RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780516|ref|YP_003064929.1| type II modification
methyltransferase [Candidatus Liberibacter asiaticus str. psy62]
(83 letters)
>gnl|CDD|161991 TIGR00675, dcm, DNA-methyltransferase (dcm). All proteins in
this family for which functions are known are
DNA-cytosine methyltransferases. This family is based
on the phylogenomic analysis of JA Eisen (1999, Ph.D.
Thesis, Stanford University).
Length = 315
Score = 122 bits (308), Expect = 2e-29
Identities = 48/80 (60%), Positives = 55/80 (68%), Gaps = 4/80 (5%)
Query: 4 ITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANFPNTLIFGDIAKIKTQD 63
DLF GIGGIRL EQ +C F+SEI+ Y+ KTY+ANF N + FGDI KI D
Sbjct: 1 FIDLFAGIGGIRLGFEQAG----FKCVFASEIDKYAQKTYEANFGNKVPFGDITKISPSD 56
Query: 64 IPDHDVLLAGFPCQPFSQAG 83
IPD D+LL GFPCQPFS AG
Sbjct: 57 IPDFDILLGGFPCQPFSIAG 76
>gnl|CDD|182476 PRK10458, PRK10458, DNA cytosine methylase; Provisional.
Length = 467
Score = 87.4 bits (217), Expect = 7e-19
Identities = 46/98 (46%), Positives = 53/98 (54%), Gaps = 24/98 (24%)
Query: 6 DLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQANF---PNTLIFG-DIAKIK- 60
DLF GIGGIR E +C F+SE N ++V+TY+AN+ P T F DI I
Sbjct: 93 DLFAGIGGIRRGFEAIGG----QCVFTSEWNKHAVRTYKANWYCDPATHRFNEDIRDITL 148
Query: 61 ---------------TQDIPDHDVLLAGFPCQPFSQAG 83
Q IPDHDVLLAGFPCQPFS AG
Sbjct: 149 SHKEGVSDEEAAEHIRQHIPDHDVLLAGFPCQPFSLAG 186
>gnl|CDD|132636 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli.
Length = 360
Score = 28.4 bits (64), Expect = 0.46
Identities = 12/32 (37%), Positives = 14/32 (43%), Gaps = 3/32 (9%)
Query: 29 CFFSSEINPYSVKTYQANFPNTLIFGDIAKIK 60
EI P KTYQ N TL G +A+
Sbjct: 232 ITPKKEIKP---KTYQLNPNQTLFLGGLARFD 260
>gnl|CDD|177857 PLN02207, PLN02207, UDP-glycosyltransferase.
Length = 468
Score = 27.3 bits (60), Expect = 0.82
Identities = 14/40 (35%), Positives = 22/40 (55%), Gaps = 2/40 (5%)
Query: 32 SSEINPYSVKTY--QANFPNTLIFGDIAKIKTQDIPDHDV 69
S +I PYSV + + N+P+ G I +K Q P+ D+
Sbjct: 220 SFDIEPYSVNHFLDEQNYPSVYAVGPIFDLKAQPHPEQDL 259
>gnl|CDD|162723 TIGR02137, HSK-PSP, phosphoserine phosphatase/homoserine
phosphotransferase bifunctional protein. This enzyme
is a member of the haloacid dehalogenase (HAD)
superfamily, specifically part of subfamily IB by
virtue of the presence of an alpha helical domain in
between motifs I and II of the HAD domain . The closest
homologs to this family are monofunctional
phosphoserine phosphatases (TIGR00338).
Length = 203
Score = 26.8 bits (59), Expect = 1.4
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 55 DIAKIKTQDIPDHDVLLAG 73
D K T+DIPD+DVL+
Sbjct: 27 DALKATTRDIPDYDVLMKQ 45
>gnl|CDD|184332 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 25.6 bits (57), Expect = 2.9
Identities = 12/26 (46%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 34 EINPYSVKTYQANFPNTLIFGDIAKI 59
EI P KTYQ N TL G +A+
Sbjct: 243 EIKP---KTYQLNEEQTLFLGGLARF 265
>gnl|CDD|129571 TIGR00479, rumA, 23S rRNA (uracil-5-)-methyltransferase RumA. This
protein family was first proposed to be RNA
methyltransferases by homology to the TrmA family. The
member from E. coli has now been shown to act as the 23S
RNA methyltransferase for the conserved U1939. The gene
is now designated rumA and was previously designated
ygcA.
