RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7155
(169 letters)
>gnl|CDD|190261 pfam02257, RFX_DNA_binding, RFX DNA-binding domain. RFX is a
regulatory factor which binds to the X box of MHC class
II genes and is essential for their expression. The
DNA-binding domain of RFX is the central domain of the
protein and binds ssDNA as either a monomer or
homodimer.
Length = 73
Score = 116 bits (292), Expect = 1e-34
Identities = 40/62 (64%), Positives = 49/62 (79%)
Query: 88 TVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLG 147
+QWL DN E +EG SLPR+ ++ HY+ HCAE L ++AASFGKLIRSVF GL+TRRLG
Sbjct: 8 ALQWLRDNCEESEGSSLPRNRVYAHYVSHCAELGLKPLSAASFGKLIRSVFPGLKTRRLG 67
Query: 148 TR 149
TR
Sbjct: 68 TR 69
>gnl|CDD|239836 cd04371, DEP, DEP domain, named after Dishevelled, Egl-10, and
Pleckstrin, where this domain was first discovered. The
function of this domain is still not clear, but it is
believed to be important for the membrane association of
the signaling proteins in which it is present. New
studies show that the DEP domain of Sst2, a yeast RGS
protein is necessary and sufficient for receptor
interaction.
Length = 81
Score = 27.3 bits (61), Expect = 1.6
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 3/32 (9%)
Query: 89 VQWLIDNYET---AEGVSLPRSSLFNHYIRHC 117
V WL+DN E E V L ++ L + I H
Sbjct: 35 VDWLLDNLEAITREEAVELGQALLKHGLIHHV 66
>gnl|CDD|152381 pfam11946, DUF3463, Domain of unknown function (DUF3463). This
presumed domain is functionally uncharacterized. This
domain is found in bacteria and archaea. This domain is
about 140 amino acids in length. This domain is found
associated with pfam04055. This domain has two conserved
sequence motifs: CTPWG and PCYL.
Length = 141
Score = 26.9 bits (60), Expect = 3.4
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 6/27 (22%)
Query: 132 KLIRSVFIGLRTRRLGTRRGWRFLSSS 158
+L R +F RLG + WRF S
Sbjct: 26 ELFREIF------RLGKGKKWRFNHSP 46
>gnl|CDD|198270 cd10407, SH2_Vav3, Src homology 2 (SH2) domain found in the Vav3
proteins. Proto-oncogene vav is a member of the Dbl
family of guanine nucleotide exchange factors (GEF) for
the Rho family of GTP binding proteins. All vavs are
activated by tyrosine phosphorylation leading to their
activation. There are three Vav mammalian family
members: Vav1 which is expressed in the hematopoietic
system, and Vav2 and Vav3 are more ubiquitously
expressed. Vav3 preferentially activates RhoA, RhoG
and, to a lesser extent, Rac1. Alternatively spliced
transcript variants encoding different isoforms have
been described for this gene. VAV3 has been shown to
interact with Grb2. Vav proteins are involved in
several processes that require cytoskeletal
reorganization, such as the formation of the
immunological synapse (IS), phagocytosis, platelet
aggregation, spreading, and transformation. Vavs
function as guanine nucleotide exchange factors (GEFs)
for the Rho/Rac family of GTPases. Vav family members
have several conserved motifs/domains including: a
leucine-rich region, a leucine-zipper, a calponin
homology (CH) domain, an acidic domain, a Dbl-homology
(DH) domain, a pleckstrin homology (PH) domain, a
cysteine-rich domain, 2 SH3 domains, a proline-rich
region, and a SH2 domain. Vavs are the only known Rho
GEFs that have both the DH/PH motifs and SH2/SH3
domains in the same protein. The leucine-rich
helix-loop-helix (HLH) domain is thought to be involved
in protein heterodimerization with other HLH proteins
and it may function as a negative regulator by forming
inactive heterodimers. The CH domain is usually
involved in the association with filamentous actin, but
in Vav it controls NFAT stimulation, Ca2+ mobilization,
and its transforming activity. Acidic domains are
involved in protein-protein interactions and contain
regulatory tyrosines. The DH domain is a GDP-GTP
exchange factor on Rho/Rac GTPases. The PH domain in
involved in interactions with GTP-binding proteins,
lipids and/or phosphorylated serine/threonine residues.
The SH3 domain is involved in localization of proteins
to specific sites within the cell interacting with
protein with proline-rich sequences. The SH2 domain
mediates a high affinity interaction with tyrosine
phosphorylated proteins. In general SH2 domains are
involved in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 103
Score = 26.5 bits (58), Expect = 3.9
Identities = 13/29 (44%), Positives = 18/29 (62%), Gaps = 1/29 (3%)
Query: 7 APAQLIGNVNGTYLIQ-QTVEPTEHATII 34
A +LI VN TYL++ +T E E+A I
Sbjct: 17 AETELINRVNSTYLVRHRTKESGEYAISI 45
>gnl|CDD|215203 PLN02355, PLN02355, probable galactinol--sucrose
galactosyltransferase 1.
