RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9655
(96 letters)
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 35.4 bits (82), Expect = 1e-04
Identities = 9/22 (40%), Positives = 16/22 (72%)
Query: 64 SCTYCSRAFKKRSDLTRHIRSH 85
C C ++F ++S+L RH+R+H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 34.7 bits (80), Expect = 3e-04
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 63 LSCTYCSRAFKKRSDLTRHIRSH 85
C C + FK +S L H+R+H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|206065 pfam13894, zf-C2H2_4, C2H2-type zinc finger. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 24
Score = 32.6 bits (74), Expect = 0.002
Identities = 8/21 (38%), Positives = 12/21 (57%)
Query: 65 CTYCSRAFKKRSDLTRHIRSH 85
C C ++F + L RH+R H
Sbjct: 3 CPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|222150 pfam13465, zf-H2C2_2, Zinc-finger double domain.
Length = 26
Score = 29.3 bits (66), Expect = 0.039
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 77 DLTRHIRSHTKEKPFK 92
+L RH+R+HT EKP+K
Sbjct: 1 NLRRHMRTHTGEKPYK 16
>gnl|CDD|204841 pfam12171, zf-C2H2_jaz, Zinc-finger double-stranded RNA-binding.
This domain family is found in archaea and eukaryotes,
and is approximately 30 amino acids in length. The
mammalian members of this group occur multiple times
along the protein, joined by flexible linkers, and are
referred to as JAZ - dsRNA-binding ZF protein -
zinc-fingers. The JAZ proteins are expressed in all
tissues tested and localise in the nucleus,
particularly the nucleolus. JAZ preferentially binds to
double-stranded (ds) RNA or RNA/DNA hybrids rather than
DNA. In addition to binding double-stranded RNA, these
zinc-fingers are required for nucleolar localisation.
Length = 27
Score = 29.1 bits (66), Expect = 0.050
Identities = 7/20 (35%), Positives = 11/20 (55%)
Query: 65 CTYCSRAFKKRSDLTRHIRS 84
C C + FK + L H++S
Sbjct: 4 CVACDKYFKSENALENHLKS 23
>gnl|CDD|240557 cd13114, POLO_box_Plk4_1, First (cryptic) polo-box domain (PBD) of
polo-like kinase 4 (Plk4/Sak). The polo-like Ser/Thr
kinases (Plk1, Plk2/Snk, Plk3/Prk/Fnk, Plk4/Sak, and the
inactive kinase Plk5) play various roles in cytokinesis
and mitosis. At their C-terminus, they contain a
tandemly repeated polo-box domain (in the case of Plk4,
a tandem repeat of cryptic PBDs is found in the middle
of the protein followed by a C-terminal single repeat),
which appears to be involved in autoinhibition and in
mediating the subcellular localization. The latter may
be controlled via interactions between the polo-box
domain and phospho-peptide motifs. The phosphopeptide
binding site is formed at the interface between the two
tandemly repeated PBDs. The PBDs of Plk4/Sak appear
unique in participating in homodimer interactions,
though it is not clear whether and how they interact
with phosphopeptides.
Length = 112
Score = 27.6 bits (62), Expect = 0.53
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 5/53 (9%)
Query: 36 NGQNQIVSEPPTDRTVSYNRPVPPNPSLSCTYC-----SRAFKKRSDLTRHIR 83
+GQ ++ +P + V P P P TY + +KK R ++
Sbjct: 56 DGQKIVIYQPNGGKGVPLEPPPLPPPGADATYSYESLPEKYWKKYQYAARFVQ 108
>gnl|CDD|232887 TIGR00232, tktlase_bact, transketolase, bacterial and yeast. This
model is designed to capture orthologs of bacterial
transketolases. The group includes two from the yeast
Saccharomyces cerevisiae but excludes dihydroxyactetone
synthases (formaldehyde transketolases) from various
yeasts and the even more distant mammalian
transketolases. Among the family of thiamine
diphosphate-dependent enzymes that includes
transketolases, dihydroxyacetone synthases, pyruvate
dehydrogenase E1-beta subunits, and
deoxyxylulose-5-phosphate synthases, mammalian and
bacterial transketolases seem not to be orthologous
[Energy metabolism, Pentose phosphate pathway].
Length = 653
Score = 28.1 bits (63), Expect = 0.63
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 20 SGVQRSMESSEKENRENGQNQIVSEPPTDR 49
S V ++E+++K EN + ++VS P D
Sbjct: 550 SEVSLAVEAAKKLAAENIKVRVVSMPSFDL 579
>gnl|CDD|233712 TIGR02079, THD1, threonine dehydratase. This model represents
threonine dehydratase, the first step in the pathway
converting threonine into isoleucine. At least two
other clades of biosynthetic threonine dehydratases
have been charcterized (TIGR01124 and TIGR01127). Those
sequences described by this model are exclusively found
in species containg the rest of the isoleucine pathway
and which are generally lacking in members of the those
other two clades of threonine dehydratases. Members of
this clade are also often gene clustered with other
elements of the isoleucine pathway [Amino acid
biosynthesis, Pyruvate family].
