RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13718
(165 letters)
>gnl|CDD|223109 COG0030, KsgA, Dimethyladenosine transferase (rRNA methylation)
[Translation, ribosomal structure and biogenesis].
Length = 259
Score = 81.9 bits (203), Expect = 1e-19
Identities = 34/126 (26%), Positives = 57/126 (45%), Gaps = 7/126 (5%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVH-PIIDLPF 59
++A G + RLS++ Q + +V+ F +P AF P P+VD VV P+ P
Sbjct: 137 LVAKPGSKDYGRLSVLVQYYADVEIVFDVPPSAFYPPPKVDSAVVRLVPKKEKPSPVKDE 196
Query: 60 KLIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
+ + V F R+K + LF + +LE A + P R LS ++F ++
Sbjct: 197 EKFFKFVKAAFSQRRKTLRNNLKNLFG------LEEVLEAAGIDPNARAENLSPEDFLKL 250
Query: 120 CLAYRD 125
A +
Sbjct: 251 ANALKG 256
>gnl|CDD|234708 PRK00274, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Reviewed.
Length = 272
Score = 79.0 bits (196), Expect = 2e-18
Identities = 38/116 (32%), Positives = 60/116 (51%), Gaps = 3/116 (2%)
Query: 12 RLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLP-FKLIERVVSCIF 70
RLS++ Q +C+V+ F +P AF+P P+VD VV PR P + + +L RVV F
Sbjct: 158 RLSVLVQYYCDVEKVFDVPPSAFVPPPKVDSAVVRLVPRKEPPVPVKDEELFFRVVKAAF 217
Query: 71 RYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQICLAYRDM 126
R+K + +L ++ + LE A + P R LSV+EF ++ A +
Sbjct: 218 AQRRKTLR--NNLKNLFGSKEKLEEALEAAGIDPNRRAETLSVEEFVRLANALAAL 271
>gnl|CDD|233115 TIGR00755, ksgA, dimethyladenosine transferase. In both E. coli
and Saccharomyces cerevisiae, this protein is
responsible for the dimethylation of two adjacent
adenosine residues in a conserved hairpin of 16S rRNA in
bacteria, 18S rRNA in eukaryotes. This adjacent
dimethylation is the only rRNA modification shared by
bacteria and eukaryotes. A single member of this family
is present in each of the first 20 completed microbial
genomes. This protein is essential in yeast, but not in
E. coli, where its deletion leads to resistance to the
antibiotic kasugamycin. Alternate name:
S-adenosylmethionine--6-N',N'-adenosyl (rRNA)
dimethyltransferase [Protein synthesis, tRNA and rRNA
base modification].
Length = 253
Score = 71.9 bits (177), Expect = 9e-16
Identities = 35/119 (29%), Positives = 58/119 (48%), Gaps = 4/119 (3%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
+ A G + RLS++ Q + NV+ F +P AF P P+VD VV PR +
Sbjct: 135 LTAKPGSKDYGRLSVLVQYFANVEIVFKVPPSAFYPPPKVDSAVVRLIPRETFPVKDEAL 194
Query: 61 LIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
E+++ F+ R+K + L PK K + +L + + P R QLS ++F ++
Sbjct: 195 F-EKLLKAAFQQRRKTLRNNLKNLLPKEK---LEEVLTQLGIDPTARAEQLSPEDFLRL 249
>gnl|CDD|237852 PRK14896, ksgA, 16S ribosomal RNA methyltransferase KsgA/Dim1
family protein; Provisional.
Length = 258
Score = 66.8 bits (164), Expect = 6e-14
Identities = 36/126 (28%), Positives = 61/126 (48%), Gaps = 11/126 (8%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
M+A G ++ RLS+M Q + +V+ +P AF PKP+VD VV TPR
Sbjct: 131 MVAKPGTKEYGRLSVMVQYYADVEIVEKVPPGAFSPKPKVDSAVVRLTPREPKYEVYDED 190
Query: 61 LIERVVSCIFRYRQKQVYKP----ASLLFPKRKRQLVVSLLERACVKPIL--RPYQLSVQ 114
+ V +F++R+K + A + + + +V +L E +L R +QLS +
Sbjct: 191 FFDDFVKALFQHRRKTLRNALKNSAHISGKEDIKAVVEALPE-----ELLNKRVFQLSPE 245
Query: 115 EFGQIC 120
E ++
Sbjct: 246 EIAELA 251
>gnl|CDD|128898 smart00650, rADc, Ribosomal RNA adenine dimethylases.
