RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4551
(321 letters)
>gnl|CDD|215998 pfam00567, TUDOR, Tudor domain.
Length = 118
Score = 85.9 bits (213), Expect = 7e-21
Identities = 38/144 (26%), Positives = 63/144 (43%), Gaps = 31/144 (21%)
Query: 48 VFMSAVANPDRFWVQIMNDRAIELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLH 107
V ++ + +P RF++Q +D +L++L E + +YY K + K G A
Sbjct: 6 VVVTHIESPGRFYIQPKSD-DKKLEKLTEELQEYYLSKPPESLP----PKVGDGCVAAFS 60
Query: 108 LDQKWYRAQVMTVKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQ 167
D KWYRA+++ +V E++F+DYG++ +P
Sbjct: 61 EDGKWYRAKILVSLDDGLV--------------------------EVFFIDYGNTETVPL 94
Query: 168 PSVYQLNPTFLGLRFQAIECSLAN 191
+ L F L QAI+CSLA
Sbjct: 95 SDLRPLPSEFASLPPQAIKCSLAG 118
>gnl|CDD|119391 cd04508, TUDOR, Tudor domains are found in many eukaryotic
organisms and have been implicated in protein-protein
interactions in which methylated protein substrates bind
to these domains. For example, the Tudor domain of
Survival of Motor Neuron (SMN) binds to symmetrically
dimethylated arginines of arginine-glycine (RG) rich
sequences found in the C-terminal tails of Sm proteins.
The SMN protein is linked to spinal muscular atrophy.
Another example is the tandem tudor domains of 53BP1,
which bind to histone H4 specifically dimethylated at
Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA
damage checkpoint signal.
Length = 48
Score = 48.0 bits (115), Expect = 7e-08
Identities = 15/44 (34%), Positives = 26/44 (59%), Gaps = 2/44 (4%)
Query: 123 GQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMP 166
G + A D KWYRA++ ++ +E++FVDYG++ +P
Sbjct: 1 GDLCLAKYSDDGKWYRAKITSILSD--GKVEVFFVDYGNTEVVP 42
>gnl|CDD|197660 smart00333, TUDOR, Tudor domain. Domain of unknown function
present in several RNA-binding proteins. 10 copies in
the Drosophila Tudor protein. Initial proposal that the
survival motor neuron gene product contain a Tudor
domain are corroborated by more recent database search
techniques such as PSI-BLAST (unpublished).
Length = 57
Score = 33.8 bits (78), Expect = 0.010
Identities = 20/81 (24%), Positives = 31/81 (38%), Gaps = 27/81 (33%)
Query: 97 KPGQIVAALLHLDQKWYRAQVMTVKPGQIVAALLHLDQKWYRAQVMTVSDSTPPTLELYF 156
K G VAA D +WYRA+++ V Q+ E++F
Sbjct: 4 KVGDKVAAR-WEDGEWYRARIVKVDGEQLY--------------------------EVFF 36
Query: 157 VDYGDSMDMPQPSVYQLNPTF 177
+DYG+ +P + QL
Sbjct: 37 IDYGNEEVVPPSDLRQLPEEL 57
>gnl|CDD|237310 PRK13222, PRK13222, phosphoglycolate phosphatase; Provisional.
Length = 226
Score = 34.0 bits (79), Expect = 0.073
Identities = 17/62 (27%), Positives = 25/62 (40%), Gaps = 5/62 (8%)
Query: 70 ELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQKWYRAQVMTVKPGQIVAAL 129
L++L E +Y + + + PG + L L Y V+T KP VA L
Sbjct: 72 LLEKLRELFDRHYAE----NVAGGSRLYPG-VKETLAALKAAGYPLAVVTNKPTPFVAPL 126
Query: 130 LH 131
L
Sbjct: 127 LE 128
>gnl|CDD|206160 pfam13990, YjcZ, YjcZ-like protein. This family of proteins is
functionally uncharacterized. The family includes the
YjcZ protein from E. coli. This family of proteins is
found in enteric bacteria. Proteins in this family are
approximately 300 amino acids in length. There are two
conserved sequence motifs: FGD and MPR.
Length = 270
Score = 32.0 bits (73), Expect = 0.34
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 70 ELDQLVESMTDYYNQKANQETHRLTEVKPGQIVAALLHLDQ--KWYRA 115
Q + ++T+ +N++A LT+V V A LHL+Q +RA
Sbjct: 94 GTRQQLLALTEQFNKRAAHLEKALTQV--DLTVRAQLHLEQIFTRWRA 139
>gnl|CDD|145503 pfam02392, Ycf4, Ycf4. This family consists of hypothetical Ycf4
proteins from various chloroplast genomes. It has been
suggested that Ycf4 is involved in the assembly and/or
stability of the photosystem I complex in chloroplasts.
Length = 180
Score = 28.6 bits (65), Expect = 2.8
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 5/41 (12%)
Query: 2 NEGI-SKRSPYRSLKNQNQAPL----EPLSVQESELRAEKL 37
EG+ +R Y LK Q PL +PL++ E E +A +L
Sbjct: 130 KEGLNPRRVIYLRLKGQRDIPLTRVGQPLTLSEIEEQAAEL 170
>gnl|CDD|187576 cd05266, SDR_a4, atypical (a) SDRs, subgroup 4. Atypical SDRs in
this subgroup are poorly defined, one member is
identified as a putative NAD-dependent
epimerase/dehydratase. Atypical SDRs are distinct from
classical SDRs. Members of this subgroup have a
glycine-rich NAD(P)-binding motif that is related to,
but is different from, the archetypical SDRs, GXGXXG.
