RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10644
(196 letters)
>gnl|CDD|203179 pfam05148, Methyltransf_8, Hypothetical methyltransferase. This
family consists of several uncharacterized eukaryotic
proteins which are related to methyltransferases
pfam01209.
Length = 219
Score = 206 bits (525), Expect = 8e-68
Identities = 85/152 (55%), Positives = 108/152 (71%), Gaps = 3/152 (1%)
Query: 46 LREKLLNKLKSARFRYLNEQLYTSKSEESKDFFTEDRESFEAYHEGFKKQVTQWPINPVD 105
L K+ +L RFR LNE+LYT K + D F ED ++F+ YHEGF QV +WP+NP+D
Sbjct: 2 LEAKMKKRLDGGRFRMLNEKLYTGKGSRAGDLFKEDPDAFDLYHEGFNLQVKKWPVNPLD 61
Query: 106 IIIKSIQERESKGRLVIADLGCGEAKLAAELTQ-HKVHSLDLVALNERVTSCDMTRTPLK 164
+II+ ++ R G VIADLGCGEA++A + VHS DLVA+N+RV CDM R PL+
Sbjct: 62 VIIRKLKRRP--GNGVIADLGCGEARIAFRKREFENVHSFDLVAVNKRVIPCDMARVPLE 119
Query: 165 PYSVDVAVFCLSLMGTDLAACIKEANRILKLG 196
SVDVAVFCLSLMGT++A +KEANRILK G
Sbjct: 120 DESVDVAVFCLSLMGTNIADFLKEANRILKNG 151
>gnl|CDD|219759 pfam08241, Methyltransf_11, Methyltransferase domain. Members of
this family are SAM dependent methyltransferases.
Length = 92
Score = 43.8 bits (104), Expect = 3e-06
Identities = 23/84 (27%), Positives = 31/84 (36%), Gaps = 13/84 (15%)
Query: 124 DLGCGEAKLAAELTQ---HKVHSLDLVA---------LNERVTSCDMTRTPLKPYSVDVA 171
D+GCG LA L + +V +DL + D P S DV
Sbjct: 2 DVGCGTGLLAEALARRGGARVTGVDLSPEMLALARKRAPRKFVVGDAEDLPFPDESFDVV 61
Query: 172 VFCLSLM-GTDLAACIKEANRILK 194
V L L D ++E R+LK
Sbjct: 62 VSSLVLHHLPDPERALREIARVLK 85
>gnl|CDD|240067 cd04716, BAH_plantDCM_I, BAH, or Bromo Adjacent Homology domain,
first copy present in DNA
(Cytosine-5)-methyltransferases (DCM) from plants. DNA
methylation, or the covalent addition of a methyl group
to cytosine within the context of the CpG dinucleotide,
has profound effects on the genome. These effects
include transcriptional repression via inhibition of
transcription factor binding, the recruitment of
methyl-binding proteins and their associated chromatin
remodeling factors, X chromosome inactivation,
imprinting, and the suppression of parasitic DNA
sequences. DNA methylation is also essential for proper
embryonic development and is an important player in both
DNA repair and genome stability. BAH domains are found
in a variety of proteins playing roles in
transcriptional silencing and the remodeling of
chromatin. It is assumed that in most or all of these
instances the BAH domain mediates protein-protein
interactions.
