RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16263
(112 letters)
>gnl|CDD|240331 PTZ00254, PTZ00254, 40S ribosomal protein SA; Provisional.
Length = 249
Score = 65.5 bits (160), Expect = 4e-14
Identities = 21/46 (45%), Positives = 32/46 (69%)
Query: 1 MSGGLDILSLKEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGE 46
+S G +L+ KEDD+ KML + HIG++N + M++YVYKR +G
Sbjct: 1 VSSGPKVLTPKEDDIKKMLACKCHIGTKNLENAMKKYVYKRTKEGV 46
>gnl|CDD|188101 TIGR01012, Sa_S2_E_A, ribosomal protein
Sa(cytosolic)/S2(archaeal). This model describes the
ribosomal protein of the cytosol and of Archaea,
homologous to S2 of bacteria. It is designated
typically as Sa in eukaryotes and Sa or S2 in the
archaea. TIGR01011 describes the related protein of
organelles and bacteria [Protein synthesis, Ribosomal
proteins: synthesis and modification].
Length = 196
Score = 55.5 bits (134), Expect = 9e-11
Identities = 16/40 (40%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 11 KEDDVTKMLGAQTHIGSENSDYQMEQYVYKRRNDGEIFVL 50
V L A HIG++N + ME+++YK R+DG ++VL
Sbjct: 2 YLVPVDMYLAAGVHIGTQNKTFDMEKFIYKVRSDG-LYVL 40
>gnl|CDD|100106 cd01425, RPS2, Ribosomal protein S2 (RPS2), involved in formation
of the translation initiation complex, where it might
contact the messenger RNA and several components of the
ribosome. It has been shown that in Escherichia coli
RPS2 is essential for the binding of ribosomal protein
S1 to the 30s ribosomal subunit. In humans, most likely
in all vertebrates, and perhaps in all metazoans, the
protein also functions as the 67 kDa laminin receptor
(LAMR1 or 67LR), which is formed from a 37 kDa
precursor, and is overexpressed in many tumors. 67LR is
a cell surface receptor which interacts with a variety
of ligands, laminin-1 and others. It is assumed that
the ligand interactions are mediated via the conserved
C-terminus, which becomes extracellular as the protein
undergoes conformational changes which are not well
understood. Specifically, a conserved palindromic
motif, LMWWML, may participate in the interactions.
67LR plays essential roles in the adhesion of cells to
the basement membrane and subsequent signalling events,
and has been linked to several diseases. Some evidence
also suggests that the precursor of 67LR, 37LRP is also
present in the nucleus in animals, where it appears
associated with histones.
Length = 193
Score = 35.3 bits (82), Expect = 0.002
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 18 MLGAQTHIGSENS--DYQMEQYVYKRRNDGEIFVL 50
+L A H+G + + +M+ Y+Y RN I L
Sbjct: 1 LLEAGVHLGHKTRRWNPKMKPYIYGERNGIHIIDL 35
>gnl|CDD|235201 PRK04020, rps2P, 30S ribosomal protein S2; Provisional.
Length = 204
Score = 33.7 bits (78), Expect = 0.010
Identities = 11/31 (35%), Positives = 19/31 (61%)
Query: 15 VTKMLGAQTHIGSENSDYQMEQYVYKRRNDG 45
+ + L A HIG++ ME+++Y+ R DG
Sbjct: 12 LEEYLAAGVHIGTQQKTKDMERFIYRVRPDG 42
>gnl|CDD|215856 pfam00318, Ribosomal_S2, Ribosomal protein S2.
Length = 205
Score = 30.6 bits (70), Expect = 0.12
Identities = 9/28 (32%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 18 MLGAQTHIGSENS--DYQMEQYVYKRRN 43
+L A H G + + +M+ Y+Y RN
Sbjct: 1 LLEAGVHFGHQTRRWNPKMKPYIYGERN 28
>gnl|CDD|223130 COG0052, RpsB, Ribosomal protein S2 [Translation, ribosomal
structure and biogenesis].
Length = 252
Score = 29.2 bits (66), Expect = 0.36
Identities = 7/29 (24%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 17 KMLGAQTHIGSENS--DYQMEQYVYKRRN 43
++L A H G + + +M+ +++ RN
Sbjct: 8 QLLEAGVHFGHQTRRWNPKMKPFIFGERN 36
>gnl|CDD|130084 TIGR01011, rpsB_bact, ribosomal protein S2, bacterial type. This
model describes the bacterial, ribosomal, and
chloroplast forms of ribosomal protein S2. TIGR01012
describes the archaeal and cytosolic forms [Protein
synthesis, Ribosomal proteins: synthesis and
modification].
