RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11495
(81 letters)
>gnl|CDD|219067 pfam06510, DUF1102, Protein of unknown function (DUF1102). This
family consists of several hypothetical archaeal
proteins of unknown function.
Length = 144
Score = 25.9 bits (57), Expect = 2.3
Identities = 9/21 (42%), Positives = 11/21 (52%)
Query: 42 GSLLVLNELLRVSNVTWERTY 62
S V +E+ VSN WE Y
Sbjct: 48 NSTYVFDEMFNVSNELWENGY 68
>gnl|CDD|218441 pfam05112, Baculo_p47, Baculovirus P47 protein. This family
consists of several Baculovirus P47 proteins which is
one of the primary components of Baculovirus encoded RNA
polymerase, which initiates transcription from late and
very late promoters.
Length = 313
Score = 25.7 bits (57), Expect = 2.5
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 53 VSNVTWERTYED 64
NV WER YED
Sbjct: 128 ACNVLWERGYED 139
>gnl|CDD|223070 PHA03391, p47, viral transcription regulator p47; Provisional.
Length = 395
Score = 25.6 bits (57), Expect = 3.4
Identities = 8/12 (66%), Positives = 8/12 (66%)
Query: 53 VSNVTWERTYED 64
NV WER YED
Sbjct: 130 ACNVLWERGYED 141
>gnl|CDD|145958 pfam03084, Sigma_1_2, Reoviral Sigma1/Sigma2 family. Reoviruses
are double-stranded RNA viruses. They lack a membrane
envelope and their capsid is organised in two
concentric icosahedral layers: an inner core and an
outer capsid layer. The sigma1 protein is found in the
outer capsid, and the sigma2 protein is found in the
core. There are four other kinds of protein (besides
sigma2) in the core, termed lambda 1-3, mu2.
Interactions between sigma2 and lambda 1 and lambda 3
are thought to initiate core formation, followed by mu2
and lambda2. Sigma1 is a trimeric protein, and is
positioned at the 12 vertices of the icosahedral outer
capsid layer. Its N-terminal fibrous tail, arranged as
a triple coiled coil, anchors it in the virion, and a
C-terminal globular head interacts with the cellular
receptor. These two parts form by separate
trimerisation events. The N-terminal fibrous tail forms
on the polysome, without the involvement of ATP or
chaperones. The post- translational assembly of the
C-terminal globular head involves the chaperone
activity of Hsp90, which is associated with
phosphorylation of Hsp90 during the process. Sigma1
protein acts as a cell attachment protein, and
determines viral virulence, pathways of spread, and
tropism. Junctional adhesion molecule has been
identified as a receptor for sigma1. In type 3
reoviruses, a small region, predicted to form a beta
sheet, in the N-terminal tail was found to bind target
cell surface sialic acid (i.e. sialic acid acts as a
co-receptor) and promote apoptosis. The sigma1 protein
also binds to the lambda2 core protein.
Length = 415
Score = 25.2 bits (55), Expect = 4.8
Identities = 11/34 (32%), Positives = 14/34 (41%)
Query: 47 LNELLRVSNVTWERTYEDLMNRLQVSTCDDSEIP 80
L+ LLR SN W+ T L E+P
Sbjct: 25 LSHLLRSSNSPWQLTQSSDTISLGRGLVSTPEVP 58
>gnl|CDD|213250 cd03283, ABC_MutS-like, ATP-binding cassette domain of MutS-like
homolog. The MutS protein initiates DNA mismatch repair
by recognizing mispaired and unpaired bases embedded in
duplex DNA and activating endo- and exonucleases to
remove the mismatch. Members of the MutS family possess
C-terminal domain with a conserved ATPase activity that
belongs to the ATP binding cassette (ABC) superfamily.
MutS homologs (MSH) have been identified in most
prokaryotic and all eukaryotic organisms examined.
Prokaryotes have two homologs (MutS1 and MutS2), whereas
seven MSH proteins (MSH1 to MSH7) have been identified
in eukaryotes. The homodimer MutS1 and heterodimers
MSH2-MSH3 and MSH2-MSH6 are primarily involved in
mitotic mismatch repair, whereas MSH4-MSH5 is involved
in resolution of Holliday junctions during meiosis. All
members of the MutS family contain the highly conserved
Walker A/B ATPase domain, and many share a common
mechanism of action. MutS1, MSH2-MSH3, MSH2-MSH6, and
MSH4-MSH5 dimerize to form sliding clamps, and
recognition of specific DNA structures or lesions
results in ADP/ATP exchange.
Length = 199
Score = 24.6 bits (54), Expect = 5.7
Identities = 12/28 (42%), Positives = 14/28 (50%), Gaps = 3/28 (10%)
Query: 24 LDEVFSREKGVNREDRIHGSLLVLNELL 51
LDE+F KG N +R S VL L
Sbjct: 111 LDEIF---KGTNSRERQAASAAVLKFLK 135
>gnl|CDD|215630 PLN03201, PLN03201, RAB geranylgeranyl transferase beta-subunit;
Provisional.
Length = 316
Score = 24.7 bits (54), Expect = 6.8
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 46 VLNELLRVSNVTWERTYEDLMNRLQVSTCDDSEI 79
V+ E LR++ W T DL+ +L D E+
Sbjct: 30 VVMEHLRMNGAYWGLTALDLLGKLDD--VDRDEV 61
>gnl|CDD|184483 PRK14063, PRK14063, exodeoxyribonuclease VII small subunit;
Provisional.
Length = 76
Score = 23.6 bits (51), Expect = 7.7
Identities = 11/29 (37%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 15 LCFEEAMSGLDEVFSR--EKGVNREDRIH 41
L FEEA+S L+ + S+ + V E+ I
Sbjct: 5 LSFEEAISQLEHLVSKLEQGDVPLEEAIS 33
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
0.318 0.132 0.377
Gapped
Lambda K H
0.267 0.0648 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,032,043
Number of extensions: 316051
Number of successful extensions: 220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 10
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
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 (21.7 bits)
S2: 53 (24.4 bits)