RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4127
(75 letters)
>gnl|CDD|216840 pfam02005, TRM, N2,N2-dimethylguanosine tRNA methyltransferase.
This enzyme EC:2.1.1.32 used S-AdoMet to methylate tRNA.
The TRM1 gene of Saccharomyces cerevisiae is necessary
for the N2,N2-dimethylguanosine modification of both
mitochondrial and cytoplasmic tRNAs. The enzyme is found
in both eukaryotes and archaebacteria.
Length = 375
Score = 119 bits (300), Expect = 3e-34
Identities = 41/68 (60%), Positives = 47/68 (69%)
Query: 7 RGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSL 66
R FD IDLDPFG+P FLD+AV S++ GGLL VT TD AVLCG PE C KY AV L
Sbjct: 117 NHRRFDVIDLDPFGSPAPFLDSAVQSVKRGGLLCVTATDTAVLCGAYPEACLRKYGAVPL 176
Query: 67 KTAACHEM 74
+ CHE+
Sbjct: 177 RGEFCHEV 184
>gnl|CDD|224780 COG1867, TRM1, N2,N2-dimethylguanosine tRNA methyltransferase
[Translation, ribosomal structure and biogenesis].
Length = 380
Score = 103 bits (258), Expect = 3e-28
Identities = 41/67 (61%), Positives = 47/67 (70%)
Query: 9 RHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSLKT 68
R FD ID+DPFG+P FLDAA+ S+R GGLL VT TD A LCG+ P C KY AV LKT
Sbjct: 120 RAFDVIDIDPFGSPAPFLDAALRSVRRGGLLCVTATDTAPLCGSYPRKCRRKYGAVPLKT 179
Query: 69 AACHEMP 75
CHE+
Sbjct: 180 EFCHEVG 186
>gnl|CDD|235286 PRK04338, PRK04338, N(2),N(2)-dimethylguanosine tRNA
methyltransferase; Provisional.
Length = 382
Score = 96.9 bits (242), Expect = 7e-26
Identities = 38/68 (55%), Positives = 47/68 (69%)
Query: 7 RGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSL 66
R FD +D+DPFG+P FLD+A+ S++ GGLL VT TD A LCG P++C KY AV L
Sbjct: 122 EERKFDVVDIDPFGSPAPFLDSAIRSVKRGGLLCVTATDTAPLCGAYPKSCLRKYGAVPL 181
Query: 67 KTAACHEM 74
KT HEM
Sbjct: 182 KTEFYHEM 189
>gnl|CDD|232913 TIGR00308, TRM1, tRNA(guanine-26,N2-N2) methyltransferase. This
enzyme is responsible for two methylations of a
characteristic guanine of most tRNA molecules. The
activity has been demonstrated for eukaryotic and
archaeal proteins, which are active when expressed in E.
coli, a species that lacks this enzyme. At least one
Eubacterium, Aquifex aeolicus, has an ortholog, as do
all completed archaeal genomes [Protein synthesis, tRNA
and rRNA base modification].
Length = 374
Score = 91.8 bits (228), Expect = 5e-24
Identities = 35/67 (52%), Positives = 46/67 (68%)
Query: 7 RGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTPETCYVKYNAVSL 66
R R F ID+DPFG P F+D+A+ + + GLLLVT TD + LCGN P++C KY A +
Sbjct: 111 RNRKFHVIDIDPFGTPAPFVDSAIQASAERGLLLVTATDTSALCGNYPKSCLRKYGANPV 170
Query: 67 KTAACHE 73
KT +CHE
Sbjct: 171 KTESCHE 177
>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 = 30.5 bits (69), Expect = 0.028
Identities = 15/47 (31%), Positives = 22/47 (46%), Gaps = 5/47 (10%)
Query: 2 QLEKIRGRHFDAIDLDP-----FGNPTRFLDAAVSSLRDGGLLLVTC 43
+L FD I DP + RFL+ A L+ GG+L++T
Sbjct: 58 ELPPEADESFDVIISDPPLHHLVEDLARFLEEARRLLKPGGVLVLTL 104
>gnl|CDD|107352 cd06357, PBP1_AmiC, Periplasmic binding domain of amidase (AmiC)
that belongs to the type I periplasmic binding fold
protein family. This group includes the periplasmic
binding domain of amidase (AmiC) that belongs to the
type I periplasmic binding fold protein family. AmiC
controls expression of the amidase operon by the
ligand-triggered conformational switch. In the absence
of ligand or presence of butyramide (repressor), AmiC
(the ligand sensor and negative regulator) adopts an
open conformation and inhibits the transcription
antitermination function of AmiR by direct
protein-protein interaction. In the presence of
inducing ligands such as acetamide, AmiC adopts a
closed conformation which disrupts a silencing
AmiC-AmiR complex and the expression of amidase and
other genes of the operon are induced.
