RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16646
(159 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 = 26.9 bits (60), Expect = 0.66
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 64 ICEICNKEFTHKSSLAEHRVLH 85
C C K F+ KS+L H H
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 26.7 bits (59), Expect = 0.88
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 65 CEICNKEFTHKSSLAEHRVLH 85
C C K F KS+L EH H
Sbjct: 3 CPECGKVFKSKSALREHMRTH 23
>gnl|CDD|213839 TIGR03629, arch_S13P, archaeal ribosomal protein S13P. This model
describes exclusively the archaeal ribosomal protein
S13P. It excludes the homologous eukaryotic 40S
ribosomal protein S18 and bacterial 30S ribosomal
protein S13 [Protein synthesis, Ribosomal proteins:
synthesis and modification].
Length = 144
Score = 28.8 bits (65), Expect = 0.90
Identities = 16/50 (32%), Positives = 22/50 (44%), Gaps = 10/50 (20%)
Query: 101 RDKHSKGDDI----REEIEREMKT------RNSIGITVRQNQTNKNHRSG 140
D H G D+ RE+I R K R+ +G+ VR +T R G
Sbjct: 86 EDLHLIGSDLDMTVREDINRMKKIRSYRGIRHELGLKVRGQRTKSTGRRG 135
>gnl|CDD|236630 PRK09853, PRK09853, putative selenate reductase subunit YgfK;
Provisional.
Length = 1019
Score = 28.8 bits (65), Expect = 1.3
Identities = 8/37 (21%), Positives = 15/37 (40%), Gaps = 2/37 (5%)
Query: 2 NEMKKKSVKNPNAKKRYRPYVPRVDSSLP-PQFHCYV 37
N + ++ +K ++P V + P CYV
Sbjct: 411 NRLAADALTMEYTQKHWKP-VESRKVAEDLPLTDCYV 446
>gnl|CDD|235215 PRK04053, rps13p, 30S ribosomal protein S13P; Reviewed.
Length = 149
Score = 27.9 bits (63), Expect = 1.5
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 10/50 (20%)
Query: 101 RDKHSKGDDI----REEIEREMKT------RNSIGITVRQNQTNKNHRSG 140
D H G D+ RE+I R K R+ +G+ VR +T R+G
Sbjct: 91 EDLHLIGSDLILTVREDINRMKKIRSYRGIRHELGLKVRGQRTRSTGRTG 140
>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 = 28.6 bits (64), Expect = 1.9
Identities = 9/29 (31%), Positives = 16/29 (55%), Gaps = 3/29 (10%)
Query: 56 HTNNYDRVICEICNKEFTHKSSLAEHRVL 84
+ ++Y +C +C EF+ LAEH+
Sbjct: 70 NPSSY---VCNVCMAEFSSMDQLAEHQRT 95
>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 = 25.5 bits (57), Expect = 2.0
Identities = 9/17 (52%), Positives = 11/17 (64%)
Query: 65 CEICNKEFTHKSSLAEH 81
CE+CN FT +S L H
Sbjct: 3 CELCNVTFTSESQLKSH 19
>gnl|CDD|227480 COG5151, SSL1, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit SSL1 [Transcription / DNA replication,
recombination, and repair].
Length = 421
Score = 26.9 bits (59), Expect = 5.4
Identities = 18/78 (23%), Positives = 32/78 (41%), Gaps = 9/78 (11%)
Query: 19 RPYVPRVDSSLPPQFHCYVCKKKYRHKRQLVRHFQVNHTNNYDRVICEICNKEFTHKSSL 78
+P+V + + + P HC+VC+ + + + + R CE+C F +
Sbjct: 349 KPFVEKPEGTNPKSTHCFVCQGPF----PKPPVSPFDESTSSGRYQCELCKSTFCSDCDV 404
Query: 79 AEHRVLHFPAQHKCSLCQ 96
H LHF C C+
Sbjct: 405 FIHETLHF-----CIGCE 417
>gnl|CDD|183221 PRK11595, PRK11595, DNA utilization protein GntX; Provisional.
Length = 227
Score = 26.2 bits (58), Expect = 8.7
Identities = 6/24 (25%), Positives = 9/24 (37%)
Query: 81 HRVLHFPAQHKCSLCQQAFKRDKH 104
L CS+C +A + K
Sbjct: 12 RMPLALSHWGICSVCSRALRTLKT 35
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
0.319 0.130 0.390
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: 7,608,375
Number of extensions: 644594
Number of successful extensions: 775
Number of sequences better than 10.0: 1
Number of HSP's gapped: 771
Number of HSP's successfully gapped: 45
Length of query: 159
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 70
Effective length of database: 6,990,096
Effective search space: 489306720
Effective search space used: 489306720
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 55 (25.1 bits)