RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15067
(80 letters)
>gnl|CDD|227395 COG5063, CTH1, CCCH-type Zn-finger protein [General function
prediction only].
Length = 351
Score = 47.4 bits (112), Expect = 7e-08
Identities = 12/48 (25%), Positives = 21/48 (43%)
Query: 13 DHDETGVCKFGTGCKFAHGAHELRVIPRHPRYRTKLCQSYHQDGFCPY 60
E C++ FAH + HP+Y+T+ + + G+ PY
Sbjct: 120 SSTEIPYCRYPDKNPFAHSKAISSLAQTHPKYKTESLEVFINPGYVPY 167
Score = 35.4 bits (81), Expect = 0.001
Identities = 11/45 (24%), Positives = 16/45 (35%), Gaps = 2/45 (4%)
Query: 18 GVCKFGTGCKFAHGAHELRVIPRHPR--YRTKLCQSYHQDGFCPY 60
G C +G C F HG + Y C++ + G P
Sbjct: 284 GYCPYGLRCCFKHGDDSDIEMYEEASLGYLDGPCRTRAKGGAFPS 328
Score = 29.2 bits (65), Expect = 0.18
Identities = 17/52 (32%), Positives = 28/52 (53%), Gaps = 6/52 (11%)
Query: 15 DETGVCKF---GTGCKFA---HGAHELRVIPRHPRYRTKLCQSYHQDGFCPY 60
G C + G C+FA HG +EL+ + +RT+ C ++ + G+CPY
Sbjct: 237 TRKGTCPYWISGVKCQFACRGHGLNELKSKKKKQNFRTEPCINWEKSGYCPY 288
>gnl|CDD|144294 pfam00642, zf-CCCH, Zinc finger C-x8-C-x5-C-x3-H type (and
similar).
Length = 27
Score = 27.9 bits (63), Expect = 0.094
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 12 PDHDETGVCKFGTGCKFAHG 31
TG CK+G CKFAHG
Sbjct: 7 RFFSRTGTCKYGDRCKFAHG 26
Score = 25.2 bits (56), Expect = 0.82
Identities = 7/17 (41%), Positives = 12/17 (70%)
Query: 44 YRTKLCQSYHQDGFCPY 60
Y+T+LC+ + + G C Y
Sbjct: 1 YKTELCRFFSRTGTCKY 17
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 28.9 bits (64), Expect = 0.24
Identities = 10/18 (55%), Positives = 12/18 (66%)
Query: 13 DHDETGVCKFGTGCKFAH 30
D+ ETG C +G CKF H
Sbjct: 146 DYKETGYCGYGDSCKFLH 163
>gnl|CDD|227577 COG5252, COG5252, Uncharacterized conserved protein, contains
CCCH-type Zn-finger protein [General function prediction
only].
Length = 299
Score = 26.2 bits (57), Expect = 1.8
Identities = 10/19 (52%), Positives = 10/19 (52%)
Query: 18 GVCKFGTGCKFAHGAHELR 36
C G CKFAHG E R
Sbjct: 94 KTCAKGDACKFAHGKEEAR 112
>gnl|CDD|241440 cd13286, PH_OPR5_ORP8, Human Oxysterol binding protein related
proteins 5 and 8 Pleckstrin homology (PH) domain.
Human ORP5 is proposed to function in efficient
nonvesicular transfer of low-density
lipoproteins-derived cholesterol (LDL-C) from late
endosomes/lysosomes to the endoplasmic reticulum (ER).
Human ORP8 is proposed to modulate lipid homeostasis
and sterol regulatory element binding proteins (SREBP)
activity. Both ORP5 and ORP8 contain a N-terminal PH
domain, a C-terminal OSBP-related domain, followed by a
transmembrane domain that localizes ORP5 to the ER.
Unlike all the other human OSBP/ORPs they lack a FFAT
motif (two phenylalanines in an acidic tract).
Oxysterol binding proteins are a multigene family that
is conserved in yeast, flies, worms, mammals and
plants. In general OSBPs and ORPs have been found to be
involved in the transport and metabolism of cholesterol
and related lipids in eukaryotes. They all contain a
C-terminal oxysterol binding domain, and most contain
an N-terminal PH domain. OSBP PH domains bind to
membrane phosphoinositides and thus likely play an
important role in intracellular targeting. They are
members of the oxysterol binding protein (OSBP) family
which includes OSBP, OSBP-related proteins (ORP),
Goodpasture antigen binding protein (GPBP), and Four
phosphate adaptor protein 1 (FAPP1). They have a wide
range of purported functions including sterol
transport, cell cycle control, pollen development and
vessicle transport from Golgi recognize both PI lipids
and ARF proteins. 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 = 130
Score = 25.4 bits (56), Expect = 2.5
Identities = 8/17 (47%), Positives = 12/17 (70%), Gaps = 5/17 (29%)
Query: 54 QDGFCPYVYFFKIFHPI 70
+DGFC FK++HP+
Sbjct: 64 KDGFC-----FKLYHPL 75
>gnl|CDD|234767 PRK00448, polC, DNA polymerase III PolC; Validated.
