKRFPQAEFIALDISAGMLAQA 74

Query: 280 RCNL-DRLHLYAEDIIEMDAFDYCPKKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIV 338
           +  L + +     D  ++   D      FD ++     +          + W  D    +
Sbjct: 75  KTKLSENVQFICGDAEKLPLED----SSFDLIV----SNLA--------LQWCDDLSQAL 118

Query: 339 KSACFQRKLLLQGISFVKPGGIVVFS 364
                           +KPGG++ FS
Sbjct: 119 SELA----------RVLKPGGLLAFS 134


>gnl|CDD|183310 PRK11779, sbcB, exonuclease I; Provisional.
          Length = 476

 Score = 28.3 bits (64), Expect = 4.5
 Identities = 25/88 (28%), Positives = 35/88 (39%), Gaps = 28/88 (31%)

Query: 384 SPIPVELVPLNS----AYWK----------SIDMAMALSPEGWIRITPDMLEKIDGVSSG 429
            P+P++LV LN     A  K           ID    L     +R  PD+ EK+  V + 
Sbjct: 292 LPVPLKLVHLNKCPVLAPAKTLRPEDAERLGIDRQQCLDNLALLRQNPDLREKVVAVFAE 351

Query: 430 M--------------DGFFAVALRRLIQ 443
                          DGFF+ A RRL++
Sbjct: 352 AEPFAPSDDVDAQLYDGFFSDADRRLME 379


>gnl|CDD|161854 TIGR00392, ileS, isoleucyl-tRNA synthetase.  The isoleucyl tRNA
           synthetase (IleS) is a class I amino acyl-tRNA ligase
           and is particularly closely related to the valyl tRNA
           synthetase. This model may recognize IleS from every
           species, including eukaryotic cytosolic and
           mitochondrial forms.
          Length = 861

 Score = 28.1 bits (63), Expect = 4.8
 Identities = 12/45 (26%), Positives = 23/45 (51%), Gaps = 5/45 (11%)

Query: 130 RVSREKIELLQRIAGISIIPEWFKERLENFYGKERVLAISDACIS 174
           +    K ++L++I  ++ +PEW + R  N+     +    D CIS
Sbjct: 427 KTKDIKDQMLEQIKKVNWVPEWGEGRFGNW-----LENRPDWCIS 466


>gnl|CDD|152360 pfam11925, DUF3443, Protein of unknown function (DUF3443).  This
           family of proteins are functionally uncharacterized.
           This protein is found in bacteria. Proteins in this
           family are typically between 400 to 434 amino acids in
           length. This protein has two conserved sequence motifs:
           NPV and DNNG.
          Length = 369

 Score = 28.1 bits (63), Expect = 5.1
 Identities = 11/44 (25%), Positives = 20/44 (45%)

Query: 222 VWWVQDASASIPVQLFGTLNNLSVLDLCAAPGGKTAQLIVSGAK 265
           V    + +++IP+Q+ G  +  SV   C++ G         GA 
Sbjct: 99  VTIGGETASNIPIQVIGDSSTASVPSSCSSGGASENTPADLGAN 142


>gnl|CDD|184932 PRK14968, PRK14968, putative methyltransferase; Provisional.
          Length = 188

 Score = 27.6 bits (62), Expect = 6.7
 Identities = 17/74 (22%), Positives = 31/74 (41%), Gaps = 2/74 (2%)

Query: 244 SVLDLCAAPGGKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDI--IEMDAFDY 301
            VL++    G        +G KV  +D++   +E  +CN    ++    +  I  D F+ 
Sbjct: 26  RVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGVEVIRSDLFEP 85

Query: 302 CPKKLFDAVLVDAP 315
                FD +L + P
Sbjct: 86  FRGDKFDVILFNPP 99


>gnl|CDD|163310 TIGR03533, L3_gln_methyl, protein-(glutamine-N5) methyltransferase,
           ribosomal protein L3-specific.  Members of this protein
           family methylate ribosomal protein L3 on a glutamine
           side chain. This family is related to HemK, a
           protein-glutamine methyltranferase for peptide chain
           release factors.
          Length = 284

 Score = 27.5 bits (62), Expect = 7.1
 Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 12/81 (14%)

Query: 244 SVLDLCAAPG--GKTAQLIVSGAKVTALDVSKRRLEKLRCNLDRLHLYAED---IIEMDA 298
            +LDLC   G            A+V A+D+S   L     N++R  L  ED   +I+ D 
Sbjct: 124 RILDLCTGSGCIAIACAYAFPEAEVDAVDISPDALAVAEINIERHGL--EDRVTLIQSDL 181

