RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 012998
(451 letters)
>gnl|CDD|237857 PRK14902, PRK14902, 16S rRNA methyltransferase B; Provisional.
Length = 444
Score = 287 bits (738), Expect = 5e-93
Identities = 128/392 (32%), Positives = 217/392 (55%), Gaps = 33/392 (8%)
Query: 61 RAVSAVRLMRIQFGGAFADL-LNKKGKGSGDNEMGYVERTLGFRTKDLDDRDLRLVTDIV 119
R ++ L++++ GA++++ LNK + +L D+D L+T++V
Sbjct: 6 RELALEVLIKVENNGAYSNIALNKV-----------------LKKSELSDKDKALLTELV 48
Query: 120 GGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEIVKLD-MPPYAVVDENVRL 178
GTI+ + LD+ L K ++P + +LR+ Y+++ LD +P +A V+E V +
Sbjct: 49 YGTIQRKLTLDYY---LAPFIKKRKKLDPWVRNLLRMSLYQLLYLDKVPDHAAVNEAVEI 105
Query: 179 AKVALRPGAGNLVNGILRKLVLLKDNNSLPLPKLEGNDRAQARALATIYSHPVWMVRRWT 238
AK G VNG+LR + LP + + L+ YSHPVW+V+RW
Sbjct: 106 AKKRGHKGIAKFVNGVLRNI----LREGLPDIDEIKDP---VKRLSIKYSHPVWLVKRWI 158
Query: 239 KYLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQLNLLKVPHELSLHLDEFIRVK 298
G+E+A K++ N P S+R N+ K ++ +L+ +L E SL E + ++
Sbjct: 159 DQYGEEKAEKILESLNEPPKASIRVNTLK-ISVEELIEKLEEEGYEVEESLLSPEALVIE 217
Query: 299 TGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQ 358
G N+ L K+GL +QDES+ LV +DP+ G +++D CAAPGGKT ++A L
Sbjct: 218 KG--NIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNT 275
Query: 359 GLVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRTFADNSTVKCDKVLLDAPCSGLG 418
G V A+DI++ +L+++ E AK + + I T D R + K DK+L+DAPCSGLG
Sbjct: 276 GKVVALDIHEHKLKLIEENAKRLGLTN-IETKALDARKVHEKFAEKFDKILVDAPCSGLG 334
Query: 419 VLSKRADLRWNRRLEDMEELKILQDELLDAAS 450
V+ ++ D+++N+ ED+E L+ +Q E+L++ +
Sbjct: 335 VIRRKPDIKYNKTKEDIESLQEIQLEILESVA 366
>gnl|CDD|237856 PRK14901, PRK14901, 16S rRNA methyltransferase B; Provisional.
Length = 434
Score = 238 bits (610), Expect = 5e-74
Identities = 130/356 (36%), Positives = 192/356 (53%), Gaps = 19/356 (5%)
Query: 102 FRTKDLDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQ-ILRIGFYE 160
R L D LVT++V G IR RR LD I L K + +P L+ +L +G Y+
Sbjct: 28 LRKYPLSGADRALVTELVYGCIRRRRTLDAWIDQLG---KKPAHKQPPDLRWLLHLGLYQ 84
Query: 161 IVKLD-MPPYAVVDENVRLAK-VALRPGAGNLVNGILRKLVLLKDN-NSLPLPKLEGNDR 217
+ +D +P A V+ V LAK L AG +VNGILR+ + ++ + LPLP D
Sbjct: 85 LRYMDRIPASAAVNTTVELAKQNGLGGLAG-VVNGILRQYLRAREAGDPLPLP----EDP 139
Query: 218 AQARALATIYSHPVWMVRRWTKYLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQ 277
+ LA ++S P W+V+ W ++LG EEA +L W N PS LR N + + ++
Sbjct: 140 IER--LAILHSFPDWLVKLWLEWLGLEEAEQLCKWFNQPPSLDLRINPLR-TSLEEVQAA 196
Query: 278 LNLLKVPHELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQPGQSI 337
L + L + +R+ ++ Q +EG VQD SA LV ++DPQPG+ I
Sbjct: 197 LAEAGITATPIPGLPQGLRLTGNPGSIRQLPGYEEGWWTVQDRSAQLVAPLLDPQPGEVI 256
Query: 338 VDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRT- 396
+D CAAPGGKT ++A + QG ++A+D + RL+ L E A+ + S I+ + AD R
Sbjct: 257 LDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKS-IKILAADSRNL 315
Query: 397 --FADNSTVKCDKVLLDAPCSGLGVLSKRADLRWNRRLEDMEELKILQDELLDAAS 450
D++LLDAPCSGLG L + D RW + E ++EL LQ ELL++ +
Sbjct: 316 LELKPQWRGYFDRILLDAPCSGLGTLHRHPDARWRQTPEKIQELAPLQAELLESLA 371
>gnl|CDD|237858 PRK14904, PRK14904, 16S rRNA methyltransferase B; Provisional.