Length = 225
Score = 26.1 bits (58), Expect = 4.2
Identities = 11/46 (23%), Positives = 23/46 (50%), Gaps = 7/46 (15%)
Query: 7 ILSLKEDDVTKMLGAQTHIGSENS--DYQMEQYVYKRRNDGEIFVL 50
++S+K+ +L A H G + + +M+ +++ RN I L
Sbjct: 1 VVSMKD-----LLEAGVHFGHQTRRWNPKMKPFIFGERNGIHIIDL 41
>gnl|CDD|212681 cd10241, HSPA5-like_NBD, Nucleotide-binding domain of human HSPA5
and similar proteins. This subfamily includes human
HSPA5 (also known as 70-kDa heat shock protein 5,
glucose-regulated protein 78/GRP78, and immunoglobulin
heavy chain-binding protein/BIP, MIF2; the gene encoding
HSPA5 maps to 9q33.3.), Sacchaormyces cerevisiae Kar2p
(also known as Grp78p), and related proteins. This
subfamily belongs to the heat shock protein 70 (HSP70)
family of chaperones that assist in protein folding and
assembly and can direct incompetent "client" proteins
towards degradation. HSPA5 and Kar2p are chaperones of
the endoplasmic reticulum (ER). Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft formed
between the two lobes of the NBD. The two subdomains of
each lobe change conformation between ATP-bound,
ADP-bound, and nucleotide-free states. ATP binding opens
up the substrate-binding site; substrate-binding
increases the rate of ATP hydrolysis. HSP70 chaperone
activity is regulated by various co-chaperones: J-domain
proteins and nucleotide exchange factors (NEFs).
Multiple ER DNAJ domain proteins have been identified
and may exist in distinct complexes with HSPA5 in
various locations in the ER, for example DNAJC3-p58IPK
in the lumen. HSPA5-NEFs include SIL1 and an atypical
HSP70 family protein HYOU1/ORP150. The ATPase activity
of Kar2p is stimulated by the NEFs: Sil1p and Lhs1p.
Length = 374
Score = 26.1 bits (58), Expect = 5.0
Identities = 7/28 (25%), Positives = 19/28 (67%), Gaps = 3/28 (10%)
Query: 23 THIGSENSDYQMEQY---VYKRRNDGEI 47
TH+G E+ D ++ ++ ++K+++ +I
Sbjct: 222 THLGGEDFDQRVMEHFIKLFKKKHGKDI 249
>gnl|CDD|177007 CHL00067, rps2, ribosomal protein S2.
Length = 230
Score = 25.6 bits (57), Expect = 5.6
Identities = 15/48 (31%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 17 KMLGAQTHIGSENSDY--QMEQYVYKRRNDGEIFVLVICYRVSLILCN 62
+ML A H G + + +M Y+Y RN I LV R C+
Sbjct: 12 EMLEAGVHFGHQTRKWNPKMAPYIYAERNGIHIINLVQTARFLSEACD 59
>gnl|CDD|132743 cd06945, NR_LBD_Nurr1_like, The ligand binding domain of Nurr1 and
related nuclear receptor proteins, members of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor Nurr1_like: This family of nuclear
receptors, including Nurr1, Nerve growth
factor-induced-B (NGFI-B) and DHR38 are involved in the
embryo development. Nurr1 is a transcription factor that
is expressed in the embryonic ventral midbrain and is
critical for the development of dopamine (DA) neurons.
Structural studies have shown that the ligand binding
pocket of Nurr1 is filled by bulky hydrophobic residues,
making it unable to bind to ligands. Therefore, it
belongs to the class of orphan receptors. However, Nurr1
forms heterodimers with RXR and can promote signaling
via its partner, RXR. NGFI-B is an early immediate gene
product of embryo development that is rapidly produced
in response to a variety of cellular signals including
nerve growth factor. It is involved in T-cell-mediated
apoptosis, as well as neuronal differentiation and
function. NGFI-B regulates transcription by binding to a
specific DNA target upstream of its target genes and
regulating the rate of tr anscriptional initiation.
Another group of receptor in this family is DHR38.
DHR38 is the Drosophila homolog to the vertebrate
NGFI-B-type orphan receptor. It interacts with the USP
component of the ecdysone receptor complex, suggesting
that DHR38 might modulate ecdysone-triggered signals in
the fly, in addition to the ECR/USP pathway. Nurr1_like
proteins exhibit a modular structure that is
characteristic for nuclear receptors; they have a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a non-conserved hinge and a
C-terminal ligand binding domain (LBD).
Length = 239
Score = 25.8 bits (57), Expect = 6.0
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 5/34 (14%)
Query: 46 EIFVLVICYRV-----SLILCNNIWQHMAELLDG 74
E+FVL + YR L+ CN + H + + G
Sbjct: 85 ELFVLRLAYRSNPVDGKLVFCNGLVLHRLQCVRG 118
>gnl|CDD|180717 PRK06833, PRK06833, L-fuculose phosphate aldolase; Provisional.
Length = 214
Score = 25.5 bits (56), Expect = 7.3
Identities = 12/44 (27%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 4 GLDILSLKEDDVTKM-LGAQTHIGSE--NSDYQMEQYVYKRRND 44
G+D +K +D+ M L + G +S+ M Y+ R D
Sbjct: 46 GIDYFEIKPEDIVIMDLDGKVVEGERKPSSELDMHLIFYRNRED 89
>gnl|CDD|215608 PLN03159, PLN03159, cation/H(+) antiporter 15; Provisional.
Length = 832
Score = 25.6 bits (56), Expect = 7.7
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 51 VICYRVSLILCNNIWQ 66
V+CY +I N IWQ
Sbjct: 17 VVCYAPMMITTNGIWQ 32
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
0.322 0.135 0.421
Gapped
Lambda K H
0.267 0.0760 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,475,395
Number of extensions: 446970
Number of successful extensions: 329
Number of sequences better than 10.0: 1
Number of HSP's gapped: 329
Number of HSP's successfully gapped: 19
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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 (24.1 bits)