Length = 360
Score = 31.1 bits (71), Expect = 0.030
Identities = 11/40 (27%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 6 IRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGGL-LLVTCT 44
+ GR + ++ DP G+P + A LR+ G+ ++ C
Sbjct: 36 VLGRELEPVEYDPGGDPDAYRALAERLLREDGVRVIFGCY 75
>gnl|CDD|234556 TIGR04345, ovoA_Cterm, putative 4-mercaptohistidine
N1-methyltranferase. Ovothiol A is
N1-methyl-4-mercaptohistidine. In the absence of
S-adenosylmethione, a methyl donor, the intermediate
produced is 4-mercaptohistidine. In both Erwinia
tasmaniensis and Trypanosoma cruzi, a protein occurs
with 5-histidylcysteine sulfoxide synthase activity, but
these two enzymes and most homologs share an additional
C-terminal methyltransferase domain. Thus OvoA may be a
bifunctional enzyme with 5-histidylcysteine sulfoxide
synthase and 4-mercaptohistidine N1-methyltranferase
activity. This model describes C-terminal putative
4-mercaptohistidine N1-methyltranferase domain
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Glutathione and analogs].
Length = 242
Score = 30.3 bits (69), Expect = 0.058
Identities = 12/39 (30%), Positives = 17/39 (43%), Gaps = 4/39 (10%)
Query: 10 HFDAI----DLDPFGNPTRFLDAAVSSLRDGGLLLVTCT 44
+D I LD +P FL + L GGLL++
Sbjct: 134 GYDLILAANLLDRLYDPAAFLSSIHERLNPGGLLVIASP 172
>gnl|CDD|222295 pfam13659, Methyltransf_26, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 117
Score = 27.8 bits (62), Expect = 0.31
Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 12/53 (22%)
Query: 1 MQLEKIRGRHFDAIDLD-PFGNPT-----------RFLDAAVSSLRDGGLLLV 41
+L ++ FD + + P+G RFL AA+ L+ GG+L+V
Sbjct: 61 RELLELPDGSFDLVLGNPPYGPRAGDPKDNRDLYDRFLAAALRLLKPGGVLVV 113
>gnl|CDD|223222 COG0144, Sun, tRNA and rRNA cytosine-C5-methylases [Translation,
ribosomal structure and biogenesis].
Length = 355
Score = 28.1 bits (63), Expect = 0.32
Identities = 9/22 (40%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 24 RFLDAAVSSLRDGGLLL-VTCT 44
L AA+ L+ GG+L+ TC+
Sbjct: 269 EILAAALKLLKPGGVLVYSTCS 290
>gnl|CDD|235399 PRK05303, flgI, flagellar basal body P-ring protein; Provisional.
Length = 367
Score = 27.8 bits (63), Expect = 0.36
Identities = 14/33 (42%), Positives = 18/33 (54%), Gaps = 5/33 (15%)
Query: 15 DLDPFGNPTRFLDAAVSSLRD-----GGLLLVT 42
L PF P + +D VSS+ D GG LL+T
Sbjct: 96 TLPPFARPGQRIDVTVSSIGDAKSLRGGTLLMT 128
>gnl|CDD|224017 COG1092, COG1092, Predicted SAM-dependent methyltransferases
[General function prediction only].
Length = 393
Score = 27.3 bits (61), Expect = 0.66
Identities = 16/58 (27%), Positives = 23/58 (39%), Gaps = 14/58 (24%)
Query: 1 MQLEKIRGRHFDAIDLDP--FGNP-----------TRFLDAAVSSLRDGGLLLV-TCT 44
++ + RG FD I LDP F D A+ L GG L+ +C+
Sbjct: 281 LRKAERRGEKFDLIILDPPSFARSKKQEFSAQRDYKDLNDLALRLLAPGGTLVTSSCS 338
>gnl|CDD|183746 PRK12789, flgI, flagellar basal body P-ring protein; Reviewed.
