RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4683
(196 letters)
>gnl|CDD|206083 pfam13912, zf-C2H2_6, C2H2-type zinc finger.
Length = 27
Score = 29.5 bits (67), Expect = 0.095
Identities = 12/23 (52%), Positives = 14/23 (60%)
Query: 141 HTCSVCKKIFVNKKNLTTHKKIH 163
HTC VC K F + + L HKK H
Sbjct: 2 HTCGVCGKTFSSLQALGGHKKSH 24
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 31.5 bits (71), Expect = 0.23
Identities = 31/163 (19%), Positives = 56/163 (34%), Gaps = 33/163 (20%)
Query: 3 EKIPSTDAHDIEIKKEGLWSFLEDENEKRNFSSEEDEESDKLDDEDNVTSDTKFPCRLCS 62
E + T + +I W +E + E+ + DE K P C
Sbjct: 108 EAVVFTASSPADITDRRQWK-GREEKVGIFYEGED------VRDEMEDLLSFKCPKSKCH 160
Query: 63 QEFDTKEQRKKHERKDHATQGLFSCDLCS------------YTSTQKYYLVKHKSRHIKD 110
+ + ++ KKH + H G C C + S+ L HK+ +++
Sbjct: 161 RRCGSLKELKKHYKAQH---GFVLCSECIGNKKDFWNEIRLFRSST---LRDHKNGGLEE 214
Query: 111 Y----NVFCKICQLGFLSKNELNVHNIKQHCAQPHTCSVCKKI 149
+ C C++ F +EL H +H C +C +
Sbjct: 215 EGFKGHPLCIFCKIYFYDDDELRRHCRLRH----EACHICDMV 253
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 28.2 bits (63), Expect = 0.25
Identities = 8/23 (34%), Positives = 12/23 (52%)
Query: 141 HTCSVCKKIFVNKKNLTTHKKIH 163
+ C C K+F +K L H + H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
Score = 25.5 bits (56), Expect = 2.8
Identities = 6/23 (26%), Positives = 8/23 (34%)
Query: 85 FSCDLCSYTSTQKYYLVKHKSRH 107
+ C C K L +H H
Sbjct: 1 YRCPECGKVFKSKSALREHMRTH 23
>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 = 28.1 bits (63), Expect = 0.27
Identities = 9/22 (40%), Positives = 10/22 (45%)
Query: 142 TCSVCKKIFVNKKNLTTHKKIH 163
C C K F K NL H + H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>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 = 30.1 bits (68), Expect = 0.83
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 3/32 (9%)
Query: 58 CRLCSQEFDTKEQRKKHERKDH---ATQGLFS 86
C +C EF + +Q +H+R H A+ L S
Sbjct: 76 CNVCMAEFSSMDQLAEHQRTTHSIGASSLLTS 107
Score = 28.6 bits (64), Expect = 2.9
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 103 HKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQH 136
K+ I + C +C F S ++L H H
Sbjct: 64 KKATPINPSSYVCNVCMAEFSSMDQLAEHQRTTH 97
>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 = 26.4 bits (58), Expect = 1.2
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 56 FPCRLCSQEFDTKEQRKKHERKDH 79
F C LC + F +K+ K+H RK H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKHH 24
Score = 23.8 bits (51), Expect = 9.3
Identities = 8/23 (34%), Positives = 11/23 (47%)
Query: 141 HTCSVCKKIFVNKKNLTTHKKIH 163
C +C K F +K L H + H
Sbjct: 1 FKCPLCGKSFSSKDALKRHLRKH 23
>gnl|CDD|222011 pfam13257, DUF4048, Domain of unknown function (DUF4048). This
presumed domain is functionally uncharacterized. This
domain family is found in eukaryotes, and is typically
between 228 and 257 amino acids in length.
Length = 242
Score = 29.4 bits (66), Expect = 1.2
Identities = 8/10 (80%), Positives = 10/10 (100%)
Query: 17 KEGLWSFLED 26
+EGLW+FLED
Sbjct: 94 REGLWTFLED 103
>gnl|CDD|218228 pfam04720, DUF506, Protein of unknown function (DUF506). Family
of uncharacterized plant proteins.
Length = 218
Score = 28.2 bits (63), Expect = 2.2
Identities = 12/40 (30%), Positives = 16/40 (40%)
Query: 22 SFLEDENEKRNFSSEEDEESDKLDDEDNVTSDTKFPCRLC 61
FLED NE S D D+ED S ++ +
Sbjct: 7 GFLEDGNETVEDESFSGSGDDSSDEEDEEDSSSEDNGDVS 46
>gnl|CDD|165133 PHA02768, PHA02768, hypothetical protein; Provisional.
