RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8167
(167 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 = 34.2 bits (79), Expect = 0.001
Identities = 10/20 (50%), Positives = 15/20 (75%)
Query: 56 CTLCDKTFTRKDSLKKHIRI 75
C C K+F+RK +LK+H+R
Sbjct: 2 CPDCGKSFSRKSNLKRHLRT 21
Score = 33.1 bits (76), Expect = 0.004
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 105 RCELCDKSFTRKDSLKKHNRI 125
+C C KSF+RK +LK+H R
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRT 21
>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 = 33.8 bits (77), Expect = 0.002
Identities = 12/23 (52%), Positives = 17/23 (73%)
Query: 55 PCTLCDKTFTRKDSLKKHIRIFH 77
C LC K+F+ KD+LK+H+R H
Sbjct: 2 KCPLCGKSFSSKDALKRHLRKHH 24
Score = 30.3 bits (68), Expect = 0.047
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 105 RCELCDKSFTRKDSLKKH 122
+C LC KSF+ KD+LK+H
Sbjct: 2 KCPLCGKSFSSKDALKRH 19
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 32.1 bits (73), Expect = 0.011
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 56 CTLCDKTFTRKDSLKKHIRI 75
C C K F K +L++H+R
Sbjct: 3 CPECGKVFKSKSALREHMRT 22
Score = 30.5 bits (69), Expect = 0.032
Identities = 9/21 (42%), Positives = 12/21 (57%)
Query: 105 RCELCDKSFTRKDSLKKHNRI 125
RC C K F K +L++H R
Sbjct: 2 RCPECGKVFKSKSALREHMRT 22
>gnl|CDD|177301 PHA00733, PHA00733, hypothetical protein.
Length = 128
Score = 32.9 bits (75), Expect = 0.025
Identities = 22/73 (30%), Positives = 27/73 (36%), Gaps = 29/73 (39%)
Query: 56 CTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTR 115
C LC F+ SLK+HIR +H+ V C +C K F
Sbjct: 76 CPLCLMPFSSSVSLKQHIRY------TEHSKV------------------CPVCGKEFRN 111
Query: 116 KDSL-----KKHN 123
DS KKHN
Sbjct: 112 TDSTLDHVCKKHN 124
>gnl|CDD|205121 pfam12874, zf-met, Zinc-finger of C2H2 type. This is a
zinc-finger domain with the CxxCx(12)Hx(6)H motif,
found in multiple copies in a wide range of proteins
from plants to metazoans. Some member proteins,
particularly those from plants, are annotated as being
RNA-binding.
Length = 25
Score = 29.8 bits (68), Expect = 0.064
Identities = 10/19 (52%), Positives = 13/19 (68%)
Query: 56 CTLCDKTFTRKDSLKKHIR 74
C LC+ TFT + LK H+R
Sbjct: 3 CELCNVTFTSESQLKSHLR 21
Score = 29.4 bits (67), Expect = 0.085
Identities = 10/20 (50%), Positives = 13/20 (65%)
Query: 105 RCELCDKSFTRKDSLKKHNR 124
CELC+ +FT + LK H R
Sbjct: 2 YCELCNVTFTSESQLKSHLR 21
>gnl|CDD|227516 COG5189, SFP1, Putative transcriptional repressor regulating G2/M
transition [Transcription / Cell division and chromosome
partitioning].
