RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6779
(144 letters)
>gnl|CDD|223640 COG0566, SpoU, rRNA methylases [Translation, ribosomal structure
and biogenesis].
Length = 260
Score = 98.1 bits (245), Expect = 6e-26
Identities = 36/145 (24%), Positives = 69/145 (47%), Gaps = 7/145 (4%)
Query: 7 RKQREKKGWLMLEGKRILIDALKANLKLKMVFFSQ-----WDILKELPLPEDVPQHRVDY 61
+K R + G ++EG+ +++AL + K+ + ++ ++ L L + +P + V
Sbjct: 13 KKLRGRAGEFLIEGEHAVLEALASGPKIVRILVTEGRLPRFEELLALAAAKGIPVYVVSE 72
Query: 62 KNIQLWSDLVTPPGIIGIFELP--AHPIASIDPASLPLNIVCDNIRDPGNMGSILRVCAA 119
+ S GI+ + + +D + PL +V D + DP N+G+I+R A
Sbjct: 73 AILDKLSGTENHQGIVAVVKKRRYPLLDDLLDAEAQPLLLVLDGVTDPHNLGAIIRTADA 132
Query: 120 VGARQVVCSRGCVDIYDNKVIRAAA 144
G V+ + D + KVIRA+A
Sbjct: 133 FGVDGVILPKRRADPLNPKVIRASA 157
>gnl|CDD|216010 pfam00588, SpoU_methylase, SpoU rRNA Methylase family. This family
of proteins probably use S-AdoMet.
Length = 142
Score = 66.0 bits (162), Expect = 1e-14
Identities = 23/50 (46%), Positives = 31/50 (62%), Gaps = 1/50 (2%)
Query: 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVV-CSRGCVDIYDNKVIRAAA 144
PL +V D +DPGN+G+I R AA GA ++ C D Y+ K IRA+A
Sbjct: 1 PLIVVLDEPQDPGNLGAIARTAAAFGADGLILVEPRCADPYNPKAIRASA 50
>gnl|CDD|214943 smart00967, SpoU_sub_bind, RNA 2'-O ribose methyltransferase
substrate binding. This domain is a RNA 2'-O ribose
methyltransferase substrate binding domain.
Length = 70
Score = 39.4 bits (93), Expect = 3e-05
Identities = 12/69 (17%), Positives = 30/69 (43%), Gaps = 5/69 (7%)
Query: 18 LEGKRILIDALKANLKLKMVFFSQ-----WDILKELPLPEDVPQHRVDYKNIQLWSDLVT 72
+EG+ + +ALK+ ++K ++ ++ L +L + V K + S
Sbjct: 1 IEGRHAVEEALKSGRRIKELYLTEGRAERLKELLKLAKERGIKVIEVSKKELDKLSGTAN 60
Query: 73 PPGIIGIFE 81
G++ + +
Sbjct: 61 HQGVVAVVK 69
>gnl|CDD|129290 TIGR00186, rRNA_methyl_3, rRNA methylase, putative, group 3. this
is part of the trmH (spoU) family of rRNA methylases
[Protein synthesis, tRNA and rRNA base modification].
Length = 237
Score = 40.8 bits (96), Expect = 7e-05
Identities = 14/59 (23%), Positives = 27/59 (45%)
Query: 86 PIASIDPASLPLNIVCDNIRDPGNMGSILRVCAAVGARQVVCSRGCVDIYDNKVIRAAA 144
+ P ++ D I DP N+G+ILR A G V+ + ++ V++ ++
Sbjct: 80 LYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGVILPKRRSAPLNSTVVKTSS 138
>gnl|CDD|203842 pfam08032, SpoU_sub_bind, RNA 2'-O ribose methyltransferase
substrate binding. This domain is a RNA 2'-O ribose
methyltransferase substrate binding domain.
Length = 74
Score = 35.3 bits (82), Expect = 0.001
Identities = 13/74 (17%), Positives = 33/74 (44%), Gaps = 8/74 (10%)
Query: 17 MLEGKRILIDALKANLKLKMVFFSQ-------WDILKELPLPEDVPQHRVDYKNIQLWSD 69
++EG+ + +ALK+ +++ ++ ++ ++LK + V K + S
Sbjct: 1 LIEGRHAVEEALKSGPEIEKLYVTEGRRDPRLKELLKLA-KKRGIKVIEVSEKVLDKLSG 59
Query: 70 LVTPPGIIGIFELP 83
V G++ + P
Sbjct: 60 TVNHQGVVAEVKPP 73
>gnl|CDD|223297 COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation,
ribosomal structure and biogenesis].