Length = 445
Score = 229 bits (586), Expect = 2e-70
Identities = 121/354 (34%), Positives = 182/354 (51%), Gaps = 31/354 (8%)
Query: 107 LDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEIVKLD- 165
L+ D L T++V G +R+R LD +I H + P+L ILR+G Y+++ LD
Sbjct: 35 LERNDRALATELVNGVLRYRLQLDFIISRFYHHD--LEKAAPVLKNILRLGVYQLLFLDR 92
Query: 166 MPPYAVVDENVRLAKVALRPGAGNLVNGILRKLVLLKDNNSLPLPKLEGNDRAQARALAT 225
+P +A V+E V+LA+ LVNG+LR + ++ L + +A L+
Sbjct: 93 VPRWAAVNECVKLARKYKGEHMAKLVNGVLRNI----SPETISLDEWLK-GMPEAERLSL 147
Query: 226 IYSHPVWMVRRWTKYLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQLNLLKVPH 285
+YSHP W++ RW G+E ++ +NN P F R N K T + V
Sbjct: 148 LYSHPEWLLERWIARYGEERTEAMLSYNNQAPLFGFRINRLKT-TPEKFLAAPADASVTF 206
Query: 286 ELSLHLDEFIRVKTGLQNVIQAG-------LLKEGLCAVQDESAGLVVAVVDPQPGQSIV 338
E K+GL N + LK GL +VQ+ + L +++PQPG +++
Sbjct: 207 E-----------KSGLPNFFLSKDFSLFEPFLKLGLVSVQNPTQALACLLLNPQPGSTVL 255
Query: 339 DCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRTFA 398
D CAAPGGK+ +MA + +G + A+D +L + A + ++I TI D R+F+
Sbjct: 256 DLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGI-TIIETIEGDARSFS 314
Query: 399 DNSTVKCDKVLLDAPCSGLGVLSKRADLRWNRRLEDMEELKILQDELLD-AASL 451
D +LLDAPC+G GVL +RA+LRW E + EL LQ ELLD AASL
Sbjct: 315 PEEQP--DAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAELLDHAASL 366
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 203 bits (519), Expect = 1e-61
Identities = 107/288 (37%), Positives = 153/288 (53%), Gaps = 18/288 (6%)
Query: 166 MPPYAVVDENVRLAKVAL-RPGAGNLVNGILRKLVLLKDNNSLPLPKLEGNDRAQARALA 224
+PP+A VDE V AK L + A VN +LR+L LE R R
Sbjct: 1 VPPHAAVDETVEAAKERLGKDRAAKFVNAVLRRLERS------EEALLEEILRPAFR--- 51
Query: 225 TIYSHPVWMVRRWTKYLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQLNLLKVP 284
YSHP W+V + LG++EA + P SLR N+ K +L+ L V
Sbjct: 52 --YSHPEWLVEKLPDALGEDEAEAIAAALLRPPPRSLRVNTLK-ADVEELLEALEEAGVL 108
Query: 285 HELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQPGQSIVDCCAAP 344
E LDE +R++ + + EGL VQDE++ L V+DP+PG+ ++D CAAP
Sbjct: 109 DEKPWVLDEVLRIEAS-GPIGRLPEFAEGLIYVQDEASQLPALVLDPKPGERVLDLCAAP 167
Query: 345 GGKTLYMASCLSGQG-LVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRTFADNS-- 401
GGKT ++A + +G +V A+D++ RL+ L E K V +VI ++ D R A+
Sbjct: 168 GGKTTHLAELMENEGAIVVAVDVSPKRLKRLRENLKRLGVRNVI-VVNKDARRLAELLPG 226
Query: 402 TVKCDKVLLDAPCSGLGVLSKRADLRWNRRLEDMEELKILQDELLDAA 449
K D++LLDAPCSG GV+ + D++W R ED+ EL LQ E+L AA
Sbjct: 227 GEKFDRILLDAPCSGTGVIRRDPDVKWRRTPEDIAELAKLQKEILAAA 274
>gnl|CDD|233025 TIGR00563, rsmB, ribosomal RNA small subunit methyltransferase
RsmB. This protein is also known as sun protein. The
reading frame was originally interpreted as two reading
frames, fmu and fmv. The recombinant protein from E.
coli was shown to methylate only C967 of small subunit
(16S) ribosomal RNA and to produce only m5C at that
position. 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 [Protein synthesis, tRNA and rRNA base
modification].
Length = 426
Score = 184 bits (469), Expect = 1e-53
Identities = 106/349 (30%), Positives = 161/349 (46%), Gaps = 22/349 (6%)
Query: 103 RTKDLDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEIV 162
+ + D+D L+ ++ G +R LD LI L +P + L + +
Sbjct: 24 LQQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDRPMK---GKPRTVHYLILVGLYQL 80
Query: 163 KLD-MPPYAVVDENVRLAKVALRPGAGNLVNGILRKLVLLKDNNSLPLPKLEGNDRAQAR 221
+P +A V E V AK R G LVNG+LR+ ++ L
Sbjct: 81 LYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRF--QREQEELLAEF---------N 129
Query: 222 ALATIYSHPVWMVRR-WTKYLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQLNL 280
AL Y HP W+V+R Y GQ + + NN P LR N K +R + + L
Sbjct: 130 ALDARYLHPEWLVKRLQKAYPGQWQ--SICEANNQRPPMWLRINRTKH-SRDEWLALLAE 186
Query: 281 LKVPHELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQPGQSIVDC 340
+ + +R++T V +EG VQD SA V + PQ ++I+D
Sbjct: 187 AGMKGFPHDLAPDAVRLETPAA-VHALPGFEEGWVTVQDASAQWVATWLAPQNEETILDA 245
Query: 341 CAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRTFADN 400
CAAPGGKT ++ L+ Q V A+DI++ RL+ + E K + T D R +
Sbjct: 246 CAAPGGKTTHILE-LAPQAQVVALDIHEHRLKRVYENLKRLGLTIKAETKDGDGRGPSQW 304
Query: 401 STV-KCDKVLLDAPCSGLGVLSKRADLRWNRRLEDMEELKILQDELLDA 448
+ + D++LLDAPCS GV+ + D++W R+ D+ EL LQ E+LDA
Sbjct: 305 AENEQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDA 353
>gnl|CDD|236790 PRK10901, PRK10901, 16S rRNA methyltransferase B; Provisional.
Length = 427
Score = 161 bits (411), Expect = 4e-45
Identities = 113/349 (32%), Positives = 174/349 (49%), Gaps = 27/349 (7%)
Query: 105 KDLDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEIVKL 164
+ + D+D L+ ++ G +R L+ LI L K + ++ +L +G Y+++
Sbjct: 31 QKVSDKDRALLQELCYGVLRRLPRLEWLIAQLLA--KPLKGKQRIVHALLLVGLYQLLYT 88
Query: 165 DMPPYAVVDENVRLAKVALRPGAGNLVNGILRKLVLLKDNNSLPLPKLEGNDRAQARALA 224
+P +A VDE V AK RP A LVN +LR+ ++ L L +L+ + A+
Sbjct: 89 RIPAHAAVDETVEAAKALKRPWAKGLVNAVLRRF--QREQEEL-LAELQADPVAR----- 140
Query: 225 TIYSHPVWMVRRWTK-YLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQLNLLKV 283
Y+HP W+++R K Y Q +AI + NN P LR N R +R + L +
Sbjct: 141 --YNHPSWLIKRLKKAYPEQWQAI--LAANNQRPPMWLRVNRRH-HSRDAYLALLAEAGI 195
Query: 284 PHELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQPGQSIVDCCAA 343
+ IR++T + V Q EG +VQD +A L ++ PQ G+ ++D CAA
Sbjct: 196 EAFPHAVGPDAIRLETPVP-VHQLPGFAEGWVSVQDAAAQLAATLLAPQNGERVLDACAA 254
Query: 344 PGGKT---LYMASCLSGQGLVYAIDINKGRLRILNET-AKLHQVNSVIRTIHADLRTFAD 399
PGGKT L +A V A+DI+ RL + E +L +VI D + D
Sbjct: 255 PGGKTAHILELAPQAQ----VVALDIDAQRLERVRENLQRLGLKATVIVGDARDPAQWWD 310
Query: 400 NSTVKCDKVLLDAPCSGLGVLSKRADLRWNRRLEDMEELKILQDELLDA 448
D++LLDAPCS GV+ + D++W RR ED+ L LQ E+LDA
Sbjct: 311 G--QPFDRILLDAPCSATGVIRRHPDIKWLRRPEDIAALAALQSEILDA 357
>gnl|CDD|184896 PRK14903, PRK14903, 16S rRNA methyltransferase B; Provisional.