Length = 409
Score = 27.8 bits (62), Expect = 0.75
Identities = 14/46 (30%), Positives = 22/46 (47%), Gaps = 7/46 (15%)
Query: 49 RTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKPFKVR 94
+ V + P+ N LS Y + + KR DL +RS +K+R
Sbjct: 11 KEVVPHTPLQLNERLSEKYGANIYLKREDLQP-VRS------YKIR 49
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 24.5 bits (54), Expect = 2.3
Identities = 7/21 (33%), Positives = 9/21 (42%)
Query: 65 CTYCSRAFKKRSDLTRHIRSH 85
C C + F L H +SH
Sbjct: 4 CGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|215642 PLN03238, PLN03238, probable histone acetyltransferase MYST;
Provisional.
Length = 290
Score = 26.0 bits (57), Expect = 3.8
Identities = 10/42 (23%), Positives = 16/42 (38%), Gaps = 6/42 (14%)
Query: 53 YNRPVPPNPSLS-----CTYCSRAFKKRSDLTRHIRSHTKEK 89
Y P P + C YC + +K+ L RH + +
Sbjct: 34 YYSPYPEPYASCTKLYICEYCLKYMRKKKSLLRH-LAKCDIR 74
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 24.3 bits (53), Expect = 4.4
Identities = 7/27 (25%), Positives = 13/27 (48%)
Query: 65 CTYCSRAFKKRSDLTRHIRSHTKEKPF 91
C C F+K+ ++ H+ S K+
Sbjct: 4 CLRCGGIFRKKKEVIEHLLSVHKQNKL 30
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase
activity and may play a role in the transcription of
the virus genome, the unwinding or reannealing of
double-stranded RNA during RNA synthesis. The RTPase
activity constitutes the first step in the capping of
RNA, resulting in a 5'-diphosphorylated RNA
plus-strand. lambda1 is an Orthoreovirus core protein,
VP3 is the homologous core protein in Aquareoviruses.
Length = 1166
Score = 25.9 bits (57), Expect = 4.7
Identities = 14/66 (21%), Positives = 19/66 (28%), Gaps = 7/66 (10%)
Query: 21 GVQRSMESSEKENRENGQNQIVSEPPTDRTVSYNRPVPP-NPS-LSCTYCSRAFKKRSDL 78
G++ S N P ++ P NPS C C F L
Sbjct: 35 GIKTQPTSDSIAAVANATKPAAVISP-----PQSKKATPINPSSYVCNVCMAEFSSMDQL 89
Query: 79 TRHIRS 84
H R+
Sbjct: 90 AEHQRT 95
>gnl|CDD|233646 TIGR01936, nqrA, NADH:ubiquinone oxidoreductase,
Na(+)-translocating, A subunit. This model represents
the NqrA subunit of the six-protein, Na(+)-pumping
NADH-quinone reductase of a number of marine and
pathogenic Gram-negative bacteria. This oxidoreductase
complex functions primarily as a sodium ion pump
[Transport and binding proteins, Cations and iron
carrying compounds].
Length = 447
Score = 25.5 bits (56), Expect = 5.9
Identities = 13/53 (24%), Positives = 22/53 (41%)
Query: 38 QNQIVSEPPTDRTVSYNRPVPPNPSLSCTYCSRAFKKRSDLTRHIRSHTKEKP 90
Q ++ E + RP S++ TY S FKKR + ++ E+
Sbjct: 322 QISVLPEGDVRELFGWLRPGLNKYSVTRTYLSGLFKKRKEYNMDTNTNGGERA 374
>gnl|CDD|206084 pfam13913, zf-C2HC_2, zinc-finger of a C2HC-type. This family
contains a number of divergent C2H2 type zinc fingers.
Length = 25
Score = 22.9 bits (50), Expect = 9.8
Identities = 6/21 (28%), Positives = 8/21 (38%), Gaps = 1/21 (4%)
Query: 64 SCTYCSRAFKKRSDLTRHIRS 84
C C R F L +H +
Sbjct: 4 PCPICGRKFAPDR-LAKHEKV 23
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 0.124 0.347
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,376,654
Number of extensions: 321102
Number of successful extensions: 264
Number of sequences better than 10.0: 1
Number of HSP's gapped: 263
Number of HSP's successfully gapped: 23
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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: 53 (24.3 bits)