RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3342
(61 letters)
>gnl|CDD|215849 pfam00307, CH, Calponin homology (CH) domain. The CH domain is
found in both cytoskeletal proteins and signal
transduction proteins. The CH domain is involved in
actin binding in some members of the family. However in
calponins there is evidence that the CH domain is not
involved in its actin binding activity. Most member
proteins have from two to four copies of the CH domain,
however some proteins such as calponin have only a
single copy.
Length = 104
Score = 56.1 bits (136), Expect = 2e-12
Identities = 14/39 (35%), Positives = 23/39 (58%)
Query: 22 RDALLKWARRTTSKYPGVRVSDFTSSWRDGLAFNAIIHR 60
ALL+W +Y G+ V++F RDGLA A++++
Sbjct: 1 EKALLRWINEVLGEYGGLPVTNFFEDLRDGLALCALLNK 39
>gnl|CDD|227401 COG5069, SAC6, Ca2+-binding actin-bundling protein fimbrin/plastin
(EF-Hand superfamily) [Cytoskeleton].
Length = 612
Score = 52.3 bits (125), Expect = 5e-10
Identities = 21/46 (45%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 16 EPNVSARDALLKWARRTTSKY-PGVRVSDFTSSWRDGLAFNAIIHR 60
E ++ LL W T Y P V DF SWRDGLAF+A+IH
Sbjct: 121 EGELTKHINLLLWCDEDTGGYKPEVDTFDFFRSWRDGLAFSALIHD 166
>gnl|CDD|237981 cd00014, CH, Calponin homology domain; actin-binding domain which
may be present as a single copy or in tandem repeats
(which increases binding affinity). The CH domain is
found in cytoskeletal and signal transduction proteins,
including actin-binding proteins like spectrin,
alpha-actinin, dystrophin, utrophin, and fimbrin,
proteins essential for regulation of cell shape
(cortexillins), and signaling proteins (Vav).
Length = 107
Score = 48.8 bits (117), Expect = 2e-09
Identities = 10/41 (24%), Positives = 25/41 (60%)
Query: 20 SARDALLKWARRTTSKYPGVRVSDFTSSWRDGLAFNAIIHR 60
S ++ LL+W + +Y V +++F++ +DG+A +++
Sbjct: 1 SQKEELLRWINKVLGEYGPVTINNFSTDLKDGIALCKLLNS 41
>gnl|CDD|214479 smart00033, CH, Calponin homology domain. Actin binding domains
present in duplicate at the N-termini of spectrin-like
proteins (including dystrophin, alpha-actinin). These
domains cross-link actin filaments into bundles and
networks. A calponin homology domain is predicted in
yeasst Cdc24p.
Length = 101
Score = 48.5 bits (116), Expect = 2e-09
Identities = 11/38 (28%), Positives = 22/38 (57%)
Query: 23 DALLKWARRTTSKYPGVRVSDFTSSWRDGLAFNAIIHR 60
LL+W ++Y V++F+S +DG+A A+++
Sbjct: 1 KTLLRWVNSLLAEYDKPPVTNFSSDLKDGVALCALLNS 38
>gnl|CDD|221350 pfam11971, CAMSAP_CH, CAMSAP CH domain. This domain is the
N-terminal CH domain from the CAMSAP proteins.
Length = 85
Score = 33.8 bits (78), Expect = 7e-04
Identities = 11/34 (32%), Positives = 14/34 (41%), Gaps = 3/34 (8%)
Query: 27 KWARRTTSKYPGVRVSDFTSSWRDGLAFNAIIHR 60
AR T V + T + DG A A+IH
Sbjct: 2 VSARCT---PLSPPVENLTRDFSDGCALAALIHF 32
>gnl|CDD|218332 pfam04929, Herpes_DNAp_acc, Herpes DNA replication accessory
factor. Replicative DNA polymerases are capable of
polymerising tens of thousands of nucleotides without
dissociating from their DNA templates. The high
processivity of these polymerases is dependent upon
accessory proteins that bind to the catalytic subunit of
the polymerase or to the substrate. The Epstein-Barr
virus (EBV) BMRF1 protein is an essential component of
the viral DNA polymerase and is absolutely required for
lytic virus replication. BMRF1 is also a transactivator.