Length = 431
Score = 153 bits (389), Expect = 4e-42
Identities = 100/341 (29%), Positives = 171/341 (50%), Gaps = 26/341 (7%)
Query: 107 LDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEIVKLD- 165
LDD+D R ++V G +R LD I L + + P + LR+G Y+++ ++
Sbjct: 34 LDDKDRRFFKELVWGVVRKEELLDWYINQLLKKK----DIPPAVRVALRMGAYQLLFMNS 89
Query: 166 MPPYAVVDENVRLAKVALRPGAGNLVNGILRKLVLLKDNNSLPLPKLEGNDRAQARALAT 225
+P YA V E V+L K LVN +LR+L ++P PK L
Sbjct: 90 VPDYAAVSETVKLVK---NENFKKLVNAVLRRL------RTVPEPK----------ELHL 130
Query: 226 IYSHPVWMVRRWTKYLGQEEAIKLMVWNNSDPSFSLRANSRKGVTRADLVMQLNLLKVPH 285
YSHP W+V W +L +E +++M WN LR NS +TR +++ L
Sbjct: 131 KYSHPKWLVNYWRSFLPEEAVLRIMEWNQEPLPTMLRVNSLA-ITREEVIKILAEEGTEA 189
Query: 286 ELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQPGQSIVDCCAAPG 345
H + V+ N+ + ++K+GL VQ ES+ +V +++ +PG ++D CAAPG
Sbjct: 190 VPGKHSPFSLIVRKLGVNMNDSRVIKDGLATVQGESSQIVPLLMELEPGLRVLDTCAAPG 249
Query: 346 GKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRTFADNSTVKC 405
GKT +A + QG + A+DI++ +++++ + AK +++S I AD +
Sbjct: 250 GKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSS-IEIKIADAERLTEYVQDTF 308
Query: 406 DKVLLDAPCSGLGVLSKRADLRWNRRLEDMEELKILQDELL 446
D++L+DAPC+ LG ++ ED ++L +Q ++
Sbjct: 309 DRILVDAPCTSLGTARNHPEVLRRVNKEDFKKLSEIQLRIV 349
>gnl|CDD|188051 TIGR00446, nop2p, NOL1/NOP2/sun family putative RNA methylase.
[Protein synthesis, tRNA and rRNA base modification].
Length = 264
Score = 107 bits (269), Expect = 1e-26
Identities = 46/138 (33%), Positives = 77/138 (55%), Gaps = 4/138 (2%)
Query: 313 GLCAVQDESAGLVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLR 372
G Q+ S+ + ++P+ + ++D AAPGGKT ++ + +G + A +I+K R +
Sbjct: 51 GYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTK 110
Query: 373 ILNETAKLHQVN-SVIRTIHADLRTFADNSTVKCDKVLLDAPCSGLGVLSKRADLRWNRR 431
L + ++++ I+AD R F +K D +LLDAPCSG GV+ K + N
Sbjct: 111 AL--ISNINRMGVLNTIVINADGRKFGA-YLLKFDAILLDAPCSGEGVIRKDPSRKRNWS 167
Query: 432 LEDMEELKILQDELLDAA 449
ED++ +LQ EL+DAA
Sbjct: 168 EEDIKYCSLLQKELIDAA 185
>gnl|CDD|201649 pfam01189, Nol1_Nop2_Fmu, NOL1/NOP2/sun family.
Length = 277
Score = 106 bits (266), Expect = 5e-26
Identities = 54/140 (38%), Positives = 78/140 (55%), Gaps = 4/140 (2%)
Query: 312 EGLCAVQDESAGLVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRL 371
G VQD S+ L ++PQ + I+D CAAPGGKT ++A + +G V A+D NK RL
Sbjct: 63 NGAVTVQDASSQLDAIALNPQEDEFILDMCAAPGGKTTHIAELMKNEGTVVAVDRNKQRL 122
Query: 372 RILNETAKLHQV-NSVIRTIHADLR-TFADNSTVKCDKVLLDAPCSGLGVLSKRADLRWN 429
+ + + ++ I D R + D++LLDAPCSG GV+ + D++W
Sbjct: 123 KRVYAN--IQRLGVFNIIVQEGDARQIDQKLLGGEFDRILLDAPCSGTGVIRRDPDIKWL 180
Query: 430 RRLEDMEELKILQDELLDAA 449
RR D+ +L LQ ELL AA
Sbjct: 181 RREADIAQLAELQKELLKAA 200
>gnl|CDD|216253 pfam01029, NusB, NusB family. The NusB protein is involved in the
regulation of rRNA biosynthesis by transcriptional
antitermination.
Length = 126
Score = 86.9 bits (216), Expect = 1e-20
Identities = 36/99 (36%), Positives = 54/99 (54%), Gaps = 2/99 (2%)
Query: 102 FRTKDLDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEI 161
DLD+RD T++V G +R LD LI L + ++P+ ILR+G YE+
Sbjct: 28 LLEADLDERDRAFATELVYGVLRNLEELDALIEKLL-ENWPLERLDPVDRAILRLGLYEL 86
Query: 162 VKL-DMPPYAVVDENVRLAKVALRPGAGNLVNGILRKLV 199
+ L D+PP+ ++E V LAK + VNG+LRK+
Sbjct: 87 LYLDDIPPHVAINEAVELAKKFGGEKSAGFVNGVLRKIA 125
>gnl|CDD|238343 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 = 77.8 bits (192), Expect = 2e-17
Identities = 39/94 (41%), Positives = 56/94 (59%), Gaps = 2/94 (2%)
Query: 105 KDLDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEIVKL 164
KD DRD L T++V GT+RW LD +I L K +P + +LR+G Y+++ L
Sbjct: 31 KDKSDRDRGLATELVYGTLRWLALLDWIINPLLK--KPDVGKDPDVRNLLRLGLYQLLYL 88
Query: 165 DMPPYAVVDENVRLAKVALRPGAGNLVNGILRKL 198
D+PP+A VDE V +AK+ G LVN +LR+
Sbjct: 89 DVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRF 122
>gnl|CDD|238253 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 = 63.1 bits (154), Expect = 3e-12
Identities = 27/97 (27%), Positives = 45/97 (46%), Gaps = 3/97 (3%)
Query: 104 TKDLDDRDLRLVTDIVGGTIRWRRYLDHLICLLCHDEKTFSSMEPLLLQILRIGFYEI-- 161
L +D ++V G +R LD +I L ++ + ILR+ YE+
Sbjct: 30 KLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKK-WLLDRLDKVDRAILRLLLYELYQ 88
Query: 162 VKLDMPPYAVVDENVRLAKVALRPGAGNLVNGILRKL 198
+ D+PP ++E V LAK + VNG+LR++
Sbjct: 89 LLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRI 125
>gnl|CDD|183387 PRK11933, yebU, rRNA (cytosine-C(5)-)-methyltransferase RsmF;
Reviewed.