Length = 122
Score = 32.8 bits (75), Expect = 0.040
Identities = 17/77 (22%), Positives = 28/77 (36%), Gaps = 7/77 (9%)
Query: 62 LNEQLYTSKSEESKDFFTEDRESFEAYHEGFKKQVTQWPINPVDIIIKSIQERESKGRLV 121
L + Y E + F + E FE +G QW D +I+ K R+
Sbjct: 6 LGDDAYVQGGEGEEPFICKITEFFEGT-DGKTYFTAQWFYRAEDTVIERQATNHDKKRVF 64
Query: 122 IAD------LGCGEAKL 132
++ L C +K+
Sbjct: 65 YSEIKNDNPLDCLISKV 81
>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 = 31.6 bits (72), Expect = 0.074
Identities = 28/96 (29%), Positives = 38/96 (39%), Gaps = 21/96 (21%)
Query: 122 IADLGCGEAKLAAELTQH---KVHSLDL---------------VALNERVTSCDMTRTPL 163
+ DLGCG LA L +V +D+ +A N V D P
Sbjct: 2 VLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPP 61
Query: 164 KPY-SVDVAVFCLSLMG--TDLAACIKEANRILKLG 196
+ S DV + L DLA ++EA R+LK G
Sbjct: 62 EADESFDVIISDPPLHHLVEDLARFLEEARRLLKPG 97
>gnl|CDD|234456 TIGR04074, bacter_Hen1, 3' terminal RNA ribose
2'-O-methyltransferase Hen1. Members of this protein
family are bacterial Hen1, a 3' terminal RNA ribose
2'-O-methyltransferase that acts in bacterial RNA
repair. All members of the seed alignment belong to a
cassette with the RNA repair enzyme polynucleotide
kinase-phosphatase (Pnkp). Chemically similar Hen1 in
eukaryotes acts instead on small regulatory RNAs
[Transcription, RNA processing, Protein synthesis, tRNA
and rRNA base modification].
Length = 462
Score = 32.3 bits (74), Expect = 0.14
Identities = 18/44 (40%), Positives = 20/44 (45%), Gaps = 9/44 (20%)
Query: 114 RESKGRLVIADLGCGEAKLAAELTQHKVHSLDLVALNERVTSCD 157
RES R V+ DLGCGE KL L K ER+ D
Sbjct: 279 RESGARSVL-DLGCGEGKLLRLLLAEKQF--------ERIAGVD 313
>gnl|CDD|184702 PRK14484, PRK14484, phosphotransferase mannnose-specific family
component IIA; Provisional.
Length = 124
Score = 29.5 bits (67), Expect = 0.61
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 13/87 (14%)
Query: 104 VDIIIKSIQERESKGRLVIADLGCGEAKLAAELTQHKVHSLDLVALNERVTSCDMTRTPL 163
D I ++I++ ES G L+ DL G A++ AE+ +++++ +++ D P+
Sbjct: 45 FDQIQEAIEKNESDGVLIFFDL--GSAEMNAEM------AIEMLDGEKKIIIID---API 93
Query: 164 KPYSVDVAVFCLSLMGTDLAACIKEAN 190
+ AV L G L + E
Sbjct: 94 VEGAFTAAV--LLSAGASLDEILAELK 118
>gnl|CDD|222415 pfam13847, Methyltransf_31, Methyltransferase domain. This family
appears to be have methyltransferase activity.
Length = 151
Score = 29.3 bits (66), Expect = 0.66
Identities = 22/99 (22%), Positives = 37/99 (37%), Gaps = 24/99 (24%)
Query: 120 LVIADLGCGEAKLAAELTQH-----KVHSLDL--VALN-----------ERVTSC----- 156
+ + DLGCG L L + +V +D+ A+ E V
Sbjct: 5 IKVLDLGCGTGYLTFILAEKLGPGAEVVGIDISEEAIEKAKENAKKLGYENVEFIQGDIE 64
Query: 157 DMTRTPLKPYSVDVAVFCLSLM-GTDLAACIKEANRILK 194
++ + L+ S DV + L D ++E R+LK
Sbjct: 65 ELPQLQLEDNSFDVVISNEVLNHLPDPDKVLEEIIRVLK 103
>gnl|CDD|223574 COG0500, SmtA, SAM-dependent methyltransferases [Secondary
metabolites biosynthesis, transport, and catabolism /
General function prediction only].