Length = 367
Score = 27.4 bits (61), Expect = 0.67
Identities = 19/46 (41%), Positives = 24/46 (52%), Gaps = 9/46 (19%)
Query: 6 IRGRHFDAI----DLDPFGNPTRFLDAAVSSLRD-----GGLLLVT 42
+R R+ A+ DL PF P +D VSSL D GG LL+T
Sbjct: 81 LRTRNVAAVMVTADLPPFTGPGSRIDVTVSSLGDATSLRGGTLLMT 126
>gnl|CDD|224620 COG1706, FlgI, Flagellar basal-body P-ring protein [Cell motility
and secretion].
Length = 365
Score = 25.7 bits (57), Expect = 2.0
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 15 DLDPFGNPTRFLDAAVSSLRD-----GGLLLVT 42
L PF +D VSS+ D GG LL+T
Sbjct: 95 SLPPFARQGSKIDVTVSSIGDAKSLRGGTLLMT 127
>gnl|CDD|222171 pfam13489, Methyltransf_23, Methyltransferase domain. This family
appears to be a methyltransferase domain.
Length = 154
Score = 25.5 bits (56), Expect = 2.1
Identities = 10/45 (22%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 2 QLEKIRGRHFDAID----LDPFGNPTRFLDAAVSSLRDGGLLLVT 42
+ +D I L+ +P L L+ GG+LL++
Sbjct: 66 PDPAVLAGKYDLITAFEVLEHLPDPPALLQQLRELLKPGGVLLIS 110
>gnl|CDD|100030 cd02194, ThiL, ThiL (Thiamine-monophosphate kinase) plays a dual
role in de novo biosynthesis and in salvage of
exogenous thiamine. Thiamine salvage occurs in two
steps, with thiamine kinase catalyzing the formation of
thiamine phosphate, and ThiL catalyzing the conversion
of this intermediate to thiamine pyrophosphate. The
N-terminal domain of ThiL binds ATP and is related to
the ATP-binding domains of hydrogen
expression/formation protein HypE, the AIR synthases,
FGAM synthase and selenophosphate synthetase (SelD).
Length = 291
Score = 25.6 bits (57), Expect = 2.1
Identities = 11/22 (50%), Positives = 12/22 (54%), Gaps = 2/22 (9%)
Query: 27 DAAVSSLRDGGLLLVTCTDMAV 48
DAAV L+ G LV TD V
Sbjct: 26 DAAV--LKPPGGRLVVTTDTLV 45
>gnl|CDD|225549 COG3004, NhaA, Na+/H+ antiporter [Inorganic ion transport and
metabolism].
Length = 390
Score = 25.7 bits (57), Expect = 2.2
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 36 GGLLLVTCTDMAVLCGNTP 54
GG+LL+ +A+L N+
Sbjct: 18 GGILLIIAAALALLVANSA 36
>gnl|CDD|224361 COG1444, COG1444, Predicted P-loop ATPase fused to an
acetyltransferase [General function prediction only].
Length = 758
Score = 25.4 bits (56), Expect = 2.8
Identities = 16/42 (38%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 2 QLEKIRGRHFDAIDLDPFG--NPTRFLDAAVSSLRDGGLLLV 41
+ E+I GR FD + LD +P L V ++R GGLL++
Sbjct: 84 ESERILGRTFDLLVLDLTEGLDPN-ALARLVGTVRGGGLLVL 124
>gnl|CDD|236568 PRK09560, nhaA, pH-dependent sodium/proton antiporter; Reviewed.