Length = 470
Score = 66.1 bits (162), Expect = 1e-11
Identities = 49/141 (34%), Positives = 76/141 (53%), Gaps = 7/141 (4%)
Query: 313 GLCAVQDESAGLVVAVV--DPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGR 370
GL +Q+ S+ L VA + D Q ++D AAPG KT +A+ ++ QG + A + + R
Sbjct: 91 GLFYIQEASSMLPVAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASR 150
Query: 371 LRILNETAKLHQ--VNSVIRTIHADLRTFADNSTVKCDKVLLDAPCSGLGVLSKRADLRW 428
+++L+ A + + V++V T H D R F D +LLDAPCSG G + K D
Sbjct: 151 VKVLH--ANISRCGVSNVALT-HFDGRVFGAALPETFDAILLDAPCSGEGTVRKDPDALK 207
Query: 429 NRRLEDMEELKILQDELLDAA 449
N E E+ Q EL+++A
Sbjct: 208 NWSPESNLEIAATQRELIESA 228
>gnl|CDD|233652 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 [Transcription, Transcription factors].
Length = 129
Score = 58.7 bits (143), Expect = 1e-10
Identities = 31/114 (27%), Positives = 54/114 (47%), Gaps = 7/114 (6%)
Query: 89 GDNEMGYVERTLGFRTKDLDDRDLRLVTDIVGGTIRWRRYLDHLI--CLLCHDEKTFSSM 146
N++ + ++LD+ D ++V G + + +D LI L ++ T +
Sbjct: 18 SGNDLEEIIEEF-LEEEELDEEDREYFRELVRGVLENQEEIDELISPHL---EDWTLERL 73
Query: 147 EPLLLQILRIGFYEIVKLDMPPYAVV-DENVRLAKVALRPGAGNLVNGILRKLV 199
+P+ ILR+ YE++ PY VV +E V LAK + VNG+L K+
Sbjct: 74 DPVDRAILRLAAYELLYRPDVPYKVVINEAVELAKKFGDDDSHKFVNGVLDKIA 127
>gnl|CDD|234686 PRK00202, nusB, transcription antitermination protein NusB;
Reviewed.
Length = 137
Score = 50.6 bits (122), Expect = 8e-08
Identities = 30/101 (29%), Positives = 46/101 (45%), Gaps = 6/101 (5%)
Query: 102 FRTKDLDDRDLRLVTDIVGGTIRWRRYLDHLI--CLLCHDEKTFSSMEPLLLQILRIGFY 159
+ D D +V G + + LD LI L + T ++P+ ILR+ Y
Sbjct: 32 LLEEQYDKADPAYFRSLVRGVVENQAELDELISPYL---KDWTLERLDPVERAILRLALY 88
Query: 160 EIVKLDMPPYAVV-DENVRLAKVALRPGAGNLVNGILRKLV 199
E++ D PY VV +E + LAK + VNG+L K+
Sbjct: 89 ELLFRDDVPYKVVINEAIELAKKFGDEDSHKFVNGVLDKIA 129
>gnl|CDD|223852 COG0781, NusB, Transcription termination factor [Transcription].
Length = 151
Score = 49.6 bits (119), Expect = 3e-07
Identities = 35/146 (23%), Positives = 59/146 (40%), Gaps = 9/146 (6%)
Query: 58 SPHRAVSAVRLMRIQ-FGGAFADLLNKKGKGSGDNEMGYVERTLGFRTKDLDDRDLRLVT 116
S R R + L+ G S ++ + +E D++ D
Sbjct: 2 SKKPPKLTRRQARELAVQALYQWELS--GSVSAEDILEDIEEEFVENELDIELADSEYFR 59
Query: 117 DIVGGTIRWRRYLDHLI--CLLCHDEKTFSSMEPLLLQILRIGFYEIVKLDMPPYAVV-D 173
+V G + + LD LI L + + ++ + ILR+ YE++ D PY VV +
Sbjct: 60 SLVKGVLENQEELDELISPHL---KKWSLERLDLVERAILRLALYELLFRDDVPYKVVIN 116
Query: 174 ENVRLAKVALRPGAGNLVNGILRKLV 199
E + LAK + VNG+L K+
Sbjct: 117 EAIELAKKFSGEDSHKFVNGVLDKIA 142
>gnl|CDD|238342 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 = 46.9 bits (112), Expect = 1e-06
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 12/87 (13%)
Query: 119 VGGTIRWRRYLDHLICLLCHDEK-----TFSSMEPLLLQILRIGFYEIVKLDMPPYAVV- 172
V G + +D LI EK + + + ILR+ YE++ L P+ VV
Sbjct: 47 VRGVLENIEEIDELI------EKHLRNWSLDRLAIVERAILRLAVYELLFLPDVPHPVVI 100
Query: 173 DENVRLAKVALRPGAGNLVNGILRKLV 199
+E + LAK + VNG+L K+
Sbjct: 101 NEAIELAKRFGGDDSHKFVNGVLDKIA 127
>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 = 45.5 bits (108), Expect = 3e-06
Identities = 20/96 (20%), Positives = 33/96 (34%), Gaps = 4/96 (4%)
Query: 337 IVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHADLRT 396
++D G L +AS + V +DI+ L + A + + + D
Sbjct: 2 VLDLGCGTGALALALASGPGAR--VTGVDISPVALELA-RKAAAALLADNVEVLKGDAEE 58
Query: 397 FADNSTVKCDKVLLDAPCSGLGVLSKRADLRWNRRL 432
+ D ++ D P L V L RRL
Sbjct: 59 LPPEADESFDVIISDPPLHHL-VEDLARFLEEARRL 93
>gnl|CDD|202251 pfam02475, Met_10, Met-10+ like-protein. The methionine-10 mutant
allele of N. crassa codes for a protein of unknown
function. However, homologous proteins have been found
in yeast suggesting this protein may be involved in
methionine biosynthesis, transport and/or utilisation.
