RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10031
(218 letters)
>gnl|CDD|227445 COG5114, COG5114, Histone acetyltransferase complex SAGA/ADA,
subunit ADA2 [Chromatin structure and dynamics].
Length = 432
Score = 45.8 bits (108), Expect = 6e-06
Identities = 35/133 (26%), Positives = 60/133 (45%), Gaps = 12/133 (9%)
Query: 12 VGTEAREEYISRFLEGTIGKVTW--EDVLKNNQVKIIDMTDQLSEGPLATLPKGGPPIHI 69
+G+ A+EE S +L+ + D+ +N V + +Q PPI+
Sbjct: 93 IGSRAKEEIKSHYLKMYDESKYYPLPDITQNIHVPQDEFLEQRRHRIETFEL---PPINP 149
Query: 70 AQEKADQ------IGYMPLRDDFEWQYDNNAESVVSGL-IHLEDTDVDTTLKLVHVDMYI 122
+ KA GYMP R +F+ +Y N AE + + + ++ LK +D+Y
Sbjct: 150 RKPKASNPYCHEIQGYMPGRLEFDVEYMNEAEVPIKDMSFDGDKEELKKKLKNATLDIYN 209
Query: 123 NKLRERARRKRVV 135
++L RARRK +
Sbjct: 210 SRLTFRARRKHAI 222
>gnl|CDD|226837 COG4403, LcnDR2, Lantibiotic modifying enzyme [Defense mechanisms].
Length = 963
Score = 36.7 bits (85), Expect = 0.009
Identities = 22/72 (30%), Positives = 31/72 (43%), Gaps = 4/72 (5%)
Query: 133 RVVKDFQLIPKFFNAQLNPETKTVKRKFNKDDSPENGAVVNVLDFGSGGWWFKFKSKSSH 192
R+ DF +I + F P K + K D+ G V +L F S +K KS S
Sbjct: 176 RLANDFSVIEEEFG----PRGKLGNVQLGKGDTHSKGQTVTILFFASAKVVYKPKSLSID 231
Query: 193 KIYQVMIILVRS 204
KI ++ V S
Sbjct: 232 KILNEILEWVNS 243
>gnl|CDD|129191 TIGR00082, rbfA, ribosome-binding factor A. Associates with free
30S ribosomal subunits (but not with 30S subunits that
are part of 70S ribosomes or polysomes). Essential for
efficient processing of 16S rRNA. May interact with the
5'terminal helix region of 16S rRNA. Mutants lacking
rbfA have a cold-sensitive phenotype [Transcription, RNA
processing].
Length = 114
Score = 30.8 bits (70), Expect = 0.16
Identities = 18/72 (25%), Positives = 30/72 (41%), Gaps = 3/72 (4%)
Query: 107 TDVDTTLKLVHVDMYINKLRERARRKRVVKDFQLIPKFFNAQLNPET---KTVKRKFNKD 163
T V+ + L H ++++ + RVVK F + L KT + F KD
Sbjct: 36 TKVEVSKDLQHAKVFVDCYGDEEAIDRVVKALNKAKGFIRSLLGQAMRLRKTPELHFVKD 95
Query: 164 DSPENGAVVNVL 175
+S + G + L
Sbjct: 96 NSLDKGMRIENL 107
>gnl|CDD|240109 cd04792, LanM-like, LanM-like proteins. LanM is a bifunctional
enzyme, involved in the synthesis of class II
lantibiotics. It is responsible for both the dehydration
and the cyclization of the precursor-peptide during
lantibiotic synthesis. The C-terminal domain shows
similarity to LanC, the cyclase component of the lan
operon, but the N terminus seems to be unrelated to the
dehydratase, LanB.
Length = 825
Score = 31.5 bits (72), Expect = 0.34
Identities = 18/80 (22%), Positives = 34/80 (42%), Gaps = 3/80 (3%)
Query: 132 KRVVKDFQLIPKFFNAQLNPETKTVKRKFNKDDSPENGAVVNVLDFGSGGWWF-KFKSKS 190
R+ D + +FF + + + D+ G VV +L F SG K +S S
Sbjct: 67 SRLANDRSELEEFFL--IGSSEGLISIQLGLGDTHNGGRVVAILTFSSGLKLVYKPRSLS 124
Query: 191 SHKIYQVMIILVRSYLSSSS 210
++Q ++ + S+L +
Sbjct: 125 VDALFQELLEWLNSFLGALP 144
>gnl|CDD|151114 pfam10583, Involucrin_N, Involucrin of squamous epithelia
N-terminus. This is the N-terminal three beta strands
of involucrin, a protein present in keratinocytes of
epidermis and other stratified squamous epithelia.