Length = 55
Score = 26.2 bits (57), Expect = 2.5
Identities = 7/23 (30%), Positives = 16/23 (69%)
Query: 141 HTCSVCKKIFVNKKNLTTHKKIH 163
+ C +C +I++ +K++ TH + H
Sbjct: 6 YECPICGEIYIKRKSMITHLRKH 28
>gnl|CDD|240287 PTZ00142, PTZ00142, 6-phosphogluconate dehydrogenase; Provisional.
Length = 470
Score = 28.2 bits (63), Expect = 3.2
Identities = 15/79 (18%), Positives = 28/79 (35%), Gaps = 14/79 (17%)
Query: 31 RNFSSEEDEESDKLDDEDNVTSDTKFPCRLCSQEFDTKEQRKKHERKDHATQGLFSCDLC 90
RN S+ ++E + ++ + E K D L+ +
Sbjct: 287 RNISALKEE---RTKASSHLAGPNPA---------NKTETEDKKYFIDDLKNALYCSKII 334
Query: 91 SYTSTQKYYLVKHKSRHIK 109
SY TQ ++L+K S+
Sbjct: 335 SY--TQGFFLIKEASKEFG 351
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 28.0 bits (63), Expect = 3.6
Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 21 WSFLEDENEKRNFSSEEDEESDK-LDDEDNVTSDTKFPCRLCSQEFDTKEQRKKHERK 77
+ LE++++ S EEDEES K DDED+ D + + + +R++ E K
Sbjct: 120 YRDLEEDDDDDEESDEEDEESSKSEDDEDDDDDDDDDDIATRERSLERRRRRREWEEK 177
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 27.8 bits (62), Expect = 4.0
Identities = 11/50 (22%), Positives = 22/50 (44%), Gaps = 1/50 (2%)
Query: 2 QEKIPSTDAHDIEIKKEGLWSFLEDENEKRNFSSEEDEESDKLDDEDNVT 51
+K + + +G+ S E + + E+ ESD D +D+V+
Sbjct: 229 PKKQAKSSKRRTIAQIDGIDSDDEGDGSDDD-DDEDAIESDLDDSDDDVS 277
>gnl|CDD|215971 pfam00524, PPV_E1_N, E1 Protein, N terminal domain.
Length = 131
Score = 26.9 bits (60), Expect = 4.6
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 8/39 (20%)
Query: 18 EGLWSFLEDENEKRNFSSEEDEE--------SDKLDDED 48
G W F+E N S +EDE+ SD +DD D
Sbjct: 14 CGGWFFVEAICSDDNISEDEDEDLFDTGSDLSDFIDDAD 52
>gnl|CDD|219900 pfam08553, VID27, VID27 cytoplasmic protein. This is a family of
fungal and plant proteins and contains many hypothetical
proteins. VID27 is a cytoplasmic protein that plays a
potential role in vacuolar protein degradation.
Length = 794
Score = 27.4 bits (61), Expect = 5.8
Identities = 12/26 (46%), Positives = 18/26 (69%)
Query: 24 LEDENEKRNFSSEEDEESDKLDDEDN 49
+ED N +R+ EEDEE ++ +DED
Sbjct: 381 IEDANTERDDEEEEDEEEEEEEDEDE 406
>gnl|CDD|201407 pfam00707, IF3_C, Translation initiation factor IF-3, C-terminal
domain.
Length = 87
Score = 25.8 bits (58), Expect = 5.8
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 6 PSTDAHDIEIKKEGLWSFLEDEN 28
P D HD+E+K + FLE +
Sbjct: 11 PKIDEHDLEVKLKHARKFLEKGD 33
>gnl|CDD|217840 pfam04006, Mpp10, Mpp10 protein. This family includes proteins
related to Mpp10 (M phase phosphoprotein 10). The U3
small nucleolar ribonucleoprotein (snoRNP) is required
for three cleavage events that generate the mature 18S
rRNA from the pre-rRNA. In Saccharomyces cerevisiae,
depletion of Mpp10, a U3 snoRNP-specific protein, halts
18S rRNA production and impairs cleavage at the three U3
snoRNP-dependent sites.