Length = 199
Score = 43.1 bits (102), Expect = 9e-05
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 332 QPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIH 391
+ G+ +VD A G ++ +A S VYA+++N ++ L E KL++V VI I
Sbjct: 99 KEGEVVVDMFAGIGPFSIPIAK-HSKAKRVYAVELNPEAVKYLKENIKLNKVEGVISPIL 157
Query: 392 ADLRTFADNSTVKCDKVLLDAP 413
D+R D+V+++ P
Sbjct: 158 GDVRDVI--LEGVADRVIMNLP 177
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 38.2 bits (89), Expect = 0.001
Identities = 18/103 (17%), Positives = 32/103 (31%), Gaps = 10/103 (9%)
Query: 328 VVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVI 387
V+DP G G L A+ V ++++ + L + +
Sbjct: 4 VLDPGAG----------SGAFLLAAARAGPDARVVGVELDPEAAALARRRLALAGLAPRV 53
Query: 388 RTIHADLRTFADNSTVKCDKVLLDAPCSGLGVLSKRADLRWNR 430
R + D R + D VL + P K ++R
Sbjct: 54 RVVVGDARELLELPDGSFDLVLGNPPYGPRAGDPKDNRDLYDR 96
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 39.9 bits (94), Expect = 0.001
Identities = 22/82 (26%), Positives = 30/82 (36%), Gaps = 9/82 (10%)
Query: 333 PGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRT--I 390
PG +VD AAPGG + A L G + A+DI + + + I
Sbjct: 45 PGMVVVDLGAAPGGWSQVAAKKLGAGGKIVAVDILPMKPI-----PGVIFLQGDITDEDT 99
Query: 391 HADLRTFADNSTVKCDKVLLDA 412
L + V D VL D
Sbjct: 100 LEKLLEALGGAPV--DVVLSDM 119
>gnl|CDD|216666 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
hypothesised that the N-terminal domain of NS5 is a
methyltransferase involved in viral RNA capping.
Length = 177
Score = 38.0 bits (89), Expect = 0.003
Identities = 13/41 (31%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 329 VDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKG 369
+ P G++++D AAPGG + + G G V A+D+
Sbjct: 18 LKPGKGKTVLDLGAAPGGFSQVLLE-RGGAGKVVAVDLGPM 57
>gnl|CDD|233880 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 [Biosynthesis of cofactors,
prosthetic groups, and carriers, Heme, porphyrin, and
cobalamin].
Length = 124
Score = 36.5 bits (85), Expect = 0.006
Identities = 21/85 (24%), Positives = 36/85 (42%), Gaps = 2/85 (2%)
Query: 324 LVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQV 383
L ++ + +PG + D A G T+ A L G VYAI+ N L ++ + V
Sbjct: 10 LTLSKLRLRPGDVLWDIGAGTGSVTIEAAR-LVPNGRVYAIERNPEALDLIERNLRRFGV 68
Query: 384 NSVIRTIHADLRTFADNSTVKCDKV 408
++ I + D ++ D V
Sbjct: 69 SN-IVIVEGDAPEAPEDLLPDPDAV 92
>gnl|CDD|225136 COG2226, UbiE, Methylase involved in ubiquinone/menaquinone
biosynthesis [Coenzyme metabolism].
Length = 238
Score = 36.1 bits (84), Expect = 0.020
Identities = 20/74 (27%), Positives = 31/74 (41%), Gaps = 6/74 (8%)
Query: 331 PQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTI 390
+PG ++D G L +A G G V +DI++ L + E K + + +
Sbjct: 49 IKPGDKVLDVACGTGDMALLLAK-SVGTGEVVGLDISESMLEVAREKLK-KKGVQNVEFV 106
Query: 391 HAD---LRTFADNS 401
D L F DNS
Sbjct: 107 VGDAENLP-FPDNS 119
>gnl|CDD|232976 TIGR00438, rrmJ, cell division protein FtsJ. Methylates the 23S
rRNA. Previously known as cell division protein ftsJ.//
Trusted cutoff too high? [SS 10/1/04] [Protein
synthesis, tRNA and rRNA base modification].
Length = 188
Score = 35.6 bits (82), Expect = 0.027
Identities = 13/36 (36%), Positives = 22/36 (61%)
Query: 332 QPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDIN 367
+PG +++D AAPGG + + G+G V A+D+
Sbjct: 31 KPGDTVLDLGAAPGGWSQVAVEQVGGKGRVIAVDLQ 66
>gnl|CDD|225317 COG2519, GCD14, tRNA(1-methyladenosine) methyltransferase and
related methyltransferases [Translation, ribosomal
structure and biogenesis].
Length = 256
Score = 35.3 bits (82), Expect = 0.038
Identities = 23/92 (25%), Positives = 37/92 (40%), Gaps = 2/92 (2%)
Query: 322 AGLVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLH 381
AG +VA + PG +++ G T Y+A + +G V +I + + E
Sbjct: 83 AGYIVARLGISPGSRVLEAGTGSGALTAYLARAVGPEGHVTTYEIREDFAKTARENLSEF 142
Query: 382 QVNSVIRTIHADLRTFADNSTVKCDKVLLDAP 413
+ + D+R D V D V LD P
Sbjct: 143 GLGDRVTLKLGDVREGIDEEDV--DAVFLDLP 172
>gnl|CDD|221804 pfam12847, Methyltransf_18, Methyltransferase domain. Protein in
this family function as methyltransferases.
Length = 104
Score = 33.4 bits (77), Expect = 0.050
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 2/68 (2%)
Query: 333 PGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHA 392
PG ++D G + +A L V +D++ L + E AKL + I +
Sbjct: 1 PGARVLDIGCGTGSLAIELAR-LFPGARVTGVDLSPEMLELARENAKLA-LGPRITFVQG 58
Query: 393 DLRTFADN 400
D D
Sbjct: 59 DAPDALDL 66
>gnl|CDD|183025 PRK11188, rrmJ, 23S rRNA methyltransferase J; Provisional.
Length = 209
Score = 34.7 bits (80), Expect = 0.055
Identities = 15/35 (42%), Positives = 22/35 (62%)
Query: 332 QPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDI 366
+PG ++VD AAPGG + Y + + +G V A DI
Sbjct: 50 KPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACDI 84
>gnl|CDD|225318 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 34.2 bits (79), Expect = 0.11
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 2/67 (2%)
Query: 332 QPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIH 391
+ G++++D A G ++ +A G+ VYAIDIN + L E +L++V + I
Sbjct: 187 KEGETVLDMFAGVGPFSIPIAK--KGRPKVYAIDINPDAVEYLKENIRLNKVEGRVEPIL 244
Query: 392 ADLRTFA 398
D R A
Sbjct: 245 GDAREVA 251
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 34.0 bits (79), Expect = 0.13
Identities = 17/80 (21%), Positives = 34/80 (42%), Gaps = 4/80 (5%)
Query: 325 VVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVN 384
+ + +PG ++D G + +A + G V +D ++G L + E + ++
Sbjct: 43 TIKWLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLDFSEGMLAVGREKLRDLGLS 102
Query: 385 SVIRTIHAD---LRTFADNS 401
+ + D L F DNS
Sbjct: 103 GNVEFVQGDAEAL-PFPDNS 121
>gnl|CDD|223352 COG0275, COG0275, Predicted S-adenosylmethionine-dependent
methyltransferase involved in cell envelope biogenesis
[Cell envelope biogenesis, outer membrane].