Length = 431
Score = 25.2 bits (55), Expect = 3.5
Identities = 12/44 (27%), Positives = 19/44 (43%), Gaps = 5/44 (11%)
Query: 3 KITDLFCGIGGIRLDLEQTFNHRNVECFFSSEINPYSVKTYQAN 46
+ D +CG+G L L + + E+ P SV+ Q N
Sbjct: 295 LVVDAYCGVGTFTLPLA-----KQAKSVVGIEVVPESVEKAQQN 333
>gnl|CDD|179588 PRK03522, rumB, 23S rRNA methyluridine methyltransferase; Reviewed.
Length = 315
Score = 25.2 bits (56), Expect = 3.5
Identities = 7/8 (87%), Positives = 8/8 (100%)
Query: 6 DLFCGIGG 13
DLFCG+GG
Sbjct: 179 DLFCGVGG 186
>gnl|CDD|140299 PTZ00273, PTZ00273, oxidase reductase; Provisional.
Length = 320
Score = 24.7 bits (54), Expect = 5.0
Identities = 7/34 (20%), Positives = 18/34 (52%)
Query: 14 IRLDLEQTFNHRNVECFFSSEINPYSVKTYQANF 47
+++D+ ++ HR F + +++P Y+ F
Sbjct: 70 LKIDIRKSRLHRGYGAFGAEQLDPSKPYDYKETF 103
>gnl|CDD|183875 PRK13168, rumA, 23S rRNA m(5)U1939 methyltransferase; Reviewed.
Length = 443
Score = 24.7 bits (55), Expect = 5.8
Identities = 6/7 (85%), Positives = 7/7 (100%)
Query: 6 DLFCGIG 12
DLFCG+G
Sbjct: 303 DLFCGLG 309
>gnl|CDD|180850 PRK07116, PRK07116, flavodoxin; Provisional.
Length = 160
Score = 24.6 bits (54), Expect = 5.9
Identities = 10/20 (50%), Positives = 15/20 (75%), Gaps = 1/20 (5%)
Query: 56 IAKIKTQDIPDHDVLLAGFP 75
IAK K ++I ++DV+ GFP
Sbjct: 67 IAK-KIENIAEYDVIFLGFP 85
>gnl|CDD|131140 TIGR02085, meth_trns_rumB, 23S rRNA (uracil-5-)-methyltransferase
RumB. This family consists of RNA methyltransferases
designated RumB, formerly YbjF. Members act on 23S rRNA
U747 and the equivalent position in other
proteobacterial species. This family is homologous to
the other 23S rRNA methyltransferase RumA and to the
tRNA methyltransferase TrmA.
Length = 374
Score = 24.0 bits (52), Expect = 8.3
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 6 DLFCGIGGIRL 16
DLFCG+GG L
Sbjct: 239 DLFCGVGGFGL 249
>gnl|CDD|184163 PRK13582, thrH, phosphoserine phosphatase; Provisional.
Length = 205
Score = 24.1 bits (53), Expect = 8.7
Identities = 8/14 (57%), Positives = 12/14 (85%)
Query: 58 KIKTQDIPDHDVLL 71
+ T+DIPD+DVL+
Sbjct: 30 RATTRDIPDYDVLM 43
>gnl|CDD|181740 PRK09267, PRK09267, flavodoxin FldA; Validated.
Length = 169
Score = 24.0 bits (53), Expect = 9.0
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 55 DIAKIKTQDIPDHDVLLAGFP 75
DIAK +D +D+L+ G P
Sbjct: 35 DIAKASKEDFEAYDLLILGIP 55
>gnl|CDD|183085 PRK11316, PRK11316, bifunctional heptose 7-phosphate kinase/heptose
1-phosphate adenyltransferase; Provisional.
Length = 473
Score = 24.0 bits (53), Expect = 9.3
Identities = 6/11 (54%), Positives = 7/11 (63%)
Query: 14 IRLDLEQTFNH 24
IRLD E+ F
Sbjct: 117 IRLDFEEGFEG 127
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
0.325 0.143 0.447
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,335,066
Number of extensions: 65513
Number of successful extensions: 141
Number of sequences better than 10.0: 1
Number of HSP's gapped: 138
Number of HSP's successfully gapped: 20
Length of query: 83
Length of database: 5,994,473
Length adjustment: 52
Effective length of query: 31
Effective length of database: 4,870,857
Effective search space: 150996567
Effective search space used: 150996567
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: 40 (21.6 bits)
S2: 50 (23.0 bits)