Length = 613
Score = 27.3 bits (60), Expect = 6.2
Identities = 17/78 (21%), Positives = 32/78 (41%)
Query: 1 MQEKIPSTDAHDIEIKKEGLWSFLEDENEKRNFSSEEDEESDKLDDEDNVTSDTKFPCRL 60
M + + D + E + ++DE+E F+ E D DDE + K
Sbjct: 109 MDSEDSADDEEEEEEDESLEDEMIDDEDEADLFNESESSLEDLSDDETEDDEEKKMEEEE 168
Query: 61 CSQEFDTKEQRKKHERKD 78
+E ++ EQ + ++ D
Sbjct: 169 AGEEKESVEQATREKKFD 186
>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein.
This family represents Cwf15/Cwc15 (from
Schizosaccharomyces pombe and Saccharomyces cerevisiae
respectively) and their homologues. The function of
these proteins is unknown, but they form part of the
spliceosome and are thus thought to be involved in mRNA
splicing.
Length = 241
Score = 26.6 bits (59), Expect = 7.7
Identities = 11/53 (20%), Positives = 24/53 (45%)
Query: 3 EKIPSTDAHDIEIKKEGLWSFLEDENEKRNFSSEEDEESDKLDDEDNVTSDTK 55
+ D + EIK++ + + + + SS + + SD D+D+ +T
Sbjct: 93 NEGDEDDDEEDEIKRKRIEEDARNSDADDSDSSSDSDSSDDDSDDDDSEDETA 145
>gnl|CDD|233115 TIGR00755, ksgA, dimethyladenosine transferase. In both E. coli
and Saccharomyces cerevisiae, this protein is
responsible for the dimethylation of two adjacent
adenosine residues in a conserved hairpin of 16S rRNA in
bacteria, 18S rRNA in eukaryotes. This adjacent
dimethylation is the only rRNA modification shared by
bacteria and eukaryotes. A single member of this family
is present in each of the first 20 completed microbial
genomes. This protein is essential in yeast, but not in
E. coli, where its deletion leads to resistance to the
antibiotic kasugamycin. Alternate name:
S-adenosylmethionine--6-N',N'-adenosyl (rRNA)
dimethyltransferase [Protein synthesis, tRNA and rRNA
base modification].
Length = 253
Score = 26.8 bits (60), Expect = 8.2
Identities = 8/36 (22%), Positives = 19/36 (52%)
Query: 100 LVKHKSRHIKDYNVFCKICQLGFLSKNELNVHNIKQ 135
L+ ++ +KD +F K+ + F + + +N+K
Sbjct: 181 LIPRETFPVKDEALFEKLLKAAFQQRRKTLRNNLKN 216
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation
[Intracellular trafficking and secretion].
Length = 776
Score = 26.9 bits (59), Expect = 8.3
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 7/80 (8%)
Query: 5 IPSTDAHDIEIKKEGLWSFLEDENEKRNF-SSEEDEESDKLDDEDNVTSDTKFPCRLCSQ 63
I + + +E + + + F + E E RN SE +EE + +DE++ + +C
Sbjct: 352 ILDSSSVPLEKQFDDILYFEKMEIENRNPEESEHEEEVEDYEDENDHSKR------ICDD 405
Query: 64 EFDTKEQRKKHERKDHATQG 83
+ R E+ H G
Sbjct: 406 DELENHFRAADEKNSHLVVG 425
>gnl|CDD|150045 pfam09237, GAGA, GAGA factor. Members of this family bind to a
5'-GAGAG-3' DNA consensus binding site, and contain a
Cys2-His2 zinc finger core as well as an N-terminal
extension containing two highly basic regions. The zinc
finger core binds in the DNA major groove and recognises
the first three GAG bases of the consensus in a manner
similar to that seen in other classical zinc finger-DNA
complexes. The second basic region forms a helix that
interacts in the major groove recognising the last G of
the consensus, while the first basic region wraps around
the DNA in the minor groove and recognises the A in the
fourth position of the consensus sequence.
Length = 54
Score = 24.5 bits (53), Expect = 10.0
Identities = 9/26 (34%), Positives = 13/26 (50%)
Query: 134 KQHCAQPHTCSVCKKIFVNKKNLTTH 159
K QP TC +C+ + +NL H
Sbjct: 18 KSQSEQPATCPICQAVIRQSRNLRRH 43
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
0.316 0.131 0.399
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: 9,302,214
Number of extensions: 798022
Number of successful extensions: 1078
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1015
Number of HSP's successfully gapped: 82
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 56 (25.5 bits)