Length = 314
Score = 32.2 bits (74), Expect = 0.44
Identities = 25/99 (25%), Positives = 40/99 (40%), Gaps = 7/99 (7%)
Query: 325 VVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVN 384
VV ++ P+P +D GG + + L G + ID + + I E K
Sbjct: 15 VVELLAPKPDGIYIDGTLGAGGHSRAILEKLPDLGRLIGIDRDPQAIAIAKERLKEFDGR 74
Query: 385 -SVIRTIHADLRTFADNSTV-KCDKVLLDAPCSGLGVLS 421
+++ A+L + K D +LLD LGV S
Sbjct: 75 VTLVHGNFANLAEALKELGIGKVDGILLD-----LGVSS 108
>gnl|CDD|129627 TIGR00536, hemK_fam, HemK family putative methylases. The gene
hemK from E. coli was found to contribute to heme
biosynthesis and originally suggested to be
protoporphyrinogen oxidase (Medline 95189105).
Functional analysis of the nearest homolog in
Saccharomyces cerevisiae, YNL063w, finds it is not
protoporphyrinogen oxidase and sequence analysis
suggests that HemK homologs have
S-adenosyl-methionine-dependent methyltransferase
activity (Medline 99237242). Homologs are found, usually
in a single copy, in nearly all completed genomes, but
varying somewhat in apparent domain architecture. Both
E. coli and H. influenzae have two members rather than
one. The members from the Mycoplasmas have an additional
C-terminal domain [Protein fate, Protein modification
and repair].
Length = 284
Score = 32.3 bits (74), Expect = 0.46
Identities = 19/81 (23%), Positives = 32/81 (39%), Gaps = 7/81 (8%)
Query: 315 CAVQDESAGLVVAVVDPQPG-QSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRI 373
V+ A L+ Q I+D G L +A V A+DI+ L +
Sbjct: 100 ELVEKALASLI-----SQNPILHILDLGTGSGCIALALAYEFP-NAEVIAVDISPDALAV 153
Query: 374 LNETAKLHQVNSVIRTIHADL 394
E A+ +Q+ + I ++L
Sbjct: 154 AEENAEKNQLEHRVEFIQSNL 174
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 31.9 bits (73), Expect = 0.46
Identities = 22/103 (21%), Positives = 39/103 (37%), Gaps = 2/103 (1%)
Query: 312 EGLCAVQDESAGLVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRL 371
G+ + E+ L+ + + I++ A G L+MA L G + I+ ++ R
Sbjct: 38 NGVPIIDPETGALLRLLARLSGPKRILEIGTAIGYSALWMALALPDDGRLTTIERDEERA 97
Query: 372 RILNETAKLHQVNSVIRTIHAD--LRTFADNSTVKCDKVLLDA 412
I E V+ I + L + D V +DA
Sbjct: 98 EIARENLAEAGVDDRIELLLGGDALDVLSRLLDGSFDLVFIDA 140
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 30.9 bits (70), Expect = 0.78
Identities = 21/89 (23%), Positives = 32/89 (35%), Gaps = 9/89 (10%)
Query: 331 PQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTI 390
+ G ++D G T +A L V IDI++ + E AK +V I
Sbjct: 1 LKSGIKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYENV-EFI 59
Query: 391 HADL-----RTFADNSTVKCDKVLLDAPC 414
D+ DNS D V+ +
Sbjct: 60 QGDIEELPQLQLEDNS---FDVVISNEVL 85
>gnl|CDD|225151 COG2242, CobL, Precorrin-6B methylase 2 [Coenzyme metabolism].
Length = 187
Score = 30.7 bits (70), Expect = 1.0
Identities = 16/64 (25%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 324 LVVAVVDPQPGQSIVDCCAAPGGKTL-YMASCLSGQGLVYAIDINKGRLRILNETAKLHQ 382
L ++ + P+PG + D A G T+ + + SG+ V AI+ ++ L ++ A
Sbjct: 25 LTLSKLRPRPGDRLWDIGAGTGSITIEWALAGPSGR--VIAIERDEEALELIERNAARFG 82
Query: 383 VNSV 386
V+++
Sbjct: 83 VDNL 86
>gnl|CDD|131799 TIGR02752, MenG_heptapren, demethylmenaquinone methyltransferase.
MenG is a generic term for a methyltransferase that
catalyzes the last step in menaquinone biosynthesis; the
exact enzymatic activity differs for different MenG
because the menaquinone differ in their prenoid side
chains in different species. Members of this MenG
protein family are 2-heptaprenyl-1,4-naphthoquinone
methyltransferase, and are found together in operons
with the two subunits of the heptaprenyl diphosphate
synthase in Bacillus subtilis and related species
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Menaquinone and ubiquinone].
Length = 231
Score = 30.9 bits (70), Expect = 1.1
Identities = 17/72 (23%), Positives = 33/72 (45%), Gaps = 3/72 (4%)
Query: 332 QPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIH 391
Q G S +D C ++ +A + +G V +D ++ L + + K +++V +H
Sbjct: 44 QAGTSALDVCCGTADWSIALAEAVGPEGHVIGLDFSENMLSVGRQKVKDAGLHNV-ELVH 102
Query: 392 ADLRT--FADNS 401
+ F DNS
Sbjct: 103 GNAMELPFDDNS 114
>gnl|CDD|233415 TIGR01444, fkbM_fam, methyltransferase, FkbM family. Members of
this family are characterized by two well-conserved
short regions separated by a variable in both sequence
and length. The first of the two regions is found in a
large number of proteins outside this subfamily, a
number of which have been characterized as
methyltransferases. One member of the present family,
FkbM, was shown to be required for a specific
methylation in the biosynthesis of the immunosuppressant
FK506 in Streptomyces strain MA6548.
Length = 144
Score = 29.6 bits (67), Expect = 1.7
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 337 IVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVI 387
++D A G +LY A +G V A + IL E KL+ + +V+
Sbjct: 2 VIDVGANIGDFSLYFAR-KGAEGRVIAFEPLPDAYEILEENVKLNNLPNVV 51
>gnl|CDD|182007 PRK09634, nusB, transcription antitermination protein NusB;
Provisional.
Length = 207
Score = 29.8 bits (68), Expect = 1.8
Identities = 17/47 (36%), Positives = 25/47 (53%)
Query: 153 ILRIGFYEIVKLDMPPYAVVDENVRLAKVALRPGAGNLVNGILRKLV 199
ILR+ EI+ L+ P ++E V LAK +NG+LR+L
Sbjct: 153 ILRLAVVEILFLNTPAAVAINEAVELAKRYSDEQGRRFINGVLRRLQ 199
>gnl|CDD|225174 COG2265, TrmA, SAM-dependent methyltransferases related to tRNA
(uracil-5-)-methyltransferase [Translation, ribosomal
structure and biogenesis].