Length = 155
Score = 33.3 bits (77), Expect = 0.020
Identities = 14/29 (48%), Positives = 16/29 (55%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVGARQV 125
LNIV P N G+I+R CAA GA
Sbjct: 3 LNIVLYQPEIPPNTGNIIRTCAATGAELH 31
>gnl|CDD|211559 TIGR00185, tRNA_yibK_trmL, tRNA
(cytidine(34)-2'-O)-methyltransferase. TrmL (previously
YibK) is responsible for 2'-O-methylation at tRNA(Leu)
position 34 [Protein synthesis, tRNA and rRNA base
modification].
Length = 153
Score = 30.5 bits (69), Expect = 0.20
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVGAR 123
LNIV P N G+I R CAA G R
Sbjct: 2 LNIVLYEPEIPPNTGNIARTCAATGTR 28
>gnl|CDD|236779 PRK10864, PRK10864, putative methyltransferase; Provisional.
Length = 346
Score = 29.4 bits (66), Expect = 0.70
Identities = 10/25 (40%), Positives = 17/25 (68%)
Query: 102 DNIRDPGNMGSILRVCAAVGARQVV 126
+++ +P N+G I+R CA G + VV
Sbjct: 204 EDVGNPHNLGGIMRSCAHFGVKGVV 228
>gnl|CDD|177093 CHL00194, ycf39, Ycf39; Provisional.
Length = 317
Score = 28.0 bits (63), Expect = 1.8
Identities = 11/24 (45%), Positives = 16/24 (66%), Gaps = 2/24 (8%)
Query: 18 LEGKRILIDALK-ANLKLKMVFFS 40
+GK LI+A K A +K + +FFS
Sbjct: 87 WDGKLALIEAAKAAKIK-RFIFFS 109
>gnl|CDD|201589 pfam01084, Ribosomal_S18, Ribosomal protein S18.
Length = 54
Score = 25.5 bits (57), Expect = 2.6
Identities = 6/23 (26%), Positives = 12/23 (52%)
Query: 55 PQHRVDYKNIQLWSDLVTPPGII 77
+DYK+++L ++ G I
Sbjct: 3 KIEYIDYKDVELLRRFISERGKI 25
>gnl|CDD|182185 PRK09989, PRK09989, hypothetical protein; Provisional.
Length = 258
Score = 27.3 bits (60), Expect = 2.8
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 18 LEGKRILIDALKANLKLKMVFFSQWDIL 45
GKRIL++AL +K +F SQ+ L
Sbjct: 135 PHGKRILVEALSPGVKPHYLFSSQYQAL 162
>gnl|CDD|182406 PRK10358, PRK10358, putative rRNA methylase; Provisional.
Length = 157
Score = 26.5 bits (58), Expect = 3.8
Identities = 13/27 (48%), Positives = 16/27 (59%)
Query: 97 LNIVCDNIRDPGNMGSILRVCAAVGAR 123
LNIV P N G+I+R+CA G R
Sbjct: 2 LNIVLFEPEIPPNTGNIIRLCANTGFR 28
>gnl|CDD|233174 TIGR00893, 2A0114, D-galactonate transporter. [Transport and
binding proteins, Carbohydrates, organic alcohols, and
acids].
Length = 399
Score = 26.9 bits (60), Expect = 4.3
Identities = 12/39 (30%), Positives = 18/39 (46%)
Query: 10 REKKGWLMLEGKRILIDALKANLKLKMVFFSQWDILKEL 48
+K WL E K I++ L A + K + +KEL
Sbjct: 173 PQKAKWLTEEEKYIVVGGLLAEQQGKGPSTPKKYQIKEL 211
>gnl|CDD|183021 PRK11181, PRK11181, 23S rRNA (guanosine-2'-O-)-methyltransferase;
Provisional.
Length = 244
Score = 26.5 bits (59), Expect = 5.0
Identities = 11/31 (35%), Positives = 17/31 (54%)
Query: 96 PLNIVCDNIRDPGNMGSILRVCAAVGARQVV 126
P ++ D + DP N+G+ LR A G V+
Sbjct: 95 PFLLILDGVTDPHNLGACLRSADAAGVHAVI 125
>gnl|CDD|177016 CHL00077, rps18, ribosomal protein S18.
Length = 86
Score = 24.9 bits (55), Expect = 7.3
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 49 PLPEDVPQHRVDYKNIQLWSDLVTPPGII 77
LP R+DYKN+ L S ++ G I
Sbjct: 18 RLPPIQSGDRIDYKNMSLLSRFISEQGKI 46
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
0.324 0.141 0.438
Gapped
Lambda K H
0.267 0.0814 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,718,944
Number of extensions: 715538
Number of successful extensions: 571
Number of sequences better than 10.0: 1
Number of HSP's gapped: 566
Number of HSP's successfully gapped: 27
Length of query: 144
Length of database: 10,937,602
Length adjustment: 88
Effective length of query: 56
Effective length of database: 7,034,450
Effective search space: 393929200
Effective search space used: 393929200
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 54 (24.4 bits)