This subgroup also lacks most of the characteristic
active site residues of the SDRs; however, the upstream
Ser is present at the usual place, and some potential
catalytic residues are present in place of the usual
YXXXK active site motif. Atypical SDRs generally lack
the catalytic residues characteristic of the SDRs, and
their glycine-rich NAD(P)-binding motif is often
different from the forms normally seen in classical or
extended SDRs. Atypical SDRs include biliverdin IX beta
reductase (BVR-B,aka flavin reductase), NMRa (a negative
transcriptional regulator of various fungi),
progesterone 5-beta-reductase like proteins,
phenylcoumaran benzylic ether and
pinoresinol-lariciresinol reductases, phenylpropene
synthases, eugenol synthase, triphenylmethane reductase,
isoflavone reductases, and others. SDRs are a
functionally diverse family of oxidoreductases that have
a single domain with a structurally conserved Rossmann
fold, an NAD(P)(H)-binding region, and a structurally
diverse C-terminal region. Sequence identity between
different SDR enzymes is typically in the 15-30% range;
they catalyze a wide range of activities including the
metabolism of steroids, cofactors, carbohydrates,
lipids, aromatic compounds, and amino acids, and act in
redox sensing. Classical SDRs have an TGXXX[AG]XG
cofactor binding motif and a YXXXK active site motif,
with the Tyr residue of the active site motif serving as
a critical catalytic residue (Tyr-151, human
15-hydroxyprostaglandin dehydrogenase numbering). In
addition to the Tyr and Lys, there is often an upstream
Ser and/or an Asn, contributing to the active site;
while substrate binding is in the C-terminal region,
which determines specificity. The standard reaction
mechanism is a 4-pro-S hydride transfer and proton relay
involving the conserved Tyr and Lys, a water molecule
stabilized by Asn, and nicotinamide. In addition to the
Rossmann fold core region typical of all SDRs, extended
SDRs have a less conserved C-terminal extension of
approximately 100 amino acids, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Length = 251
Score = 28.4 bits (64), Expect = 4.6
Identities = 11/44 (25%), Positives = 18/44 (40%)
Query: 125 IVAALLHLDQKWYRAQVMTVSDSTPPTLELYFVDYGDSMDMPQP 168
+V AL Q+ V V D P T ++ + + +P P
Sbjct: 185 LVGALAFALQRPAPGPVYNVVDDLPVTRGEFYQAAAELLGLPPP 228
>gnl|CDD|218673 pfam05642, Sporozoite_P67, Sporozoite P67 surface antigen. This
family consists of several Theileria P67 surface
antigens. A stage specific surface antigen of Theileria
parva, p67, is the basis for the development of an
anti-sporozoite vaccine for the control of East Coast
fever (ECF) in cattle. The antigen has been shown to
contain five distinct linear peptide sequences
recognised by sporozoite-neutralising murine monoclonal
antibodies.
Length = 727
Score = 28.9 bits (64), Expect = 5.0
Identities = 16/49 (32%), Positives = 27/49 (55%), Gaps = 2/49 (4%)
Query: 246 DTSGEQDVNISQELISRGFAVSSKSGSELPDGRPNGNTSAGSNSSDSDT 294
T E+D + S+E ++ + SSK G +P +TS+GS +S +D
Sbjct: 113 KTDSEEDDDDSEEEDNK--STSSKDGKGSKKTQPGVSTSSGSTTSGTDL 159
>gnl|CDD|151320 pfam10871, DUF2748, Protein of unknown function (DUF2748). This is
a bacterial family of proteins with unknown function.
Length = 452
Score = 28.4 bits (63), Expect = 5.3
Identities = 21/67 (31%), Positives = 32/67 (47%), Gaps = 8/67 (11%)
Query: 174 NPTFLGLRFQA-IECSLANVRPVGDVW------SEEAISCFEDLTHVAQWKVLLARVESY 226
N ++ L A + +AN+ P DV+ +EEAI+C E L V Q + + +
Sbjct: 326 NDEYMALMIDAMFKDMIANLEPAADVYKNDDPDAEEAIACIEALARVPQQTIKWGHITT- 384
Query: 227 KETSTDL 233
KE DL
Sbjct: 385 KEIMHDL 391
>gnl|CDD|234978 PRK01747, mnmC, bifunctional tRNA
(mnm(5)s(2)U34)-methyltransferase/FAD-dependent
cmnm(5)s(2)U34 oxidoreductase; Reviewed.
Length = 662
Score = 27.9 bits (63), Expect = 9.7
Identities = 13/41 (31%), Positives = 18/41 (43%), Gaps = 5/41 (12%)
Query: 96 VKPGQIVAALLHLDQKWYRAQVMTVKPGQIVAALLHLDQKW 136
+ P ++ ALL L Q +T+ G VA L D W
Sbjct: 405 LCPAELCRALLALAG-----QQLTIHFGHEVARLEREDDGW 440
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
0.312 0.127 0.369
Gapped
Lambda K H
0.267 0.0748 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,677,402
Number of extensions: 1436266
Number of successful extensions: 852
Number of sequences better than 10.0: 1
Number of HSP's gapped: 843
Number of HSP's successfully gapped: 14
Length of query: 321
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 224
Effective length of database: 6,635,264
Effective search space: 1486299136
Effective search space used: 1486299136
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 (21.9 bits)
S2: 59 (26.5 bits)