Length = 169
Score = 55.6 bits (135), Expect = 2e-10
Identities = 18/50 (36%), Positives = 26/50 (52%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPR 50
+ A G + RLS++ Q + +V F +P AF P P+VD VV R
Sbjct: 119 LAAKPGSKDYGRLSVLLQPYADVKILFKVPPSAFRPPPKVDSAVVRLERR 168
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 47.6 bits (114), Expect = 4e-07
Identities = 25/119 (21%), Positives = 54/119 (45%), Gaps = 6/119 (5%)
Query: 10 RCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFKLIERVVSCI 69
R RL+++ + + ++ +P +F P P+VD +V R P+ K + +V +
Sbjct: 142 RSRLTVLTEPFTDIKLVAKVPRSSFRPPPKVDSALVRLERRDTPLPVKDLKKYDYLVRKL 201
Query: 70 FRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQICLAYRDMCE 128
F + + ++ LFP + Q +L +RA + +LS Q ++++ +
Sbjct: 202 FNGKGRSLFTSLRSLFPGGQVQ---ALSKRARINDNALVGKLS---PEQWLNIFKELAK 254
>gnl|CDD|240367 PTZ00338, PTZ00338, dimethyladenosine transferase-like protein;
Provisional.
Length = 294
Score = 46.1 bits (110), Expect = 2e-06
Identities = 29/98 (29%), Positives = 48/98 (48%), Gaps = 8/98 (8%)
Query: 1 MIATEGMEQRCRLSIMCQNWCNVDHRFTIPGKAFIPKPQVDVGVVHFTPRVHPIIDLPFK 60
++A G E CRLS+ Q C V H + +F P P+V+ VV P+ +P D+ F+
Sbjct: 143 LLAQPGDELYCRLSVNTQLLCRVTHLMKVSKNSFNPPPKVESSVVRIEPK-NPPPDVDFE 201
Query: 61 LIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLE 98
+ ++ F + K + S +F K + V+ LE
Sbjct: 202 EWDGLLRICFSRKNKTL----SAIF---KTKSVLQTLE 232
>gnl|CDD|200593 cd10971, CE4_DAC_u2_5s, Putative catalytic NodB homology domain
of uncharacterized prokaryotic polysaccharide
deacetylases which consist of a 5-stranded beta/alpha
barrel. This family contains many uncharacterized
prokaryotic polysaccharide deacetylases. Although their
biological functions remain unknown, all members of
this family are predicted to contain a conserved domain
with a 5-stranded beta/alpha barrel, which is similar
to the catalytic NodB homology domain of rhizobial
NodB-like proteins, belonging to the larger
carbohydrate esterase 4 (CE4) superfamily.
Length = 198
Score = 28.4 bits (64), Expect = 1.3
Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 5/61 (8%)
Query: 27 FTIPGKAFIPKPQVDVGVVHFTPRVHPII--DLPFKLIERVVSCIFRYRQKQVYKPASLL 84
F +P K +DV +HF + ++ +LP KL ++ +F+ K V
Sbjct: 30 FFVPAKPVEEHKVLDVNKIHFILFIKRLLQYELPEKLRTEILDKLFK---KYVDISEEAF 86
Query: 85 F 85
Sbjct: 87 A 87
>gnl|CDD|223331 COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and
metabolism].
Length = 272
Score = 28.4 bits (64), Expect = 1.8
Identities = 9/38 (23%), Positives = 15/38 (39%), Gaps = 4/38 (10%)
Query: 39 QVDVGVVHFTPRVHP----IIDLPFKLIERVVSCIFRY 72
VD+G+ F P P ++ + L E V+
Sbjct: 115 SVDMGLPSFKPAEIPLLEEKVEEQYGLGEETVTFYAVS 152
>gnl|CDD|236208 PRK08262, PRK08262, hypothetical protein; Provisional.
Length = 486
Score = 28.4 bits (64), Expect = 2.1
Identities = 6/42 (14%), Positives = 16/42 (38%), Gaps = 3/42 (7%)
Query: 32 KAFIPKPQVDVGVVHFT---PRVHPIIDLPFKLIERVVSCIF 70
+ + +V++ V+ V +KL+ + +F
Sbjct: 374 RRAVADDRVEIEVLGGNSEPSPVSSTDSAAYKLLAATIREVF 415
>gnl|CDD|220410 pfam09798, LCD1, DNA damage checkpoint protein. This is a family
of proteins which regulate checkpoint kinases. In
Schizosaccharomyces pombe this protein is called Rad26
and in Saccharomyces cerevisiae it is called LCD1.