Length = 758
Score = 27.2 bits (60), Expect = 4.9
Identities = 19/53 (35%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 101 GVSLPRSSLF---NHYIRHCAENKLDAVNAASFGKLIRSVFIGLRTRRLGTRR 150
G+S+ +L N + +N L V AS G LI FIG+R+ ++G+RR
Sbjct: 6 GISVADGNLVVLGNRVLHDVHDNVL--VTPASGGALINGAFIGVRSDQVGSRR 56
>gnl|CDD|143323 cd07699, IgC_L, Immunoglobulin Constant domain. IgC_L:
Immunoglobulin (Ig) light chain constant (C) domain. The
basic structure of Ig molecules is a tetramer of two
light chains and two heavy chains linked by disulfide
bonds. In Ig, each chain is composed of one variable
domain (IgV) and one or more constant domains (IgC);
these names reflect the fact that the variability in
sequences is higher in the variable domain than in the
constant domain. There are five types of heavy chains
(alpha, gamma, delta, epsilon, and mu), which determine
the type of immunoglobulin: IgA, IgG, IgD, IgE, and
IgM, respectively. In higher vertebrates, there are two
types of light chain, designated kappa and lambda, which
seem to be functionally identical, and can associate
with any of the heavy chains.
Length = 100
Score = 26.2 bits (58), Expect = 4.9
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 3/33 (9%)
Query: 74 NQASL-SHVTKISP--ATVQWLIDNYETAEGVS 103
+A+L + P ATVQW +D + GV
Sbjct: 18 GKATLVCLINDFYPGFATVQWKVDGATVSSGVQ 50
>gnl|CDD|218792 pfam05880, Fiji_64_capsid, Fijivirus 64 kDa capsid protein. This
family consists of several Fijivirus 64 kDa capsid
proteins.
Length = 559
Score = 27.1 bits (60), Expect = 5.6
Identities = 17/78 (21%), Positives = 31/78 (39%), Gaps = 1/78 (1%)
Query: 71 SPDNQASLSHVT-KISPATVQWLIDNYETAEGVSLPRSSLFNHYIRHCAENKLDAVNAAS 129
+P + + V I ++ L D T + +LP S F +I +N++ +
Sbjct: 51 APHVASDQNTVNIYIKTELLKRLHDRLSTVDTSTLPNISQFKEHITSFFQNEIQPIFQTL 110
Query: 130 FGKLIRSVFIGLRTRRLG 147
I F+G+ T L
Sbjct: 111 GNNEIDPSFVGVTTFGLS 128
>gnl|CDD|177271 PHA00360, II, replication initiation protein.
Length = 421
Score = 26.5 bits (58), Expect = 7.2
Identities = 14/38 (36%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 76 ASLSHVTKISPATVQWLIDNYETAEGVSLPRSSLFNHY 113
A LS + ++ TV++ ID T G+ P SL +HY
Sbjct: 36 ARLSGLN-LAAHTVEYAIDGDLTVSGLKHPFESLPSHY 72
>gnl|CDD|203711 pfam07654, C1-set, Immunoglobulin C1-set domain.
Length = 83
Score = 25.3 bits (56), Expect = 7.6
Identities = 13/39 (33%), Positives = 15/39 (38%), Gaps = 3/39 (7%)
Query: 68 DPLSPDNQASLS-HVTKISPA--TVQWLIDNYETAEGVS 103
P +L VT P TV WL + E EGV
Sbjct: 3 SPEELGKPNTLVCLVTGFYPPDITVTWLKNGQEVTEGVE 41
>gnl|CDD|214651 smart00407, IGc1, Immunoglobulin C-Type.
Length = 75
Score = 25.0 bits (55), Expect = 8.1
Identities = 11/26 (42%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 80 HVTKISPA--TVQWLIDNYETAEGVS 103
V+ P TV WL + E EGVS
Sbjct: 7 LVSGFYPPDITVTWLRNGQEVTEGVS 32
>gnl|CDD|233709 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily
of the penicillin binding proteins includes the member
from E. coli designated penicillin-binding protein 1C.
Members have both transglycosylase and transpeptidase
domains and are involved in forming cross-links in the
late stages of peptidoglycan biosynthesis. All members
of this subfamily are presumed to have the same basic
function [Cell envelope, Biosynthesis and degradation of
murein sacculus and peptidoglycan].
Length = 727
Score = 26.6 bits (59), Expect = 8.1
Identities = 7/50 (14%), Positives = 19/50 (38%), Gaps = 5/50 (10%)
Query: 6 NAPAQLIGNVNGTYLIQQTVEPTEHATIIATTASRDSPHENTEVAYIVDE 55
NA + ++G Y+++ P ++ A + + + +D
Sbjct: 642 NASLIISPPLDGIYILRDPDGPKAALLLVLIAAG-----GASGLYWFLDG 686
>gnl|CDD|129794 TIGR00711, efflux_EmrB, drug resistance transporter, EmrB/QacA
subfamily. This subfamily of drug efflux proteins, a
part of the major faciliator family, is predicted to
have 14 potential membrane-spanning regions. Members
with known activities include EmrB (multiple drug
resistance efflux pump) in E. coli, FarB (antibacterial
fatty acid resistance) in Neisseria gonorrhoeae, TcmA
(tetracenomycin C resistance) in Streptomyces
glaucescens, etc. In most cases, the efflux pump is
described as having a second component encoded in the
same operon, such as EmrA of E. coli [Cellular
processes, Toxin production and resistance, Transport
and binding proteins, Other].
Length = 485
Score = 26.2 bits (58), Expect = 10.0
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 85 SPATVQWLIDNYETAEGVSLP 105
S + VQW+I +Y A +S+P
Sbjct: 35 SLSQVQWVITSYMLANAISIP 55
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
0.314 0.127 0.361
Gapped
Lambda K H
0.267 0.0728 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,062,894
Number of extensions: 688389
Number of successful extensions: 593
Number of sequences better than 10.0: 1
Number of HSP's gapped: 593
Number of HSP's successfully gapped: 24
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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: 55 (25.0 bits)