This family is predicted to have a UL42 like structure.
Length = 381
Score = 27.7 bits (62), Expect = 0.24
Identities = 9/19 (47%), Positives = 11/19 (57%)
Query: 24 ALLKWARRTTSKYPGVRVS 42
L KW R+ +K VRVS
Sbjct: 165 MLQKWLRQQKTKERTVRVS 183
>gnl|CDD|215575 PLN03100, PLN03100, Permease subunit of ER-derived-lipid
transporter; Provisional.
Length = 292
Score = 27.1 bits (60), Expect = 0.52
Identities = 17/57 (29%), Positives = 21/57 (36%), Gaps = 17/57 (29%)
Query: 5 SILISDIVMGAEPNV---SARDALLKWARRTTSKYPGVRVSDFTSSWRDGLAFNAII 58
S L++D V G N+ SA AL W D S+ F AII
Sbjct: 203 SALLADSVYGVSANIILDSAARALRPW--------------DIVSAMIKSQVFGAII 245
>gnl|CDD|236657 PRK10150, PRK10150, beta-D-glucuronidase; Provisional.
Length = 604
Score = 25.7 bits (57), Expect = 1.4
Identities = 9/35 (25%), Positives = 13/35 (37%)
Query: 8 ISDIVMGAEPNVSARDALLKWARRTTSKYPGVRVS 42
I DI + E A + W+ T V V+
Sbjct: 184 IDDITVVTELAQDLNHASVDWSVETNGDVDSVSVT 218
>gnl|CDD|215277 PLN02501, PLN02501, digalactosyldiacylglycerol synthase.
Length = 794
Score = 24.9 bits (54), Expect = 2.8
Identities = 7/37 (18%), Positives = 17/37 (45%)
Query: 15 AEPNVSARDALLKWARRTTSKYPGVRVSDFTSSWRDG 51
AE + R ++++ R + VR ++F ++
Sbjct: 127 AEMELDDRGGIVEFDRVRRRRNSRVRFTEFWGEAKEE 163
>gnl|CDD|197330 cd09096, Deadenylase_nocturnin, C-terminal deadenylase domain of
nocturnin and related domains. This subfamily contains
the C-terminal catalytic domain of the deadenylase,
nocturnin, and related domains. Nocturnin is a
poly(A)-specific 3' exonuclease that specifically
degrades the 3' poly(A) tail of RNA in a process known
as deadenylation. This nuclease activity is manganese
dependent. Nocturnin is expressed in the cytoplasm of
Xenopus laevis retinal photoreceptor cells in a
rhythmic fashion, and it has been proposed that it
participates in posttranscriptional regulation of the
circadian clock or its outputs, and that the mRNA
target(s) of this deadenylase are circadian
clock-related. In mouse, the nocturnin gene, mNoc, is
expressed in a circadian pattern in a range of tissues
including retina, spleen, heart, kidney, and liver. It
is highly expressed in bone-marrow stromal cells,
adipocytes and hepatocytes. In mammals, nocturnin plays
a role in regulating mesenchymal stem-cell lineage
allocation, perhaps through regulating PPAR-gamma
(peroxisome proliferator-activated receptor-gamma)
nuclear translocation. This subfamily belongs to the
large EEP (exonuclease/endonuclease/phosphatase)
superfamily that contains functionally diverse enzymes
that share a common catalytic mechanism of cleaving
phosphodiester bonds.
Length = 280
Score = 24.7 bits (54), Expect = 3.0
Identities = 10/31 (32%), Positives = 14/31 (45%)
Query: 1 MEQWSILISDIVMGAEPNVSARDALLKWARR 31
+ QW+IL + G + V LKW R
Sbjct: 2 VMQWNILAQALGEGKDGFVRCPCEALKWEER 32
>gnl|CDD|99723 cd06402, PB1_p62, The PB1 domain is an essential part of p62
scaffold protein (alias sequestosome 1,SQSTM) involved
in cell signaling, receptor internalization, and
protein turnover. The PB1 domain is a modular domain
mediating specific protein-protein interaction which
play roles in many critical cell processes. A canonical
PB1-PB1 interaction, which involves heterodimerization
of two PB1 domains, is required for the formation of
macromolecular signaling complexes ensuring specificity
and fidelity during cellular signaling. The interaction
between two PB1 domain depends on the type of PB1.