Length = 389
Score = 24.8 bits (55), Expect = 4.7
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 4/32 (12%)
Query: 23 TRFLDAAVSSLRDGGLLLVTCTDMAVLCGNTP 54
RFL + + GG+LL+ +A++ N+P
Sbjct: 6 RRFLKSEAA----GGILLMAAAALAMIVANSP 33
>gnl|CDD|212072 cd11503, SLC5sbd_NIS, Na(+)/iodide cotransporter NIS and related
proteins; solute-binding domain. NIS (product of the
SLC5A5 gene) transports I-, and other anions including
ClO4-, SCN-, and Br-. NIS is expressed in the thyroid,
colon, ovary, and in human breast cancers. It mediates
the active transport and the concentration of iodide
from the blood into thyroid follicular cells, a
fundamental step in thyroid hormone biosynthesis, and is
the basis of radioiodine therapy for thyroid cancer.
Mutation in the SLC5A5 gene can result in a form of
thyroid hormone dysgenesis. Human NIS exists mainly as a
dimer stabilized by a disulfide bridge. This subgroup
belongs to the solute carrier 5 (SLC5) transporter
family.
Length = 535
Score = 24.8 bits (54), Expect = 5.4
Identities = 12/24 (50%), Positives = 16/24 (66%)
Query: 28 AAVSSLRDGGLLLVTCTDMAVLCG 51
AA+SSL GG+L + T M V+ G
Sbjct: 388 AALSSLLGGGVLQGSFTVMGVISG 411
>gnl|CDD|233387 TIGR01379, thiL, thiamine-monophosphate kinase. This model
describes thiamine-monophosphate kinase, an enzyme that
converts thiamine monophosphate into thiamine
pyrophosphate (TPP, coenzyme B1), an enzyme cofactor.
Thiamine monophosphate may be derived from de novo
synthesis or from unphosphorylated thiamine, known as
vitamin B1. Proteins scoring between the trusted and
noise cutoff for this model include short forms from
the Thermoplasmas (which lack the N-terminal region)
and a highly derived form from Campylobacter jejuni.
Eukaryotes lack this enzyme, and add pyrophosphate from
ATP to unphosphorylated thiamine in a single step
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Thiamine].
Length = 317
Score = 24.6 bits (54), Expect = 5.5
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 27 DAAVSSLRDGGLLLVTCTDMAV 48
DAA+ S +G L++T TD V
Sbjct: 26 DAALVSAPEGRDLVLT-TDTLV 46
>gnl|CDD|213874 TIGR03857, F420_MSMEG_2249, probable F420-dependent oxidoreductase,
MSMEG_2249 family. Coenzyme F420 has a limited
phylogenetic distribution, including methanogenic
archaea, Mycobacterium tuberculosis and related species,
Colwellia psychrerythraea 34H, Rhodopseudomonas
palustris HaA2, and others. Partial phylogenetic
profiling identifies protein subfamilies, within the
larger family called luciferase-like monooxygenanases
(pfam00296), that appear only in F420-positive genomes
and are likely to be F420-dependent. This model
describes a distinctive subfamily, found only in
F420-biosynthesizing members of the Actinobacteria of
the bacterial luciferase-like monooxygenase (LLM)
superfamily [Unknown function, Enzymes of unknown
specificity].
Length = 329
Score = 24.8 bits (54), Expect = 5.6
Identities = 10/28 (35%), Positives = 15/28 (53%), Gaps = 1/28 (3%)
Query: 8 GRHFDAIDLDPFGNPTRFLDAAVSSLRD 35
GR FD + L PF P + +V+ +R
Sbjct: 168 GRAFDGVILHPFLTPEA-VARSVAIVRR 194
>gnl|CDD|238355 cd00659, Topo_IB_C, DNA topoisomerase IB, C-terminal catalytic
domain. Topoisomerase I promotes the relaxation of both
positive and negative DNA superhelical tension by
introducing a transient single-stranded break in duplex
DNA. This function is vital for the processes of
replication, transcription, and recombination. Unlike
Topo IA enzymes, Topo IB enzymes do not require a
single-stranded region of DNA or metal ions for their
function. The type IB family of DNA topoisomerases
includes eukaryotic nuclear topoisomerase I,
topoisomerases of poxviruses and bacterial versions of
Topo IB. They belong to the superfamily of DNA
breaking-rejoining enzymes, which share the same fold in
their C-terminal catalytic domain and the overall
reaction mechanism with tyrosine recombinases. The
C-terminal catalytic domain in topoisomerases is linked
to a divergent N-terminal domain that shows no sequence
or structure similarity to the N-terminal domains of
tyrosine recombinases.