Length = 432
Score = 30.4 bits (69), Expect = 2.0
Identities = 20/98 (20%), Positives = 39/98 (39%), Gaps = 6/98 (6%)
Query: 323 GLVVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQ 382
+ ++ G+ ++D G L +A V+ ++I+ + E A +
Sbjct: 283 ETALEWLELAGGERVLDLYCGVGTFGLPLAK---RVKKVHGVEISPEAVEAAQENAAANG 339
Query: 383 VNSVIRTIHADLRTF--ADNSTVKCDKVLLDAPCSGLG 418
+++V I D F A K D V++D P +G
Sbjct: 340 IDNV-EFIAGDAEEFTPAWWEGYKPDVVVVDPPRAGAD 376
>gnl|CDD|223363 COG0286, HsdM, Type I restriction-modification system
methyltransferase subunit [Defense mechanisms].
Length = 489
Score = 30.5 bits (69), Expect = 2.1
Identities = 39/198 (19%), Positives = 65/198 (32%), Gaps = 33/198 (16%)
Query: 264 NSRKGVTRADLVMQLNLLKVPHELSLHLDEFIRVKTGLQNVIQAGLLKEGLCA----VQD 319
+ + D L L + L+ + +F + + G E L +
Sbjct: 103 DLKGVFADLDFNDALKLGSLLKLLNKVILKFDEIDGRALDRDLFGDAYEYLLRKFAEAEG 162
Query: 320 ESAG----------LVVAVVDPQPGQSIVDCCAAPGG---KTLYMASCLSGQGLVYAIDI 366
+ AG L+V ++DP+P SI D GG + + +Y +I
Sbjct: 163 KEAGEFYTPREVSELIVELLDPEPRNSIYDPACGSGGMLLQAAKYLKRHQDEIFIYGQEI 222
Query: 367 NKGRLRILNETAK----LHQVNSVIRTIHADLRTFADN------STVKCDKVLLDAPCSG 416
N R+ AK LH + H D T ++ K D V+ + P SG
Sbjct: 223 NDTTYRL----AKMNLILHGIEGDANIRHGD--TLSNPKHDDKDDKGKFDFVIANPPFSG 276
Query: 417 LGVLSKRADLRWNRRLED 434
G + + R
Sbjct: 277 KGWGGDLLESEQDERFFF 294
>gnl|CDD|220246 pfam09445, Methyltransf_15, RNA cap guanine-N2 methyltransferase.
RNA cap guanine-N2 methyltransferases such as
Schizosaccharomyces pombe Tgs1 and Giardia lamblia Tgs2
catalyze methylation of the exocyclic N2 amine of
7-methylguanosine.
Length = 165
Score = 29.2 bits (66), Expect = 2.5
Identities = 17/57 (29%), Positives = 24/57 (42%), Gaps = 3/57 (5%)
Query: 337 IVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRTIHAD 393
I+D GG T+ A+ V IDIN L A+++ V+ I I D
Sbjct: 4 ILDVFCGAGGNTIQFANVFCS---VIGIDINPEHLACAQHNAEVYGVSDRIWFILGD 57
>gnl|CDD|216706 pfam01795, Methyltransf_5, MraW methylase family. Members of this
family are probably SAM dependent methyltransferases
based on Escherichia coli rsmH. This family appears to
be related to pfam01596.
Length = 310
Score = 29.2 bits (66), Expect = 4.1
Identities = 23/101 (22%), Positives = 40/101 (39%), Gaps = 11/101 (10%)
Query: 325 VVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVN 384
VV +++ +P +DC GG + + L +G + ID + + E K +
Sbjct: 12 VVELLNIKPDGIYIDCTLGGGGHSEAILEQLPEEGRLIGIDRDPQAIANAKERLKPFKGR 71
Query: 385 SVIRTIHADLRTF----ADNSTVKCDKVLLDAPCSGLGVLS 421
+ IH++ + K D +L D LGV S
Sbjct: 72 VTL--IHSNFANLFAYLKELGVGKVDGILFD-----LGVSS 105
>gnl|CDD|181382 PRK08317, PRK08317, hypothetical protein; Provisional.
Length = 241
Score = 29.1 bits (66), Expect = 4.1
Identities = 18/74 (24%), Positives = 28/74 (37%), Gaps = 4/74 (5%)
Query: 330 DPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNSVIRT 389
QPG ++D PG +A + +G V ID ++ L + E A +
Sbjct: 16 AVQPGDRVLDVGCGPGNDARELARRVGPEGRVVGIDRSEAMLALAKERAAGL--GPNVEF 73
Query: 390 IHADLRT--FADNS 401
+ D F D S
Sbjct: 74 VRGDADGLPFPDGS 87
>gnl|CDD|234022 TIGR02813, omega_3_PfaA, polyketide-type polyunsaturated fatty acid
synthase PfaA. Members of the seed for this alignment
are involved in omega-3 polyunsaturated fatty acid
biosynthesis, such as the protein PfaA from the
eicosapentaenoic acid biosynthesis operon in
Photobacterium profundum strain SS9. PfaA is encoded
together with PfaB, PfaC, and PfaD, and the functions of
the individual polypeptides have not yet been described.
More distant homologs of PfaA, also included with the
reach of this model, appear to be involved in
polyketide-like biosynthetic mechanisms of
polyunsaturated fatty acid biosynthesis, an alternative
to the more familiar iterated mechanism of chain
extension and desaturation, and in most cases are encoded
near genes for homologs of PfaB, PfaC, and/or PfaD.
Length = 2582
Score = 29.6 bits (66), Expect = 4.4
Identities = 12/43 (27%), Positives = 21/43 (48%)
Query: 11 RILVSTDASKALSKQAASTRKPRTSISTKKRAKVSPSRRTQNL 53
++LV TD + + AS +KP+ S T + + R + L
Sbjct: 2261 QLLVGTDMQGNDTAEDASVKKPQVSRLTARVPQPMAIRVMRTL 2303
>gnl|CDD|223990 COG1062, AdhC, Zn-dependent alcohol dehydrogenases, class III
[Energy production and conversion].
Length = 366
Score = 29.1 bits (66), Expect = 4.6
Identities = 24/99 (24%), Positives = 39/99 (39%), Gaps = 21/99 (21%)
Query: 274 LVMQLNLLKVPHELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQP 333
+V +++L+K+ + L A LL C V G VV +P
Sbjct: 145 VVHEISLVKIDPDAPLEK---------------ACLLG---CGVT-TGIGAVVNTAKVEP 185
Query: 334 GQSI-VDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRL 371
G ++ V G + A +G G + A+DIN +L
Sbjct: 186 GDTVAVFGLGGVGLAAIQGAK-AAGAGRIIAVDINPEKL 223
>gnl|CDD|166839 PRK00178, tolB, translocation protein TolB; Provisional.