Length = 648
Score = 28.2 bits (63), Expect = 2.3
Identities = 15/53 (28%), Positives = 27/53 (50%)
Query: 45 VHFTPRVHPIIDLPFKLIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLL 97
F + DL KLIE ++ I+R ++ + S + P+ + +L+VSL
Sbjct: 496 TVFIDQDSNNGDLRIKLIEVLLRIIYRAWKEYEEQLLSEMIPEVESELIVSLW 548
>gnl|CDD|218238 pfam04739, AMPKBI, 5'-AMP-activated protein kinase beta subunit,
interation domain. This region is found in the beta
subunit of the 5'-AMP-activated protein kinase complex,
and its yeast homologues Sip1, Sip2 and Gal83, which
are found in the SNF1 kinase complex. This region is
sufficient for interaction of this subunit with the
kinase complex, but is not solely responsible for the
interaction, and the interaction partner is not known.
The isoamylase N-terminal domain (pfam02922) is
sometimes found in proteins belonging to this family.
Length = 94
Score = 26.4 bits (59), Expect = 3.5
Identities = 7/21 (33%), Positives = 9/21 (42%), Gaps = 4/21 (19%)
Query: 65 VVSCIFRYRQKQV----YKPA 81
+ RY+ K V YKP
Sbjct: 74 ALGATTRYKSKYVTTVLYKPL 94
>gnl|CDD|87993 pfam09448, MmlI, Methylmuconolactone methyl-isomerase. MmlI is a
short, approx 115 residue, protein of two alpha helices
and four beta strands. It is involved in the catabolism
of methyl-substituted aromatics via a modified
oxo-adipate pathway in bacteria. The enzyme appears to
be monomeric in some species and tetrameric in others.
The known structure shows two copies of the protein form
a dimeric alpha beta barrel.
Length = 112
Score = 26.6 bits (58), Expect = 4.4
Identities = 10/39 (25%), Positives = 22/39 (56%)
Query: 105 ILRPYQLSVQEFGQICLAYRDMCEEMPGLYEYTLEDTPG 143
+++P +S + F CL + +M ++PGL++Y +
Sbjct: 7 LVKPAGMSDETFRAECLRHYEMSHDVPGLHKYEVRLVAE 45
>gnl|CDD|147079 pfam04737, Lant_dehyd_N, Lantibiotic dehydratase, N terminus.
Lantibiotics are ribosomally synthesised antimicrobial
agents derived from ribosomally synthesised peptides.
They are produced by bacteria of the Firmicutes phylum,
and include mutacin, subtilin, and nisin. Lantibiotic
peptides contain thioether bridges termed lanthionines
that are thought to be generated by dehydration of
serine and threonine residues followed by addition of
cysteine residues. This family constitutes the
N-terminus of the enzyme proposed to catalyze the
dehydration step.
Length = 97
Score = 26.1 bits (58), Expect = 5.0
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 72 YRQKQVYKPASLLFPKRKRQLVVSL---LERACVKP 104
Y Q Y + L K+KR+L SL L+R C +
Sbjct: 13 YASIQRYLDGTPLRRKKKRRLERSLYRYLQRMCTRN 48
>gnl|CDD|223101 COG0022, AcoB, Pyruvate/2-oxoglutarate dehydrogenase complex,
dehydrogenase (E1) component, eukaryotic type, beta
subunit [Energy production and conversion].
Length = 324
Score = 27.1 bits (61), Expect = 5.1
Identities = 14/46 (30%), Positives = 24/46 (52%), Gaps = 1/46 (2%)
Query: 24 DHRFTIP-GKAFIPKPQVDVGVVHFTPRVHPIIDLPFKLIERVVSC 68
+ +TIP GKA I + DV +V + VH ++ +L + +S
Sbjct: 184 EEDYTIPLGKAKIVREGSDVTIVTYGAMVHTALEAAEELEKEGISA 229
>gnl|CDD|129242 TIGR00136, gidA, glucose-inhibited division protein A. GidA, the
longer of two forms of GidA-related proteins, appears to
be present in all complete eubacterial genomes so far,
as well as Saccharomyces cerevisiae. A subset of these
organisms have a closely related protein. GidA is absent
in the Archaea. It appears to act with MnmE, in an
alpha2/beta2 heterotetramer, in the
5-carboxymethylaminomethyl modification of uridine 34 in
certain tRNAs. The shorter, related protein, previously
called gid or gidA(S), is now called TrmFO (see model
TIGR00137) [Protein synthesis, tRNA and rRNA base
modification].
Length = 617
Score = 27.3 bits (61), Expect = 5.1
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 27 FTIPGKAFIPKPQVDVGVVHFTPRVHPIID 56
F+ K F+P Q+ + H P+ H +I
Sbjct: 222 FSFMNKNFLPLQQLPCYLTHTNPKTHDLIR 251
>gnl|CDD|182536 PRK10546, PRK10546, pyrimidine (deoxy)nucleoside triphosphate
pyrophosphohydrolase; Provisional.
