RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13508
(621 letters)
>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 = 147 bits (373), Expect = 3e-41
Identities = 70/213 (32%), Positives = 105/213 (49%), Gaps = 36/213 (16%)
Query: 281 FLNRAAMKMANMDKRLNSMFTQPVRENGSPLLGPGELLYFADVCAGPGGFSEYVLYRKKW 340
+++RAA K+ +D+R L PG+ D+ A PGGFS+ +L R
Sbjct: 1 YVSRAAYKLLEIDERFG--------------LKPGKGKTVLDLGAAPGGFSQVLLERGG- 45
Query: 341 RAKGIGFTLTGSHDFKLDDFFAGPSETFEPYYGVKGNGDVYDPENILSLHEFVMKSTKGR 400
K + L GP E + Y ++G D+ DPE + L E +
Sbjct: 46 AGKVVAVDL-------------GPMEPIQGVYFLRG--DITDPETLEKLRELL-----PG 85
Query: 401 GVHFMMADGGFSVEGQENIQEILSKRLYLCQFLVSLFIVRPEGHFVCKVFDMFTPFSAGL 460
V +++DG +V G EN +S +L L L++L ++RP G+FV KVF F FS L
Sbjct: 86 KVDLVLSDGAPNVSGIENTDSFISLQLVLAALLLALEVLRPGGNFVVKVFKGFE-FSVEL 144
Query: 461 LYLLYRSYKQVCIFKPNTSRPANSERYIVCKWK 493
L L + +++V IFKP SRP++SE Y+VC
Sbjct: 145 LEKLKKGFEKVGIFKPPASRPSSSEEYLVCLGF 177
Score = 107 bits (270), Expect = 5e-27
Identities = 46/116 (39%), Positives = 67/116 (57%), Gaps = 6/116 (5%)
Query: 53 GDVYDPENILSLHEFVMKSSKGRGVHFMMADGGFSVEGQENIQEILSKRLYLCQFLVSLF 112
GD+ DPE + L E + V +++DG +V G EN +S +L L L++L
Sbjct: 68 GDITDPETLEKLRELL-----PGKVDLVLSDGAPNVSGIENTDSFISLQLVLAALLLALE 122
Query: 113 IVRPEGHFVCKVFDMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIVCKWK 168
++RP G+FV KVF F FS LL L + +++V IFKP SRP++SE Y+VC
Sbjct: 123 VLRPGGNFVVKVFKGFE-FSVELLEKLKKGFEKVGIFKPPASRPSSSEEYLVCLGF 177
>gnl|CDD|223370 COG0293, FtsJ, 23S rRNA methylase [Translation, ribosomal structure
and biogenesis].
Length = 205
Score = 61.1 bits (149), Expect = 1e-10
Identities = 57/236 (24%), Positives = 101/236 (42%), Gaps = 49/236 (20%)
Query: 261 MDKRLNSMFTQPVRENGNGPFLNRAAMKMANMDKRLNSMFTQPVRENGSPLLGPGELLYF 320
+ + L + + ++ G + +RAA K+ ++++ L PG ++
Sbjct: 8 LAEHLRDPYYKKAKKEG---YRSRAAYKLLELNEKFK-------------LFKPGMVV-- 49
Query: 321 ADVCAGPGGFSEYVLYRKKWRAKGIGFTLTGSHDFKLDDFFAGPSETFEPYYGVKG-NGD 379
D+ A PGG+S+ + K + + P + P GV GD
Sbjct: 50 VDLGAAPGGWSQVAAKKLGAGGKIVAVDI-------------LPMK---PIPGVIFLQGD 93
Query: 380 VYDPENILSLHEFVMKSTKGRGVHFMMADGGFSVEGQENIQEILSKRLYLCQ--FLVSLF 437
+ D + + L E + G V +++D + G ++ S +YLC+ +L
Sbjct: 94 ITDEDTLEKLLEAL----GGAPVDVVLSDMAPNTSGNRSVDHARS--MYLCELALEFALE 147
Query: 438 IVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIVCK 491
+++P G FV KVF + F LL L R +++V IFKP SR + E Y+V K