Involucrin first appears in the cell cytosol, but
ultimately becomes cross-linked to membrane proteins by
transglutaminase thus helping in the formation of an
insoluble envelope beneath the plasma membrane.
Apigenin is a plant-derived flavanoid that has
significant promise as a skin cancer chemopreventive
agent. It has been found that apigenin regulates normal
human keratinocyte differentiation by suppressing it
and this is associated with reduced cell proliferation
without apoptosis. The downstream part of the protein
is represented by the family Involucrin, pfam00904.
Length = 69
Score = 28.4 bits (63), Expect = 0.73
Identities = 10/25 (40%), Positives = 14/25 (56%), Gaps = 3/25 (12%)
Query: 52 LSEGPLATLPKGGPPIHIAQEKADQ 76
LS+ PL T+ PP + QE+ Q
Sbjct: 15 LSQEPLKTVS---PPANTQQEQRKQ 36
>gnl|CDD|212790 cd11856, SH3_p47phox_like, Src homology 3 domains of the p47phox
subunit of NADPH oxidase and similar domains. This
family is composed of the tandem SH3 domains of p47phox
subunit of NADPH oxidase and Nox Organizing protein 1
(NoxO1), the four SH3 domains of Tks4 (Tyr kinase
substrate with four SH3 domains), the five SH3 domains
of Tks5, the SH3 domain of obscurin, Myosin-I, and
similar domains. Most members of this group also contain
Phox homology (PX) domains, except for obscurin and
Myosin-I. p47phox and NoxO1 are regulators of the
phagocytic NADPH oxidase complex (also called Nox2 or
gp91phox) and nonphagocytic NADPH oxidase Nox1,
respectively. They play roles in the activation of their
respective NADPH oxidase, which catalyzes the transfer
of electrons from NADPH to molecular oxygen to form
superoxide. Tks proteins are Src substrates and
scaffolding proteins that play important roles in the
formation of podosomes and invadopodia, the dynamic
actin-rich structures that are related to cell migration
and cancer cell invasion. Obscurin is a giant muscle
protein that plays important roles in the organization
and assembly of the myofibril and the sarcoplasmic
reticulum. Type I myosins (Myosin-I) are actin-dependent
motors in endocytic actin structures and actin patches.
They play roles in membrane traffic in endocytic and
secretory pathways, cell motility, and mechanosensing.
Myosin-I contains an N-terminal actin-activated ATPase,
a phospholipid-binding TH1 (tail homology 1) domain, and
a C-terminal extension which includes an F-actin-binding
TH2 domain, an SH3 domain, and an acidic peptide that
participates in activating the Arp2/3complex. The SH3
domain of myosin-I is required for myosin-I-induced
actin polymerization. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 53
Score = 26.1 bits (58), Expect = 2.9
Identities = 8/16 (50%), Positives = 10/16 (62%)
Query: 169 GAVVNVLDFGSGGWWF 184
G VV VL+ GWW+
Sbjct: 21 GEVVEVLEKNDSGWWY 36
>gnl|CDD|213007 cd12074, SH3_Tks5_1, First Src homology 3 domain of Tyrosine kinase
substrate with five SH3 domains. Tks5, also called SH3
and PX domain-containing protein 2A (SH3PXD2A) or Five
SH (FISH), is a scaffolding protein and Src substrate
that is localized in podosomes, which are electron-dense
structures found in Src-transformed fibroblasts,
osteoclasts, macrophages, and some invasive cancer
cells. It binds and regulates some members of the ADAMs
family of transmembrane metalloproteases, which function
as sheddases and mediators of cell and matrix
interactions. It is required for podosome formation,
degradation of the extracellular matrix, and cancer cell
invasion. Tks5 contains an N-terminal Phox homology (PX)
domain and five SH3 domains. This model characterizes
the first SH3 domain of Tks5. SH3 domains are protein
interaction domains that bind to proline-rich ligands
with moderate affinity and selectivity, preferentially
to PxxP motifs. They play versatile and diverse roles in
the cell including the regulation of enzymes, changing
the subcellular localization of signaling pathway
components, and mediating the formation of multiprotein
complex assemblies.
Length = 53
Score = 25.8 bits (56), Expect = 3.7
Identities = 10/28 (35%), Positives = 18/28 (64%)
Query: 157 KRKFNKDDSPENGAVVNVLDFGSGGWWF 184
+++ N + S + G VV+V++ GWWF
Sbjct: 9 EKQENSEISLQAGEVVDVIEKNESGWWF 36
>gnl|CDD|173231 PRK14770, PRK14770, lipoprotein signal peptidase; Provisional.
