RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13055
(97 letters)
>gnl|CDD|239095 cd02412, 30S_S3_KH, K homology RNA-binding (KH) domain of the
prokaryotic 30S small ribosomal subunit protein S3. S3
is part of the head region of the 30S ribosomal subunit
and is believed to interact with mRNA as it threads its
way from the latch into the channel. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In general, KH
binds single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA.
Length = 109
Score = 32.1 bits (74), Expect = 0.014
Identities = 9/33 (27%), Positives = 18/33 (54%)
Query: 15 VEDEFIRRFLRGTWHNLFLSEIIIKRQHNIIRI 47
ED IR+F++ +S I I+R+ + + +
Sbjct: 33 HEDLKIRKFIKKKLKKAGISRIEIERKADRVEV 65
>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
Length = 232
Score = 32.4 bits (75), Expect = 0.019
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 15 VEDEFIRRFLRGTWHNLFLSEIIIKRQHNIIRI 47
ED IR+FL+ +S I I+R +R+
Sbjct: 34 HEDLKIRKFLKKKLKKAGVSRIEIERPAKRVRV 66
>gnl|CDD|222340 pfam13718, GNAT_acetyltr_2, GNAT acetyltransferase 2. This domain
has N-acetyltransferase activity. It has a GCN5-related
N-acetyltransferase (GNAT) fold.
Length = 169
Score = 30.1 bits (69), Expect = 0.10
Identities = 10/20 (50%), Positives = 11/20 (55%), Gaps = 3/20 (15%)
Query: 65 GYTEELLSFWLQC---PVKL 81
G T ELL FW + PV L
Sbjct: 130 GATPELLKFWQKNGFVPVYL 149
>gnl|CDD|224361 COG1444, COG1444, Predicted P-loop ATPase fused to an
acetyltransferase [General function prediction only].
Length = 758
Score = 29.3 bits (66), Expect = 0.27
Identities = 13/20 (65%), Positives = 14/20 (70%), Gaps = 3/20 (15%)
Query: 65 GYTEELLSFWLQC---PVKL 81
GYTEELL FWL+ PV L
Sbjct: 572 GYTEELLRFWLRNGFVPVHL 591
>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type. This
model describes the bacterial type of ribosomal protein
S3. Chloroplast and mitochondrial forms have large,
variable inserts between conserved N-terminal and
C-terminal domains. This model recognizes all bacterial
forms and many chloroplast forms above the trusted
cutoff score. TIGRFAMs model TIGR01008 describes S3 of
the eukaryotic cytosol and of the archaea [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 211
Score = 28.4 bits (64), Expect = 0.48
Identities = 14/55 (25%), Positives = 27/55 (49%), Gaps = 6/55 (10%)
Query: 11 SETAVEDEFIRRFLRGTWHNLFLSEIIIKRQHNIIRIGGIVERAIHPRKIYFLIG 65
++ ED IR +++ N +S++ I+R + IR+ IH + +IG
Sbjct: 30 AKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVT------IHTARPGIVIG 78
>gnl|CDD|241414 cd13260, PH_RASA1, RAS p21 protein activator (GTPase activating
protein) 1 Pleckstrin homology (PH) domain. RASA1
(also called RasGap1 or p120) is a member of the RasGAP
family of GTPase-activating proteins. RASA1 contains
N-terminal SH2-SH3-SH2 domains, followed by two C2
domains, a PH domain, a RasGAP domain, and a BTK
domain. Splice variants lack the N-terminal domains. It
is a cytosolic vertebrate protein that acts as a
suppressor of RAS via its C-terminal GAP domain
function, enhancing the weak intrinsic GTPase activity
of RAS proteins resulting in the inactive GDP-bound
form of RAS, allowing control of cellular proliferation
and differentiation. Additionally, it is involved in
mitogenic signal transmission towards downstream
interacting partners through its N-terminal SH2-SH3-SH2
domains. RASA1 interacts with a number of proteins
including: G3BP1, SOCS3, ANXA6, Huntingtin, KHDRBS1,
Src, EPHB3, EPH receptor B2, Insulin-like growth factor
1 receptor, PTK2B, DOK1, PDGFRB, HCK, Caveolin 2,
DNAJA3, HRAS, GNB2L1 and NCK1. PH domains have diverse
functions, but in general are involved in targeting
proteins to the appropriate cellular location or in the
interaction with a binding partner. They share little
sequence conservation, but all have a common fold,
which is electrostatically polarized. Less than 10% of
PH domains bind phosphoinositide phosphates (PIPs) with
high affinity and specificity. PH domains are
distinguished from other PIP-binding domains by their
specific high-affinity binding to PIPs with two vicinal
phosphate groups: PtdIns(3,4)P2, PtdIns(4,5)P2 or
PtdIns(3,4,5)P3 which results in targeting some PH
domain proteins to the plasma membrane. A few display
strong specificity in lipid binding. Any specificity is
usually determined by loop regions or insertions in the
N-terminus of the domain, which are not conserved
across all PH domains. PH domains are found in cellular
signaling proteins such as serine/threonine kinase,
tyrosine kinases, regulators of G-proteins, endocytotic
GTPases, adaptors, as well as cytoskeletal associated
molecules and in lipid associated enzymes.
Length = 103
Score = 24.6 bits (54), Expect = 6.9
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 50 IVERAIHPRKIYFLIGYTEELLSFWLQC 77
IV RA++ IY+L T EL W++
Sbjct: 71 IVVRALNESTIYYLCADTAELAQDWMKA 98
>gnl|CDD|218697 pfam05694, SBP56, 56kDa selenium binding protein (SBP56). This
family consists of several eukaryotic selenium binding
proteins as well as three sequences from archaea. The
exact function of this protein is unknown although it is
thought that SBP56 participates in late stages of
intra-Golgi protein transport. The Lotus japonicus
homologue of SBP56, LjSBP is thought to have more than
one physiological role and can be implicated in
controlling the oxidation/reduction status of target
proteins, in vesicular Golgi transport.
Length = 461
Score = 24.9 bits (55), Expect = 8.1
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 11/29 (37%)
Query: 40 RQHNI-----------IRIGGIVERAIHP 57
RQ++I +R+GGI+ RA HP
Sbjct: 337 RQYDISDPFNPKLTGQVRLGGIIRRAPHP 365
>gnl|CDD|99965 cd03791, GT1_Glycogen_synthase_DULL1_like, This family is most
closely related to the GT1 family of
glycosyltransferases. Glycogen synthase catalyzes the
formation and elongation of the alpha-1,4-glucose
backbone using ADP-glucose, the second and key step of
glycogen biosynthesis. This family includes starch
synthases of plants, such as DULL1 in Zea mays and
glycogen synthases of various organisms.
Length = 476
Score = 24.8 bits (55), Expect = 9.8
Identities = 7/15 (46%), Positives = 10/15 (66%)
Query: 56 HPRKIYFLIGYTEEL 70
+P ++ LIGY E L
Sbjct: 349 YPGRVAVLIGYDEAL 363
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
0.328 0.146 0.445
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,239,981
Number of extensions: 470511
Number of successful extensions: 509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 509
Number of HSP's successfully gapped: 26
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.1 bits)