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)