Length = 430
Score = 29.3 bits (66), Expect = 4.8
Identities = 14/34 (41%), Positives = 18/34 (52%)
Query: 344 PGGKTLYMASCLSGQGLVYAIDINKGRLRILNET 377
GKTL M G V A D+ +G +RIL +T
Sbjct: 340 ADGKTLVMVHRQDGNFHVAAQDLQRGSVRILTDT 373
>gnl|CDD|176182 cd05279, Zn_ADH1, Liver alcohol dehydrogenase and related
zinc-dependent alcohol dehydrogenases.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Alcohol dehydrogenase in the
liver converts ethanol and NAD+ to acetaldehyde and
NADH, while in yeast and some other microorganisms ADH
catalyzes the conversion acetaldehyde to ethanol in
alcoholic fermentation. There are 7 vertebrate ADH 7
classes, 6 of which have been identified in humans.
Class III, glutathione-dependent formaldehyde
dehydrogenase, has been identified as the primordial
form and exists in diverse species, including plants,
micro-organisms, vertebrates, and invertebrates. Class
I, typified by liver dehydrogenase, is an evolving
form. Gene duplication and functional specialization of
ADH into ADH classes and subclasses created numerous
forms in vertebrates. For example, the A, B and C
(formerly alpha, beta, gamma) human class I subunits
have high overall structural similarity, but differ in
the substrate binding pocket and therefore in substrate
specificity. In human ADH catalysis, the zinc ion helps
coordinate the alcohol, followed by deprotonation of a
histidine (His-51), the ribose of NAD, a serine
(Ser-48), then the alcohol, which allows the transfer of
a hydride to NAD+, creating NADH and a zinc-bound
aldehyde or ketone. In yeast and some bacteria, the
active site zinc binds an aldehyde, polarizing it, and
leading to the reverse reaction. ADH is a member of the
medium chain alcohol dehydrogenase family (MDR), which
has a NAD(P)(H)-binding domain in a Rossmann fold of an
beta-alpha form. The NAD(H)-binding region is comprised
of 2 structurally similar halves, each of which contacts
a mononucleotide. A GxGxxG motif after the first
mononucleotide contact half allows the close contact of
the coenzyme with the ADH backbone. The N-terminal
catalytic domain has a distant homology to GroES.
These proteins typically form dimers (typically higher
plants, mammals) or tetramers (yeast, bacteria), and
have 2 tightly bound zinc atoms per subunit, a catalytic
zinc at the active site and a structural zinc in a lobe
of the catalytic domain. NAD(H) binding occurs in the
cleft between the catalytic and coenzyme-binding domains
at the active site, and coenzyme binding induces a
conformational closing of this cleft. Coenzyme binding
typically precedes and contributes to substrate binding.
Length = 365
Score = 29.3 bits (66), Expect = 4.8
Identities = 19/112 (16%), Positives = 35/112 (31%), Gaps = 19/112 (16%)
Query: 274 LVMQLNLLKVPHELSLHLDEFIRVKTGLQNVIQAGLLKEGLCAVQDESAGLVVAVVDPQP 333
+V +++L K+ + L L+ C G V P
Sbjct: 143 VVSEISLAKIDPDAPLEK---------------VCLIG---CGFS-TGYGAAVNTAKVTP 183
Query: 334 GQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKGRLRILNETAKLHQVNS 385
G + G ++ M +G + A+DINK + + +N
Sbjct: 184 GSTCAVFGLGGVGLSVIMGCKAAGASRIIAVDINKDKFEKAKQLGATECINP 235
>gnl|CDD|140001 PRK13944, PRK13944, protein-L-isoaspartate O-methyltransferase;
Provisional.
Length = 205
Score = 28.6 bits (64), Expect = 5.3
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 4/53 (7%)
Query: 321 SAGLVVAV----VDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAIDINKG 369
SA +VA+ ++P+PG I++ G + A + +G VY ++I K
Sbjct: 56 SAPHMVAMMCELIEPRPGMKILEVGTGSGYQAAVCAEAIERRGKVYTVEIVKE 108
>gnl|CDD|234597 PRK00050, PRK00050, 16S rRNA m(4)C1402 methyltranserfase;
Provisional.
Length = 296
Score = 28.9 bits (66), Expect = 5.4
Identities = 24/100 (24%), Positives = 37/100 (37%), Gaps = 15/100 (15%)
Query: 325 VVAVVDPQPGQSIVDCCAAPGGKTLYMASCLSGQGLVYAID-----INKGRLRILNETAK 379
VV + +P VD GG + + L +G + AID I + L +
Sbjct: 11 VVDALAIKPDGIYVDGTFGGGGHSRAILERLGPKGRLIAIDRDPDAIAAAK-DRLKPFGR 69
Query: 380 LHQVNSVIRTIHADLRTFADNSTVKCDKVLLDAPCSGLGV 419
V+ ++L+ K D +LLD LGV
Sbjct: 70 FTLVHGNF----SNLKEVLAEGLGKVDGILLD-----LGV 100
>gnl|CDD|165200 PHA02866, PHA02866, Hypothetical protein; Provisional.
Length = 333
Score = 28.8 bits (64), Expect = 6.1
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 3/72 (4%)
Query: 71 IQFGGAFADLLNKKGKGSGDNEMGYVERTLGFRTKDLDDRDLRLVTDIVGGTIRWRRYLD 130
I F G F +L N +GK E+ V+ L + + D + LR + D V ++ + +
Sbjct: 251 ISFDG-FYNLSNVEGKDMAWKELKAVKEDLWVPSSEEDYKFLRELVDYVSSNLKTK--VG 307
Query: 131 HLICLLCHDEKT 142
+ + C D++T
Sbjct: 308 YYVLSTCDDDET 319
>gnl|CDD|234248 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 [Protein fate, Protein modification
and repair].
Length = 251
Score = 28.2 bits (64), Expect = 8.8
Identities = 8/34 (23%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 361 VYAIDINKGRLRILNETAKLHQVNSVIRTIHADL 394
V A+DI+ L + + A +++V + +D
Sbjct: 114 VTAVDISPEALAVARKNAARLGLDNV-EFLQSDW 146
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.320 0.135 0.392
Gapped
Lambda K H
0.267 0.0668 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,768,334
Number of extensions: 2243268
Number of successful extensions: 1898
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1845
Number of HSP's successfully gapped: 62
Length of query: 451
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 351
Effective length of database: 6,502,202
Effective search space: 2282272902
Effective search space used: 2282272902
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 61 (27.4 bits)