Length = 135
Score = 26.2 bits (58), Expect = 5.8
Identities = 13/38 (34%), Positives = 22/38 (57%), Gaps = 5/38 (13%)
Query: 117 GQICLAYRDMCEEMPGLYEYT---LEDTPGDIEPEAVA 151
G+I LA R + GL+E+ +E PG+ +P+A+
Sbjct: 15 GKILLAQRPAHSDQAGLWEFAGGKVE--PGESQPQALI 50
>gnl|CDD|177087 CHL00185, ycf59, magnesium-protoporphyrin IX monomethyl ester
cyclase; Provisional.
Length = 351
Score = 26.6 bits (59), Expect = 6.7
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 85 FPKRKRQLVVSLLERAC 101
++ + L V LER+C
Sbjct: 72 LDEKTKSLFVEFLERSC 88
>gnl|CDD|198188 cd09934, SH2_Tec_family, Src homology 2 (SH2) domain found in
Tec-like proteins. The Tec protein tyrosine kinase is
the founding member of a family that includes Btk, Itk,
Bmx, and Txk. The members have a PH domain, a
zinc-binding motif, a SH3 domain, a SH2 domain, and a
protein kinase catalytic domain. Btk is involved in
B-cell receptor signaling with mutations in Btk
responsible for X-linked agammaglobulinemia (XLA) in
humans and X-linked immunodeficiency (xid) in mice. Itk
is involved in T-cell receptor signaling. Tec is
expressed in both T and B cells, and is thought to
function in activated and effector T lymphocytes to
induce the expression of genes regulated by NFAT
transcription factors. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 104
Score = 25.4 bits (56), Expect = 7.5
Identities = 11/43 (25%), Positives = 18/43 (41%)
Query: 94 VSLLERACVKPILRPYQLSVQEFGQICLAYRDMCEEMPGLYEY 136
VSL + P ++ Y + + LA + E +P L Y
Sbjct: 44 VSLFTKVPGSPHVKHYHIKQNARSEFYLAEKHCFETIPELINY 86
>gnl|CDD|214973 smart01010, AMPKBI, 5'-AMP-activated protein kinase beta subunit,
interation domain. This region is found in the beta
subunit of the 5'-AMP-activated protein kinase complex,
and its yeast homologues Sip1, Sip2 and Gal83, which are
found in the SNF1 kinase complex. This region is
sufficient for interaction of this subunit with the
kinase complex, but is not solely responsible for the
interaction, and the interaction partner is not known.
The isoamylase N-terminal domain is sometimes found in
proteins belonging to this family.
Length = 100
Score = 25.4 bits (56), Expect = 9.1
Identities = 9/21 (42%), Positives = 10/21 (47%), Gaps = 4/21 (19%)
Query: 65 VVSCIFRYRQKQV----YKPA 81
V+ RYR K V YKP
Sbjct: 80 AVAATTRYRGKYVTQVLYKPL 100
>gnl|CDD|218755 pfam05796, Chordopox_G2, Chordopoxvirus protein G2. This family
consists of several Chordopoxvirus
isatin-beta-thiosemicarbazone dependent protein (protein
G2) sequences. Inactivation of the gene coding for this
protein renders the virus dependent upon
isatin-beta-thiosemicarbazone (IBT) for growth.
Length = 216
Score = 26.1 bits (58), Expect = 9.7
Identities = 23/100 (23%), Positives = 34/100 (34%), Gaps = 20/100 (20%)
Query: 60 KLIERVVSCIFRYRQKQVYKPASLLFPKRKRQLVVSLLERACVKPILRPYQLSVQEFGQI 119
K I + + C + SL FP + +V L R K I R Y+L G
Sbjct: 51 KRITKALEC------ADLLPELSLEFPDDILRELVRLRLRKFSKTIKRSYKLPNNMKGIA 104
Query: 120 -----CLAYRDMCEEM---------PGLYEYTLEDTPGDI 145
+ R +E+ P +Y Y D P +
Sbjct: 105 VVKDREVYVRRANDELLDFLFKEYNPQIYRYAEGDKPSAL 144
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
0.325 0.142 0.443
Gapped
Lambda K H
0.267 0.0724 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,619,891
Number of extensions: 793741
Number of successful extensions: 682
Number of sequences better than 10.0: 1
Number of HSP's gapped: 676
Number of HSP's successfully gapped: 28
Length of query: 165
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 75
Effective length of database: 6,945,742
Effective search space: 520930650
Effective search space used: 520930650
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: 55 (25.0 bits)