Query: 299 FDYCPKKLFDAVL-----VDA 314
           F   P + +D ++     VDA
Sbjct: 182 FAALPGRKYDLIVSNPPYVDA 202


>gnl|CDD|161832 TIGR00348, hsdR, type I site-specific deoxyribonuclease, HsdR
           family.  Members of this family are assumed to differ
           from each other in DNA site specificity.
          Length = 667

 Score = 27.4 bits (61), Expect = 8.4
 Identities = 19/91 (20%), Positives = 35/91 (38%), Gaps = 11/91 (12%)

Query: 89  SVAQILYLDVADYAVVDLAVEQAKRDKENRHFAKLVNSILRRVSREKIELL----QRIAG 144
                 +LD      +D   ++       R   ++    L+    +K + +     R+  
Sbjct: 443 DRLPEDHLDRKK---LDAFFDEIFELLPER-IREITKESLKEK-LQKTKKILFNEDRLES 497

Query: 145 IS-IIPEWFKERLENFYGKERVLAIS-DACI 173
           I+  I E + +  E F  K  V+AIS  AC+
Sbjct: 498 IAKDIAEHYAKFKELFKFKAMVVAISRYACV 528


>gnl|CDD|152126 pfam11690, DUF3287, Protein of unknown function (DUF3287).  This
           eukaryotic family of proteins has no known function.
          Length = 144

 Score = 27.3 bits (60), Expect = 8.7
 Identities = 13/33 (39%), Positives = 17/33 (51%)

Query: 106 LAVEQAKRDKENRHFAKLVNSILRRVSREKIEL 138
           LAV+  KR  E R   K +N +L  V+    EL
Sbjct: 66  LAVQHQKRSLEKRKIRKKINRMLLIVTAISREL 98


>gnl|CDD|149353 pfam08241, Methyltransf_11, Methyltransferase domain.  Members of
           this family are SAM dependent methyltransferases.
          Length = 95

 Score = 27.3 bits (61), Expect = 9.2
 Identities = 29/120 (24%), Positives = 44/120 (36%), Gaps = 27/120 (22%)

Query: 246 LDLCAAPGGKTAQLI-VSGAKVTALDVSKRRLEKLRCNLDRLHLYAEDIIEMDAFDY-CP 303
           LD+    G  T  L  + GA+VT +D+S   L   R       L     +  DA D   P
Sbjct: 1   LDVGCGTGLLTEALARLPGAQVTGVDLSPEMLALARKRAQEDGL---TFVVGDAEDLPFP 57

Query: 304 KKLFDAVLVDAPCSSTGTIRRHPDVLWTRDTDDIVKSACFQRKLLLQGISFVKPGGIVVF 363
            + FD V+     S          +    D +  ++      ++L       KPGG +V 
Sbjct: 58  DESFDVVV----SSLV--------LHHLPDPERALREI---ARVL-------KPGGKLVI 95


>gnl|CDD|147828 pfam05890, Ebp2, Eukaryotic rRNA processing protein EBP2.  This
           family consists of several Eukaryotic rRNA processing
           protein EBP2 sequences. Ebp2p is required for the
           maturation of 25S rRNA and 60S subunit assembly. Ebp2p
           may be one of the target proteins of Rrs1p for executing
           the signal to regulate ribosome biogenesis. This family
           also plays a role in chromosome segregation.
          Length = 268

 Score = 26.9 bits (60), Expect = 9.9
 Identities = 17/66 (25%), Positives = 31/66 (46%), Gaps = 7/66 (10%)

Query: 107 AVEQAKRDKENRHFAKLV-NSILRRVSREKIELLQRIAGISIIPEWFKERLENFYGKERV 165
           A E+A++ +E + F K V    L+  ++EK ++L++I          K+R     G    
Sbjct: 133 ASEEARKQRELKKFGKQVQVEKLQERAKEKKDMLEKIKK------LKKKRKGGGEGDLFD 186

Query: 166 LAISDA 171
             + DA
Sbjct: 187 FLLDDA 192


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.323    0.138    0.406 

Gapped
Lambda     K      H
   0.267   0.0672    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 7,459,791
Number of extensions: 498766
Number of successful extensions: 1079
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1040
Number of HSP's successfully gapped: 45
Length of query: 445
Length of database: 5,994,473
Length adjustment: 96
Effective length of query: 349
Effective length of database: 3,920,105
Effective search space: 1368116645
Effective search space used: 1368116645
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 (26.6 bits)