Length = 257
Score = 29.9 bits (64), Expect = 0.84
Identities = 28/141 (19%), Positives = 44/141 (31%), Gaps = 24/141 (17%)
Query: 80 EDRESFEAYHEGFKK--QVTQWPINPVDIIIKSIQERESKGRLVIADLGC--GEAKLAAE 135
E Y + +D+++ R G L + D+GC G L A
Sbjct: 8 LLSRILELYDRLAELLDAFLLLAEELLDLLLVLRLLRLLPGGLGVLDIGCGTGRLALLAR 67
Query: 136 LTQHKVH------SLDLVAL-----------NERVTSCDMTRTPL---KPYSVDVAVFCL 175
L + S +++AL D L S D+ + L
Sbjct: 68 LGGRGAYVVGVDLSPEMLALARARAEGAGLGLVDFVVADALGGVLPFEDSASFDLVISLL 127
Query: 176 SLMGTDLAACIKEANRILKLG 196
L A ++E R+LK G
Sbjct: 128 VLHLLPPAKALRELLRVLKPG 148
>gnl|CDD|234318 TIGR03704, PrmC_rel_meth, putative protein-(glutamine-N5)
methyltransferase, unknown substrate-specific. This
protein family is closely related to two different
families of protein-(glutamine-N5) methyltransferase.
The first is PrmB, which modifies ribosomal protein L3
in some bacteria. The second is PrmC (HemK), which
modifies peptide chain release factors 1 and 2 in most
bacteria and also in eukaryotes. The glutamine side
chain-binding motif NPPY shared by PrmB and PrmC is
N[VAT]PY in this family. The protein substrate is
unknown [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 251
Score = 28.6 bits (64), Expect = 1.8
Identities = 15/37 (40%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 114 RESKGRLVIADLGCGE----AKLAAELTQHKVHSLDL 146
R G LV+ DL CG A LAA L ++H+ D+
Sbjct: 82 RPRSGTLVVVDLCCGSGAVGAALAAALDGIELHAADI 118
>gnl|CDD|233430 TIGR01477, RIFIN, variant surface antigen, rifin family. This
model represents the rifin branch of the rifin/stevor
family (pfam02009) of predicted variant surface
antigens as found in Plasmodium falciparum. This model
is based on a set of rifin sequences kindly provided by
Matt Berriman from the Sanger Center. This is a global
model and assesses a penalty for incomplete sequence.
Additional fragmentary sequences may be found with the
fragment model and a cutoff of 20 bits.
Length = 353
Score = 28.9 bits (65), Expect = 1.8
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 24 NILATSSGGHKKEKYYNSKHTP 45
NIL S HK ++ S TP
Sbjct: 16 NILVNSQRNHKNTPHHTSNTTP 37
>gnl|CDD|211985 TIGR04262, orph_peri_GRRM, extracellular substrate-binding orphan
protein, GRRM family. This subfamily belongs to
bacterial extracellular solute-binding protein family 3
(pfam00497). In that family, most members are ABC
transporter periplasmic substrate-binding proteins.
However, members of the present subfamily are orphans in
the sense of being adjacent to neither ABC transporter
ATP-binding proteins or permease subunits. Instead, most
members are encoded next to the two signature proteins
of the proposed Glycine-Rich Repeat Modification (GRRM)
system, a radical SAM/SPASM protein GrrM (TIGR04261) and
the Gly-rich repeat protein itself GrrA (TIGR04260).
Length = 257
Score = 28.1 bits (63), Expect = 2.9
Identities = 15/66 (22%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 72 EESKDFFTEDRESFEAYH----EGFKKQVTQWPINPVDI---IIKSIQERESKGRLVIAD 124
+ + +D ++ E + Q+ P+ I ++ S+QE K R AD
Sbjct: 9 GDVLPLYQKDDAGYDGLSFDVLELIRDQLQAELGKPITIQFVVVNSVQEGLPKLRSGKAD 68
Query: 125 LGCGEA 130
+ CG A
Sbjct: 69 IACGVA 74
>gnl|CDD|234537 TIGR04313, aro_clust_Mycop, aromatic cluster surface protein.