Sbjct: 148 VLKPGGSFVAKVFQGEDF----EDLLKALRRLFRKVKIFKPKASRKRSREIYLVAK 199
Score = 55.3 bits (134), Expect = 1e-08
Identities = 37/118 (31%), Positives = 59/118 (50%), Gaps = 14/118 (11%)
Query: 53 GDVYDPENILSLHEFVMKSSKGRGVHFMMADGGFSVEGQENIQEILSKRLYLCQ--FLVS 110
GD+ D + + L E + G V +++D + G ++ S +YLC+ +
Sbjct: 92 GDITDEDTLEKLLEAL----GGAPVDVVLSDMAPNTSGNRSVDHARS--MYLCELALEFA 145
Query: 111 LFIVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIVCK 166
L +++P G FV KVF + F LL L R +++V IFKP SR + E Y+V K
Sbjct: 146 LEVLKPGGSFVAKVFQGEDF----EDLLKALRRLFRKVKIFKPKASRKRSREIYLVAK 199
>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 = 44.8 bits (106), Expect = 3e-05
Identities = 45/184 (24%), Positives = 81/184 (44%), Gaps = 29/184 (15%)
Query: 311 LLGPGELLYFADVCAGPGGFSEYVLYRKKWRAKGIGFTLTGSHDFKLDDFFAGPSETFEP 370
L+ PG+ + D+ A PGG+S+ + + + + I L + +P
Sbjct: 29 LIKPGDTV--LDLGAAPGGWSQVAVEQVGGKGRVIAVDL----------------QPMKP 70
Query: 371 YYGVKG-NGDVYDPENILSLHEFVMKSTKGRGVHFMMADGGFSVEGQENIQEILSKRLYL 429
V GD D E + + E V V +M+D ++ G +I + S L
Sbjct: 71 IENVDFIRGDFTDEEVLNKIRERV----GDDKVDVVMSDAAPNISGYWDIDHLRSIDLVE 126
Query: 430 CQFLVSLFIVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERY 487
++ +++P+G+FV KVF + + L L + +++V + KP SR ++E Y
Sbjct: 127 LALDIAKEVLKPKGNFVVKVFQGEEIDEY----LNELRKLFEKVKVTKPQASRKRSAEVY 182
Query: 488 IVCK 491
IV K
Sbjct: 183 IVAK 186
Score = 40.6 bits (95), Expect = 7e-04
Identities = 32/116 (27%), Positives = 56/116 (48%), Gaps = 10/116 (8%)
Query: 53 GDVYDPENILSLHEFVMKSSKGRGVHFMMADGGFSVEGQENIQEILSKRLYLCQFLVSLF 112
GD D E + + E V V +M+D ++ G +I + S L ++
Sbjct: 79 GDFTDEEVLNKIRERV----GDDKVDVVMSDAAPNISGYWDIDHLRSIDLVELALDIAKE 134
Query: 113 IVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIVCK 166
+++P+G+FV KVF + + L L + +++V + KP SR ++E YIV K
Sbjct: 135 VLKPKGNFVVKVFQGEEIDEY----LNELRKLFEKVKVTKPQASRKRSAEVYIVAK 186
>gnl|CDD|225409 COG2853, VacJ, Surface lipoprotein [Cell envelope biogenesis, outer
membrane].
Length = 250
Score = 33.4 bits (77), Expect = 0.22
Identities = 24/79 (30%), Positives = 37/79 (46%), Gaps = 12/79 (15%)
Query: 504 MFKLNKRLDRYG----STSKRDIVSCVPLDIMKSDANFFDYLVTSNNVINRIA-GLGKHA 558
MFK N LDRY + R + P + +NFF+ L ++N + G K A
Sbjct: 44 MFKFNDVLDRYILRPVAVGYRAV---TPKPVRSGVSNFFNNLGEPATMVNNLLQGKPKKA 100
Query: 559 IYRYREDSNRWVSETSLGI 577
+ E NR++ T+LG+
Sbjct: 101 M----EHFNRFLINTTLGL 115
>gnl|CDD|222777 PHA00144, PHA00144, major head protein.