There are three types of PB1 domains: type I which
contains an OPCA motif, acidic aminoacid cluster, type
II which contains a basic cluster, and type I/II which
contains both an OPCA motif and a basic cluster.
Interactions of PB1 domains with other protein domains
have been described as noncanonical PB1-interactions.
The PB1 domain module is conserved in amoebas, fungi,
animals, and plants.
Length = 87
Score = 24.2 bits (53), Expect = 3.4
Identities = 5/22 (22%), Positives = 11/22 (50%)
Query: 29 ARRTTSKYPGVRVSDFTSSWRD 50
+ + +P +R +F W+D
Sbjct: 33 VEKVAAVFPSLRGKNFQLFWKD 54
>gnl|CDD|220598 pfam10142, PhoPQ_related, PhoPQ-activated pathogenicity-related
protein. Members of this family of bacterial proteins
are involved in the virulence of some pathogenic
proteobacteria.
Length = 363
Score = 24.6 bits (54), Expect = 3.5
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 3/34 (8%)
Query: 19 VSARDALLKWARRTTSKYPGVRVS--DFTS-SWR 49
V D LK+ +T++ GV + + TS +W
Sbjct: 5 VEKEDQPLKYTLTSTTELAGVTIYILELTSQTWS 38
>gnl|CDD|240640 cd12163, 2-Hacid_dh_5, Putative D-isomer specific 2-hydroxyacid
dehydrogenases. 2-Hydroxyacid dehydrogenases catalyze
the conversion of a wide variety of D-2-hydroxy acids
to their corresponding keto acids. The general
mechanism is (R)-lactate + acceptor to pyruvate +
reduced acceptor. Formate/glycerate and related
dehydrogenases of the D-specific 2-hydroxyacid
dehydrogenase superfamily include groups such as
formate dehydrogenase, glycerate dehydrogenase,
L-alanine dehydrogenase, and S-adenosylhomocysteine
hydrolase. Despite often low sequence identity, these
proteins typically have a characteristic arrangement of
2 similar subdomains of the alpha/beta Rossmann fold
NAD+ binding form. The NAD+ binding domain is inserted
within the linear sequence of the mostly N-terminal
catalytic domain, which has a similar domain structure
to the internal NAD binding domain. Structurally, these
domains are connected by extended alpha helices and
create a cleft in which NAD is bound, primarily to the
C-terminal portion of the 2nd (internal) domain. Some
related proteins have similar structural subdomain but
with a tandem arrangement of the catalytic and
NAD-binding subdomains in the linear sequence. While
many members of this family are dimeric, alanine DH is
hexameric and phosphoglycerate DH is tetrameric.
Length = 334
Score = 23.8 bits (52), Expect = 6.8
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 28 WARRTTSKYPGVRVSDFTSSWRDGLA 53
W + ++PG+ + S+ DG
Sbjct: 1 WLAKLRKRFPGLEIRWVESAPPDGPP 26
>gnl|CDD|234819 PRK00711, PRK00711, D-amino acid dehydrogenase small subunit;
Validated.
Length = 416
Score = 23.6 bits (52), Expect = 7.7
Identities = 6/17 (35%), Positives = 12/17 (70%)
Query: 7 LISDIVMGAEPNVSARD 23
L++D++ G +P + A D
Sbjct: 394 LLADLISGRKPAIDADD 410
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
0.321 0.131 0.411
Gapped
Lambda K H
0.267 0.0727 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,147,180
Number of extensions: 209600
Number of successful extensions: 162
Number of sequences better than 10.0: 1
Number of HSP's gapped: 162
Number of HSP's successfully gapped: 14
Length of query: 61
Length of database: 10,937,602
Length adjustment: 32
Effective length of query: 29
Effective length of database: 9,518,274
Effective search space: 276029946
Effective search space used: 276029946
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 (21.9 bits)
S2: 53 (24.2 bits)