Length = 423
Score = 32.0 bits (72), Expect = 0.12
Identities = 22/69 (31%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 59 CDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDS 118
C+K + ++ LK H+ H QNQ H N + +A RCE+CDK + +
Sbjct: 357 CNKKYKNQNGLKYHMLHGH-QNQKLHENPSPEKM--NIFSAKDKPYRCEVCDKRYKNLNG 413
Query: 119 LKKHNRIFH 127
LK H + H
Sbjct: 414 LKYHRKHSH 422
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 30.9 bits (71), Expect = 0.32
Identities = 14/31 (45%), Positives = 20/31 (64%), Gaps = 6/31 (19%)
Query: 135 MDEQMARGSADFLEVVLNEDGEGEPVSITVY 165
+DE +A G AD ++V L+EDG SI+V
Sbjct: 49 IDEALA-GYADRIDVTLHEDG-----SISVE 73
>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 = 27.6 bits (62), Expect = 0.36
Identities = 8/24 (33%), Positives = 14/24 (58%), Gaps = 1/24 (4%)
Query: 52 DRIPCTLCDKTFTRKDSLKKHIRI 75
+ +PC +C + F D L KH ++
Sbjct: 1 ELVPCPICGRKF-APDRLAKHEKV 23
>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 = 27.2 bits (61), Expect = 0.59
Identities = 7/19 (36%), Positives = 13/19 (68%)
Query: 56 CTLCDKTFTRKDSLKKHIR 74
C CDK F +++L+ H++
Sbjct: 4 CVACDKYFKSENALENHLK 22
Score = 24.8 bits (55), Expect = 3.1
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 106 CELCDKSFTRKDSLKKH 122
C CDK F +++L+ H
Sbjct: 4 CVACDKYFKSENALENH 20
>gnl|CDD|221755 pfam12756, zf-C2H2_2, C2H2 type zinc-finger (2 copies). This
family contains two copies of a C2H2-like zinc finger
domain.
Length = 100
Score = 28.4 bits (64), Expect = 0.88
Identities = 13/72 (18%), Positives = 28/72 (38%), Gaps = 9/72 (12%)
Query: 56 CTLCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVA-----LGARANAAFIDRIRCELCD 110
C C+ T + +H+ H P+ ++++ L + + C C
Sbjct: 2 CLFCNHTSDTVEENLEHMFKSHGFFIPEREYLVDLEGLLNYLREKIHEGN----ECLYCG 57
Query: 111 KSFTRKDSLKKH 122
K F ++L++H
Sbjct: 58 KQFKSLEALRQH 69
>gnl|CDD|235542 PRK05644, gyrB, DNA gyrase subunit B; Validated.
Length = 638
Score = 29.3 bits (67), Expect = 0.89
Identities = 15/29 (51%), Positives = 18/29 (62%), Gaps = 6/29 (20%)
Query: 136 DEQMARGSADFLEVVLNEDGEGEPVSITV 164
DE +A G D +EV +NEDG SITV
Sbjct: 51 DEALA-GYCDHIEVTINEDG-----SITV 73
>gnl|CDD|115579 pfam06933, SSP160, Special lobe-specific silk protein SSP160. This
family consists of several special lobe-specific silk
protein SSP160 sequences which appear to be specific to
Chironomus (Midge) species.
Length = 758
Score = 29.4 bits (65), Expect = 0.96
Identities = 13/35 (37%), Positives = 22/35 (62%)
Query: 17 NSTSVENSTSVENSTSVENTSSVDNRTSVGPVVPI 51
NST+ NST+ NST+ N++S N +++ + I
Sbjct: 294 NSTTNSNSTTTTNSTTSTNSTSSSNSSTIAGCIDI 328
Score = 29.4 bits (65), Expect = 0.99
Identities = 16/41 (39%), Positives = 25/41 (60%)
Query: 4 LQNVQNHFVSGKKNSTSVENSTSVENSTSVENTSSVDNRTS 44
+Q +Q+ S NS+S NSTS NST+ N+++ N T+
Sbjct: 95 IQAIQSGSGSASGNSSSSANSTSNSNSTTSNNSTTSSNSTT 135
Score = 28.6 bits (63), Expect = 1.7
Identities = 13/28 (46%), Positives = 18/28 (64%)
Query: 17 NSTSVENSTSVENSTSVENTSSVDNRTS 44
NS S NST+ NST+ N+++ N TS
Sbjct: 288 NSNSTSNSTTNSNSTTTTNSTTSTNSTS 315
Score = 28.6 bits (63), Expect = 2.1
Identities = 12/34 (35%), Positives = 20/34 (58%)
Query: 11 FVSGKKNSTSVENSTSVENSTSVENTSSVDNRTS 44
F +G ++ S NS S NST+ N+++ N T+
Sbjct: 276 FANGSASANSTSNSNSTSNSTTNSNSTTTTNSTT 309
>gnl|CDD|235501 PRK05559, PRK05559, DNA topoisomerase IV subunit B; Reviewed.