Members of this family are absolutely restricted to the
Mollicutes (Mycoplasma and Ureaplasma). All have a
signal peptide, usually of the lipoprotein type,
suggesting surface expression. Most members have lengths
of about 280 residues but some members have a nearly
full-length duplication. The mostly nearly invariant
residue, a Trp,is part of a strongly conserved 9-residue
motif, [ND]-W-[LY]-[WF]-X-[LF]-X-N-[LI], where X usually
is hydrophobic. Because the hydrophobic six-residue core
of this motif almost always contains three to four
aromatic residues, we name this family aromatic cluster
surface protein. Multiple paralogs may occur in a given
Mycoplasma, usually clustered on the genome.
Length = 297
Score = 28.1 bits (63), Expect = 3.0
Identities = 22/79 (27%), Positives = 33/79 (41%), Gaps = 4/79 (5%)
Query: 18 SNSNVPNILATSSGGHK--KEKYYNSKHTPLREKLLNKLKSARFRYLNEQLYTSKSEESK 75
+N + N+L + K KY S+ E L LK + YLN + S S +S
Sbjct: 56 NNKYINNLLNLVFKNDEDEKNKYIKSQKNINSELYLKLLKLSLE-YLN-NINNSSSNDSD 113
Query: 76 DFFTEDRESFEAYHEGFKK 94
F +S + +E F K
Sbjct: 114 FFSYLYEKSKKKLNELFSK 132
>gnl|CDD|220744 pfam10421, OAS1_C, 2'-5'-oligoadenylate synthetase 1, domain 2,
C-terminus. This is the largely alpha-helical,
C-terminal half of 2'-5'-oligoadenylate synthetase 1,
being described as domain 2 of the enzyme and homologous
to a tandem ubiquitin repeat. It carries the region of
enzymic activity between 320 and 344 at the extreme
C-terminal end. Oligoadenylate synthetases are antiviral
enzymes that counteract vial attack by degrading viral
RNA. The enzyme uses ATP in 2'-specific nucleotidyl
transfer reactions to synthesise 2'.5'-oligoadenylates,
which activate latent ribonuclease, resulting in
degradation of viral RNA and inhibition of virus
replication. This domain is often associated with
NTP_transf_2 pfam01909.
Length = 191
Score = 27.2 bits (61), Expect = 4.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 36 EKYYNSKHTPLREKLLNKLKSAR 58
KYY+ + +R LL +LK R
Sbjct: 115 TKYYDFEDETVRNYLLRQLKKPR 137
>gnl|CDD|236312 PRK08617, PRK08617, acetolactate synthase; Reviewed.
Length = 552
Score = 27.1 bits (61), Expect = 6.2
Identities = 16/46 (34%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 129 EAKLAAELTQHKVHSLDLV-ALNERVTSCDMTRTPLKPYSVDVAVF 173
A+ A L + VH L ++ AL + VT D T T VDV
Sbjct: 353 LAERPARLEEGAVHPLRIIRALQDIVTD-DTTVT------VDVGSH 391
>gnl|CDD|235548 PRK05657, PRK05657, RNA polymerase sigma factor RpoS; Validated.
Length = 325
Score = 26.8 bits (60), Expect = 7.9
Identities = 15/33 (45%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 134 AELTQHKVHSL-DLVALNERVTSCDMTRTPLKP 165
AEL V + ++ALNER+TS D TPL
Sbjct: 196 AELLDKPVDDVSRMLALNERITSLD---TPLGG 225
>gnl|CDD|226888 COG4485, COG4485, Predicted membrane protein [Function unknown].