Length = 1437
Score = 25.6 bits (57), Expect = 2.8
Identities = 5/13 (38%), Positives = 9/13 (69%)
Query: 63 FFKIFHPIPYYTT 75
+FK+ +P+ YY
Sbjct: 1280 YFKVHYPLAYYAA 1292
>gnl|CDD|214632 smart00356, ZnF_C3H1, zinc finger.
Length = 27
Score = 23.7 bits (52), Expect = 3.5
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 16 ETGVCKFGTGCKFAHG 31
+ G C G CKFAH
Sbjct: 11 KRGYCPRGDRCKFAHP 26
>gnl|CDD|225087 COG2176, PolC, DNA polymerase III, alpha subunit (gram-positive type)
[DNA replication, recombination, and repair].
Length = 1444
Score = 25.0 bits (55), Expect = 4.8
Identities = 6/15 (40%), Positives = 10/15 (66%)
Query: 61 VYFFKIFHPIPYYTT 75
+ +FK+ HP+ YY
Sbjct: 1285 IAYFKVHHPLEYYAA 1299
>gnl|CDD|178317 PLN02715, PLN02715, lipid phosphate phosphatase.
Length = 327
Score = 25.0 bits (54), Expect = 5.2
Identities = 9/20 (45%), Positives = 12/20 (60%)
Query: 44 YRTKLCQSYHQDGFCPYVYF 63
YR YH++G+ PY YF
Sbjct: 265 YRQFYPNPYHEEGWGPYAYF 284
>gnl|CDD|233397 TIGR01405, polC_Gram_pos, DNA polymerase III, alpha chain,
Gram-positive type. This model describes a polypeptide
chain of DNA polymerase III. Full-length homologs of this
protein are restricted to the Gram-positive lineages,
including the Mycoplasmas. This protein is designated
alpha chain and given the gene symbol polC, but is not a
full-length homolog of other polC genes. The N-terminal
region of about 200 amino acids is rich in low-complexity
sequence, poorly alignable, and not included n this model
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1213
Score = 25.0 bits (55), Expect = 5.8
Identities = 5/15 (33%), Positives = 10/15 (66%)
Query: 61 VYFFKIFHPIPYYTT 75
+ +FK+ +P+ YY
Sbjct: 1053 IAYFKVHYPLEYYAA 1067
>gnl|CDD|235785 PRK06365, PRK06365, acetyl-CoA acetyltransferase; Provisional.
Length = 430
Score = 24.9 bits (54), Expect = 6.0
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 34 ELRVIPRHPRYRTKLCQSYHQDGFCPYVY 62
+L +I H Y + Q+Y G C Y
Sbjct: 314 DLDLIELHDAYTSSEIQTYEDLGLCKYGE 342
>gnl|CDD|215900 pfam00398, RrnaAD, Ribosomal RNA adenine dimethylase.
Length = 254
Score = 24.2 bits (53), Expect = 8.5
Identities = 16/55 (29%), Positives = 19/55 (34%), Gaps = 11/55 (20%)
Query: 32 AHELRVIPR-HPRYRTKLCQS-----YHQDGF---CPYVYFFKIFHPIPYYTTEA 77
A E+ PR R + KL HQD P F + IPY T
Sbjct: 56 AIEID--PRLAKRLQEKLALHPNVEVVHQDFLKFSFPKDDPFLVVGNIPYNITTP 108
>gnl|CDD|200540 cd11279, Sema_RON, The Sema domain, a protein interacting module,
of RON Receptor Tyrosine Kinase. RON receptor tyrosine
kinase is a Macrophage-stimulating protein (MSP)
receptor. Upon binding of MSP, RON is activated via
autophosphorylation within its kinase catalytic domain,
resulting in a wide range of effects, including
proliferation, tubular morphogenesis, angiogenesis,
cellular motility and invasiveness. By interacting with
downstream signaling molecules, it regulates macrophage
migration, phagocytosis, and nitric oxide production.
RON has been implicated in cancers of the breast, colon,
pancreas and ovaries because both splice variants and
receptor overexpression have been identified in these
tumors. The Sema domain is located at the N-terminus and
contains four disulfide bonds formed by eight conserved
cysteine residues. It serves as ligand recognition and
binding model. RON is composed of an alpha-beta
heterodimer. The extracellular alpha chain is disulfide
linked to the beta chain, which contains an
extracellular ligand-binding region with a Sema domain,
a PSI domain and four IPT repeats, a transmembrane
segment, and an intracellular catalytic tyrosine kinase
domain. The Sema domain of RON may be necessary for
receptor dimerization and activation.
Length = 493
Score = 24.4 bits (53), Expect = 9.1
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 4/40 (10%)
Query: 28 FAHGAHELRVIPRH-PRYRTKLCQSYHQDGFCPYVYFFKI 66
FA G H L V+P++ Y S+ +VYF +
Sbjct: 200 FAPGFHSLTVLPKYLDSYPIHYVHSFTSGD---FVYFLTV 236
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
0.327 0.147 0.510
Gapped
Lambda K H
0.267 0.0763 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,193,594
Number of extensions: 311564
Number of successful extensions: 292
Number of sequences better than 10.0: 1
Number of HSP's gapped: 292
Number of HSP's successfully gapped: 19
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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)