Length = 631
Score = 28.9 bits (66), Expect = 1.2
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 6/30 (20%)
Query: 135 MDEQMARGSADFLEVVLNEDGEGEPVSITV 164
+DE +A G +EV L+ DG S++V
Sbjct: 50 VDEALA-GHGKRIEVTLHADG-----SVSV 73
>gnl|CDD|222041 pfam13312, DUF4081, Domain of unknown function (DUF4081). This
domain is often found N-terminal to the GNAT
acetyltransferase domain, pfam00583 and FR47, pfam08445.
Length = 107
Score = 28.0 bits (63), Expect = 1.2
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 85 TNVIEVALGARANAAFIDRIR 105
N++ VA A AF DR R
Sbjct: 21 ANLVPVAADPAALRAFADRAR 41
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 28.4 bits (63), Expect = 2.0
Identities = 18/70 (25%), Positives = 24/70 (34%), Gaps = 6/70 (8%)
Query: 58 LCDKTFTRKDSLKKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKD 117
LC + K IR+F + H N G F C C F D
Sbjct: 181 LCSECIGNKKDFWNEIRLFRSSTLRDHKN------GGLEEEGFKGHPLCIFCKIYFYDDD 234
Query: 118 SLKKHNRIFH 127
L++H R+ H
Sbjct: 235 ELRRHCRLRH 244
>gnl|CDD|227381 COG5048, COG5048, FOG: Zn-finger [General function prediction
only].
Length = 467
Score = 28.1 bits (62), Expect = 2.3
Identities = 24/113 (21%), Positives = 40/113 (35%), Gaps = 18/113 (15%)
Query: 12 VSGKKNSTSVENSTSVENSTSVENT--SSVDNRTSVGPVVPIDRIPCTLCDKTFTRKDSL 69
S + +S S S +S ++ SS + S I C+ +F+R L
Sbjct: 246 SSLSSSDSSSSASESPRSSLPTASSQSSSPNESDSSSEKGFSLPIKSKQCNISFSRSSPL 305
Query: 70 KKHIRIFHTQNQPQHTNVIEVALGARANAAFIDRIRCELCDKSFTRKDSLKKH 122
+H+R + + LC K F+R D+LK+H
Sbjct: 306 TRHLRSVNHSGESLKPFSCPY----------------SLCGKLFSRNDALKRH 342
>gnl|CDD|182965 PRK11103, PRK11103, PTS system mannose-specific transporter subunit
IID; Provisional.
Length = 282
Score = 27.8 bits (62), Expect = 2.8
Identities = 16/45 (35%), Positives = 21/45 (46%), Gaps = 12/45 (26%)
Query: 65 RKDSLKKHIRIFHTQNQPQHTNVIEVALGA-------RANAAFID 102
RK ++K+H+ F+T H V LG RAN A ID
Sbjct: 61 RKQAIKRHLEFFNT-----HPYVAAPILGVTLAMEEQRANGAEID 100
>gnl|CDD|203029 pfam04495, GRASP55_65, GRASP55/65 PDZ-like domain. GRASP55 (Golgi
re-assembly stacking protein of 55 kDa) and GRASP65 (a
65 kDa) protein are highly homologous. GRASP55 is a
component of the Golgi stacking machinery. GRASP65, an
N-ethylmaleimide- sensitive membrane protein required
for the stacking of Golgi cisternae in a cell-free
system. This region appears to be related to the PDZ
domain.
Length = 136
Score = 27.2 bits (61), Expect = 3.1
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 2/31 (6%)
Query: 135 MDEQMARGSADFLEVVLNEDGEGEPVSITVY 165
D + RG D E+V E EG P+ + VY
Sbjct: 69 TDSGLLRGEDDLFELV--ESHEGRPLKLYVY 97
>gnl|CDD|177288 PHA00616, PHA00616, hypothetical protein.
Length = 44
Score = 25.5 bits (56), Expect = 3.2
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 56 CTLCDKTFTRKDSLKKHIRIFHTQN 80
C C F +K + +H+ H QN
Sbjct: 4 CLRCGGIFRKKKEVIEHLLSVHKQN 28
>gnl|CDD|237860 PRK14939, gyrB, DNA gyrase subunit B; Provisional.