Length = 858
Score = 27.1 bits (60), Expect = 7.9
Identities = 15/64 (23%), Positives = 21/64 (32%), Gaps = 2/64 (3%)
Query: 9 SETAHSTSTSNSNVPNILATSSGGHKKEKYYNSKHTPLRE-KLLNKLKSARFRYLNEQLY 67
SE ++T N I S+ + K N K T + +LN L S Y
Sbjct: 577 SEHKNNTLYENHYSLPIAVPSANIYNDVK-LNKKSTLDNQQAMLNGLVSKNTTYFTHFPA 635
Query: 68 TSKS 71
Sbjct: 636 NKIL 639
>gnl|CDD|219850 pfam08455, SNF2_assoc, Bacterial SNF2 helicase associated. This
domain is found in bacterial proteins of the SWF/SNF/SWI
helicase family to the N-terminus of the SNF2 family
N-terminal domain (pfam00176) and together with the
Helicase conserved C-terminal domain (pfam00271). The
function of the domain is not clear.
Length = 376
Score = 26.8 bits (60), Expect = 9.1
Identities = 9/42 (21%), Positives = 13/42 (30%), Gaps = 1/42 (2%)
Query: 48 EKLLNKLKSARFRYLNEQLYTSKSEESK-DFFTEDRESFEAY 88
EK+L L+ F Y EE +F +
Sbjct: 192 EKILKLLEQFGFAKDGNSFYLLLDEEELYNFLYTGLPKLQEL 233
>gnl|CDD|234689 PRK00216, ubiE, ubiquinone/menaquinone biosynthesis
methyltransferase; Reviewed.
Length = 239
Score = 26.3 bits (59), Expect = 9.7
Identities = 23/99 (23%), Positives = 31/99 (31%), Gaps = 18/99 (18%)
Query: 105 DIIIKSIQERESKGRLVIAD-----LGCGEAKLAAELTQHKVHSLDLVALNERVTSCDMT 159
D+ I + G +V D L G KL V V D
Sbjct: 64 DLAIALAKAVGKTGEVVGLDFSEGMLAVGREKLRDLGLSGNVE---FVQ-------GDAE 113
Query: 160 RTPLKPYSVDVAV--FCLSLMGTDLAACIKEANRILKLG 196
P S D F L + D+ ++E R+LK G
Sbjct: 114 ALPFPDNSFDAVTIAFGLRNV-PDIDKALREMYRVLKPG 151
>gnl|CDD|225370 COG2813, RsmC, 16S RNA G1207 methylase RsmC [Translation, ribosomal
structure and biogenesis].
Length = 300
Score = 26.5 bits (59), Expect = 9.8
Identities = 19/73 (26%), Positives = 27/73 (36%), Gaps = 7/73 (9%)
Query: 113 ERESKGRLVIADLGCGEAKLAAELTQHK-VHSLDLVALNER-VTSCDMTRTPLKPYSVDV 170
+ G+ + DLGCG L L + L LV +N R V S R L V+
Sbjct: 155 PPDLGGK--VLDLGCGYGVLGLVLAKKSPQAKLTLVDVNARAVESA---RKNLAANGVEN 209
Query: 171 AVFCLSLMGTDLA 183
S + +
Sbjct: 210 TEVWASNLYEPVE 222
>gnl|CDD|181649 PRK09103, PRK09103, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 758
Score = 26.9 bits (60), Expect = 9.9
Identities = 13/49 (26%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 76 DFFTEDRESFEAYHEGFKK--QVTQWPINPVDIIIKSIQERESKGRLVI 122
D F D++ FE + +++ + + + V++ +QER S GR+ I
Sbjct: 363 DAFFADQDEFERLYTKYEQDDSIRKKRVKAVELFSLMMQERASTGRIYI 411
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
0.314 0.129 0.364
Gapped
Lambda K H
0.267 0.0790 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,318,510
Number of extensions: 832709
Number of successful extensions: 648
Number of sequences better than 10.0: 1
Number of HSP's gapped: 643
Number of HSP's successfully gapped: 31
Length of query: 196
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 104
Effective length of database: 6,857,034
Effective search space: 713131536
Effective search space used: 713131536
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 56 (25.2 bits)