Length = 438
Score = 33.3 bits (76), Expect = 0.38
Identities = 28/112 (25%), Positives = 43/112 (38%), Gaps = 21/112 (18%)
Query: 177 DFMFKLNKRLDRYGSTSKRDIVSCVPLDIMKSDA-NFFD-----YLVTSNNTVFDELEGD 230
+F+ L ++R GST + + PL I K F D Y + +D E +
Sbjct: 53 EFITAL---VNRIGSTVIKALSLENPLAIFKKGTLEFGDTIEEIYTDITKEKTYDAEEAE 109
Query: 231 Q------------FFRARNRSNPFELIKNGPFLNRAAMKMANMDKRLNSMFT 270
Q F RNR N ++ L A + N D+ L+S+ T
Sbjct: 110 QKVFKRAIPNVKTLFHTRNRQNFYKQTIQRDSLKTAFVSDGNFDEFLSSIIT 161
>gnl|CDD|113116 pfam04333, VacJ, VacJ like lipoprotein. VacJ is required for the
intercellular spreading of Shigella flexneri. It is
attached to the outer membrane by a lipid anchor.
Length = 200
Score = 31.5 bits (72), Expect = 0.83
Identities = 21/79 (26%), Positives = 36/79 (45%), Gaps = 12/79 (15%)
Query: 504 MFKLNKRLDRY----GSTSKRDIVSCVPLDIMKSDANFFDYLVTSNNVINRIA-GLGKHA 558
M+K N LDRY + ++ VP + +NFF+ L ++N + G K A
Sbjct: 16 MWKFNSVLDRYVLRPVAVGYVNV---VPKPVRSGVSNFFNNLGEPATMVNNLLQGKPKKA 72
Query: 559 IYRYREDSNRWVSETSLGI 577
+ NR++ T+ G+
Sbjct: 73 M----VHFNRFLINTTFGL 87
>gnl|CDD|183025 PRK11188, rrmJ, 23S rRNA methyltransferase J; Provisional.
Length = 209
Score = 28.9 bits (65), Expect = 6.3
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 113 IVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIV 164
++ P G FV KVF + F + L + + +V + KP++SR + E YIV
Sbjct: 154 VLAPGGSFVVKVFQGEGFDEY----LREIRSLFTKVKVRKPDSSRARSREVYIV 203
Score = 28.9 bits (65), Expect = 6.3
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 6/54 (11%)
Query: 438 IVRPEGHFVCKVF--DMFTPFSAGLLYLLYRSYKQVCIFKPNTSRPANSERYIV 489
++ P G FV KVF + F + L + + +V + KP++SR + E YIV
Sbjct: 154 VLAPGGSFVVKVFQGEGFDEY----LREIRSLFTKVKVRKPDSSRARSREVYIV 203
>gnl|CDD|211840 TIGR03566, FMN_reduc_MsuE, FMN reductase, MsuE subfamily. Members
of this protein family use NAD(P)H to reduce FMN and
regenerate FMNH2. Members include the NADH-dependent
enzyme MsuE from Pseudomonas aeruginosa, which serves as
a partner to an FMNH2-dependent alkanesulfonate
monooxygenase. The NADP-dependent enzyme from E. coli is
outside the scope of this model.
Length = 174
Score = 28.8 bits (65), Expect = 6.4
Identities = 11/27 (40%), Positives = 16/27 (59%)
Query: 526 VPLDIMKSDANFFDYLVTSNNVINRIA 552
+P + SDA+F DY + S + RIA
Sbjct: 135 LPTGVYASDADFADYRLASEALRARIA 161
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
0.323 0.139 0.425
Gapped
Lambda K H
0.267 0.0726 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 31,899,115
Number of extensions: 3138903
Number of successful extensions: 2299
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2285
Number of HSP's successfully gapped: 18
Length of query: 621
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 518
Effective length of database: 6,369,140
Effective search space: 3299214520
Effective search space used: 3299214520
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 (21.9 bits)
S2: 62 (27.7 bits)