Length = 756
Score = 27.8 bits (63), Expect = 3.7
Identities = 10/29 (34%), Positives = 16/29 (55%), Gaps = 6/29 (20%)
Query: 136 DEQMARGSADFLEVVLNEDGEGEPVSITV 164
DE +A G D + V ++ DG S++V
Sbjct: 51 DEALA-GHCDDITVTIHADG-----SVSV 73
>gnl|CDD|214659 smart00433, TOP2c, TopoisomeraseII. Eukaryotic DNA topoisomerase
II, GyrB, ParE.
Length = 594
Score = 27.1 bits (61), Expect = 4.5
Identities = 9/31 (29%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 135 MDEQMARGSADFLEVVLNEDGEGEPVSITVY 165
DE + G D ++V +++D SI+V
Sbjct: 14 ADEAL-AGYMDTIKVTIDKDN-----SISVE 38
>gnl|CDD|202452 pfam02892, zf-BED, BED zinc finger.
Length = 43
Score = 24.9 bits (55), Expect = 4.7
Identities = 7/28 (25%), Positives = 11/28 (39%), Gaps = 3/28 (10%)
Query: 103 RIRCELCDKSFTRKDS---LKKHNRIFH 127
+ RC+ C K + LK+H
Sbjct: 15 KARCKYCGKILSGGGGTSNLKRHLVRKC 42
>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The second LIM
domain of LMO1 and LMO3 (LIM domain only protein 1 and
3): LMO1 and LMO3 are highly homologous and belong to
the LMO protein family. LMO1 and LMO3 are nuclear
protein that plays important roles in transcriptional
regulation and development. As LIM domains lack
intrinsic DNA-binding activity, nuclear LMOs are
involved in transcriptional regulation by forming
complexes with other transcription factors or cofactors.
For example, LMO1 interacts with the the bHLH domain of
bHLH transcription factor, TAL1 (T-cell acute
leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the
expression of TAL1/SCL target genes. LMO3 facilitates
p53 binding to its response elements, which suggests
that LMO3 acts as a co-repressor of p53, suppressing
p53-dependent transcriptional regulation. In addition,
LMO3 interacts with neuronal transcription factor, HEN2,
and acts as an oncogene in neuroblastoma. Another
binding partner of LMO3 is calcium- and integrin-binding
protein CIB, which binds via the second LIM domain
(LIM2) of LMO3. One role of the CIB/LMO3 complex is to
inhibit cell proliferation. Although LMO1 and LMO3 are
highly homologous proteins, they play different roles in
the regulation of the pituitary glycoprotein hormone
alpha-subunit (alpha GSU) gene. Alpha GSU promoter
activity was markedly repressed by LMO1 but activated by
LMO3. All LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 25.0 bits (54), Expect = 5.9
Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 89 EVALGARANAAFIDRIRCELCDKSFTRKDS-LKKHNRIF 126
E+ + A+ N +D C+LC++ F D K+N I
Sbjct: 12 EMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMIL 50
>gnl|CDD|150637 pfam09986, DUF2225, Uncharacterized protein conserved in bacteria
(DUF2225). This domain, found in various hypothetical
bacterial proteins, has no known function.
Length = 214
Score = 26.5 bits (59), Expect = 5.9
Identities = 6/23 (26%), Positives = 11/23 (47%)
Query: 53 RIPCTLCDKTFTRKDSLKKHIRI 75
+I C +C+ F K +R+
Sbjct: 5 KIVCPVCNNEFKTKKVKSSGLRL 27
>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 = 26.7 bits (59), Expect = 8.2
Identities = 17/71 (23%), Positives = 30/71 (42%), Gaps = 11/71 (15%)
Query: 18 STSVENSTSVENSTSVENTSSVDNRT---------SVGPVVPIDRIP--CTLCDKTFTRK 66
S+SV+N ++ + ++ ++V N T PI+ C +C F+
Sbjct: 27 SSSVDNDGGIKTQPTSDSIAAVANATKPAAVISPPQSKKATPINPSSYVCNVCMAEFSSM 86
Query: 67 DSLKKHIRIFH 77
D L +H R H
Sbjct: 87 DQLAEHQRTTH 97
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
0.315 0.130 0.369
Gapped
Lambda K H
0.267 0.0672 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,906,845
Number of extensions: 674618
Number of successful extensions: 671
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 49
Length of query: 167
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 77
Effective length of database: 6,945,742
Effective search space: 534822134
Effective search space used: 534822134
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.1 bits)