Length = 218
Score = 24.5 bits (54), Expect = 5.7
Identities = 8/34 (23%), Positives = 14/34 (41%), Gaps = 1/34 (2%)
Query: 29 AVSSLRDGGLLLV-TCTDMAVLCGNTPETCYVKY 61
A SL + ++A+L +TP + Y
Sbjct: 172 ASLSLAEKKKAYNDANREVAILLNHTPAISKINY 205
>gnl|CDD|239637 cd03582, NTR_complement_C5, NTR/C345C domain, complement C5
subfamily; The NTR domain found in complement C5 is
also known as C345C because it occurs at the C-terminus
of complement C3, C4 and C5. Complement C5 is activated
by C5 convertase, which itself is a complex between C3b
and C3 convertase. The small cleavage fragment, C5a, is
the most important small peptide mediator of
inflammation, and the larger active fragment, C5b,
initiates late events of complement activation. The
NTR/C345C domain is important in the function of C5 as
it interacts with enzymes that convert C5 to the active
form, C5b. The domain has also been found to bind to
complement components C6 and C7, and may specifically
interact with their factor I modules.
Length = 150
Score = 24.4 bits (53), Expect = 6.0
Identities = 8/28 (28%), Positives = 10/28 (35%)
Query: 46 MAVLCGNTPETCYVKYNAVSLKTAACHE 73
+A C C V A K+ C E
Sbjct: 2 VAAQCQCFAAACDVTITAARRKSETCKE 29
>gnl|CDD|107326 cd06331, PBP1_AmiC_like, Type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF). This group
includes the type I periplasmic components of
amide-binding protein (AmiC) and the active transport
system for short-chain and urea (FmdDEF), found in
bacteria and Archaea. AmiC controls expression of the
amidase operon by a ligand-triggered conformational
switch. In the absence of ligand or presence of
butyramide (repressor), AmiC (the ligand sensor and
negative regulator) adopts an open conformation and
inhibits the transcription antitermination function of
AmiR by direct protein-protein interaction. In the
presence of inducing ligands such as acetamide, AmiC
adopts a closed conformation which disrupts a silencing
AmiC-AmiR complex and the expression of amidase and
other genes of the operon is induced. FmdDEF is
predicted to be an ATP-dependent transporter and
closely resembles the periplasmic binding protein and
the two transmembrane proteins present in various
hydrophobic amino acid-binding transport systems.
Length = 333
Score = 24.4 bits (54), Expect = 7.1
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 6 IRGRHFDAIDLDPFGNPTRFLDAAVSSLRDGG 37
I GR + + DP +P AA +RD
Sbjct: 36 ILGRPLELVVEDPASDPAFAAKAARRLIRDDK 67
>gnl|CDD|181955 PRK09561, nhaA, pH-dependent sodium/proton antiporter; Reviewed.
Length = 388
Score = 24.1 bits (53), Expect = 7.8
Identities = 8/19 (42%), Positives = 13/19 (68%)
Query: 36 GGLLLVTCTDMAVLCGNTP 54
GG+LL+ +A+L N+P
Sbjct: 15 GGILLIIAAALAMLMANSP 33
>gnl|CDD|226607 COG4122, COG4122, Predicted O-methyltransferase [General function
prediction only].
Length = 219
Score = 23.8 bits (52), Expect = 9.0
Identities = 11/28 (39%), Positives = 16/28 (57%), Gaps = 1/28 (3%)
Query: 14 IDLDPFGNPTRFLDAAVSSLRDGGLLLV 41
ID D P +L+ A+ LR GGL++
Sbjct: 138 IDADKADYP-EYLERALPLLRPGGLIVA 164
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 0.138 0.430
Gapped
Lambda K H
0.267 0.0669 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,748,527
Number of extensions: 276969
Number of successful extensions: 397
Number of sequences better than 10.0: 1
Number of HSP's gapped: 397
Number of HSP's successfully gapped: 30
Length of query: 75
Length of database: 10,937,602
Length adjustment: 45
Effective length of query: 30
Effective length of database: 8,941,672
Effective search space: 268250160
Effective search space used: 268250160
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 (21.5 bits)
S2: 53 (24.3 bits)