Length = 167
Score = 27.5 bits (61), Expect = 3.8
Identities = 13/40 (32%), Positives = 21/40 (52%), Gaps = 1/40 (2%)
Query: 169 GAVVNVLDFGSGGW-WFKFKSKSSHKIYQVMIILVRSYLS 207
GAVV+ L + GW W+ F + V ++L+ S L+
Sbjct: 120 GAVVDFLHAHAFGWSWYVFNLADAAIDCGVAVLLIDSLLA 159
>gnl|CDD|163483 TIGR03771, anch_rpt_ABC, anchored repeat-type ABC transporter,
ATP-binding subunit. This protein family is the
ATP-binding cassette subunit of binding
protein-dependent ABC transporter complex that strictly
co-occurs with TIGR03769. TIGRFAMs model TIGR03769
describes a protein domain that occurs singly or as one
of up to three repeats in proteins of a number of
Actinobacteria, including Propionibacterium acnes
KPA171202. The TIGR03769 domain occurs both in an
adjacent gene for the substrate-binding protein and in
additional (often nearby) proteins, often with
LPXTG-like sortase recognition signals. Homologous
ATP-binding subunits outside the scope of this family
include manganese transporter MntA in Synechocystis sp.
PCC 6803 and chelated iron transporter subunits. The
function of this transporter complex is unknown
[Transport and binding proteins, Unknown substrate].
Length = 223
Score = 27.5 bits (61), Expect = 4.7
Identities = 11/46 (23%), Positives = 19/46 (41%), Gaps = 4/46 (8%)
Query: 57 LATLPKGGPPIHIA----QEKADQIGYMPLRDDFEWQYDNNAESVV 98
L +P + +A + IGY+P R +F W + + V
Sbjct: 27 LGLIPPAKGTVKVAGASPGKGWRHIGYVPQRHEFAWDFPISVAHTV 72
>gnl|CDD|212950 cd12017, SH3_Tks_3, Third Src homology 3 domain of Tyrosine kinase
substrate (Tks) proteins. Tks proteins are Src
substrates and scaffolding proteins that play important
roles in the formation of podosomes and invadopodia, the
dynamic actin-rich structures that are related to cell
migration and cancer cell invasion. Vertebrates contain
two Tks proteins, Tks4 (Tyr kinase substrate with four
SH3 domains) and Tks5 (Tyr kinase substrate with five
SH3 domains), which display partially overlapping but
non-redundant functions. Both associate with the ADAMs
family of transmembrane metalloproteases, which function
as sheddases and mediators of cell and matrix
interactions. Tks5 interacts with N-WASP and Nck, while
Tks4 is essential for the localization of MT1-MMP
(membrane-type 1 matrix metalloproteinase) to
invadopodia. Tks proteins contain an N-terminal Phox
homology (PX) domain and four or five SH3 domains. This
model characterizes the third SH3 domain of Tks
proteins. SH3 domains are protein interaction domains
that bind to proline-rich ligands with moderate affinity
and selectivity, preferentially to PxxP motifs. They
play versatile and diverse roles in the cell including
the regulation of enzymes, changing the subcellular
localization of signaling pathway components, and
mediating the formation of multiprotein complex
assemblies.
Length = 53
Score = 24.7 bits (54), Expect = 8.3
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 165 SPENGAVVNVLDFGSGGWWF 184
S + G V V+D GWW+
Sbjct: 17 SFQKGQKVEVIDKNPSGWWY 36
>gnl|CDD|237625 PRK14147, PRK14147, heat shock protein GrpE; Provisional.
Length = 172
Score = 26.5 bits (58), Expect = 8.5
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 4/29 (13%)
Query: 125 LRERA----RRKRVVKDFQLIPKFFNAQL 149
LRERA +RKR+ +D + KF N +L
Sbjct: 42 LRERADLENQRKRIARDVEQARKFANEKL 70
>gnl|CDD|236686 PRK10416, PRK10416, signal recognition particle-docking protein
FtsY; Provisional.
Length = 318
Score = 27.0 bits (61), Expect = 9.1
Identities = 19/73 (26%), Positives = 34/73 (46%), Gaps = 15/73 (20%)
Query: 106 DTDVDTTLKLVHVDMYINKLRERARRKRVVKDFQLIPKFFNAQLNPETKTVKRKFN-KDD 164
D V+TT ++ I +LRER +RK +KD + + + +L + V++ N ++
Sbjct: 60 DVGVETTEEI------IEELRERVKRKN-LKDPEELKELLKEELAEILEPVEKPLNIEEK 112
Query: 165 SPE-------NGA 170
P NG
Sbjct: 113 KPFVILVVGVNGV 125
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
0.317 0.134 0.394
Gapped
Lambda K H
0.267 0.0583 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,104,657
Number of extensions: 1037782
Number of successful extensions: 963
Number of sequences better than 10.0: 1
Number of HSP's gapped: 961
Number of HSP's successfully gapped: 24
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
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 (21.6 bits)
S2: 57 (26.1 bits)