RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1815
(238 letters)
>gnl|CDD|198182 cd09928, SH2_Cterm_SPT6_like, C-terminal Src homology 2 (SH2)
domain found in Spt6. Spt6 is an essential
transcription elongation factor and histone chaperone
that binds the C-terminal repeat domain (CTD) of RNA
polymerase II. Spt6 contains a tandem SH2 domain with a
novel structure and CTD-binding mode. The tandem SH2
domain binds to a serine 2-phosphorylated CTD peptide in
vitro, whereas its N-terminal SH2 subdomain does not.
CTD binding requires a positively charged crevice in the
C-terminal SH2 subdomain, which lacks the canonical
phospho-binding pocket of SH2 domains. The tandem SH2
domain is apparently required for transcription
elongation in vivo as its deletion in cells is lethal in
the presence of 6-azauracil. 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 = 89
Score = 126 bits (319), Expect = 1e-37
Identities = 50/93 (53%), Positives = 67/93 (72%), Gaps = 5/93 (5%)
Query: 75 RELLSFRYYREECGGMRDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYLPAS-RS 133
L +Y+R +++ E++L++EK+ NP +I Y +SK YPGKFLLSYLPA+ R
Sbjct: 1 EMLNHHKYFRGT----KEEVEKLLKEEKKANPKRIPYAFCVSKKYPGKFLLSYLPANTRV 56
Query: 134 RHEFISVTPEGFRFRGQQFDSVNSLFRWFKEHF 166
RHE++ VTP+GFRFRGQ F SV+SL WFKEHF
Sbjct: 57 RHEYVKVTPDGFRFRGQVFPSVDSLLNWFKEHF 89
>gnl|CDD|198174 cd09918, SH2_Nterm_SPT6_like, N-terminal Src homology 2 (SH2)
domain found in Spt6. N-terminal SH2 domain in Spt6.
Spt6 is an essential transcription elongation factor
and histone chaperone that binds the C-terminal repeat
domain (CTD) of RNA polymerase II. Spt6 contains a
tandem SH2 domain with a novel structure and
CTD-binding mode. The tandem SH2 domain binds to a
serine 2-phosphorylated CTD peptide in vitro, whereas
its N-terminal SH2 subdomain does not. CTD binding
requires a positively charged crevice in the C-terminal
SH2 subdomain, which lacks the canonical
phospho-binding pocket of SH2 domains. The tandem SH2
domain is apparently required for transcription
elongation in vivo as its deletion in cells is lethal
in the presence of 6-azauracil. 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 = 85
Score = 122 bits (309), Expect = 3e-36
Identities = 48/66 (72%), Positives = 54/66 (81%)
Query: 1 MDQGEVIVRPSSKGADHLTVTWKVADDLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLD 60
D GEV++RPSSKG DHLTVTWKVAD +YQHID+ E KEN FSLG+ L IG EE+EDLD
Sbjct: 20 KDVGEVVIRPSSKGVDHLTVTWKVADGVYQHIDIEELNKENPFSLGKELIIGGEEYEDLD 79
Query: 61 EIIARH 66
EIIAR
Sbjct: 80 EIIARF 85
>gnl|CDD|214585 smart00252, SH2, Src homology 2 domains. Src homology 2 domains
bind phosphotyrosine-containing polypeptides via 2
surface pockets. Specificity is provided via
interaction with residues that are distinct from the
phosphotyrosine. Only a single occurrence of a SH2
domain has been found in S. cerevisiae.
Length = 84
Score = 40.3 bits (95), Expect = 6e-05
Identities = 13/71 (18%), Positives = 26/71 (36%), Gaps = 7/71 (9%)
Query: 1 MDQGEVIVRPSSKGADHLTVTWKVADDLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLD 60
G+ +VR S ++ +V +H +R ++ F L G +F L
Sbjct: 20 EGDGDFLVRDSESSPGDYVLSVRV-KGKVKHYRIRRN-EDGKFYLE-----GGRKFPSLV 72
Query: 61 EIIARHVSPMA 71
E++ +
Sbjct: 73 ELVEHYQKNSL 83
Score = 28.3 bits (64), Expect = 0.97
Identities = 18/77 (23%), Positives = 40/77 (51%), Gaps = 7/77 (9%)
Query: 91 RDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYLPASRSRHEFISVTPEGFRF--R 148
R++AE++L+ E + + V S++ PG ++LS + +H I +G +
Sbjct: 10 REEAEKLLKNEGDGD-----FLVRDSESSPGDYVLSVRVKGKVKHYRIRRNEDGKFYLEG 64
Query: 149 GQQFDSVNSLFRWFKEH 165
G++F S+ L ++++
Sbjct: 65 GRKFPSLVELVEHYQKN 81
>gnl|CDD|198173 cd00173, SH2, Src homology 2 (SH2) domain. In general, SH2
domains are involved in signal transduction; they bind
pTyr-containing polypeptide ligands via two surface
pockets, a pTyr and hydrophobic binding pocket,
allowing proteins with SH2 domains to localize to
tyrosine phosphorylated sites. They are present in a
wide array of proteins including: adaptor proteins
(Nck1, Crk, Grb2), scaffolds (Slp76, Shc, Dapp1),
kinases (Src, Syk, Fps, Tec), phosphatases (Shp-1,
Shp-2), transcription factors (STAT1), Ras signaling
molecules (Ras-Gap), ubiquitination factors (c-Cbl),
cytoskeleton regulators (Tensin), signal regulators
(SAP), and phospholipid second messengers (PLCgamma),
amongst others.
Length = 79
Score = 33.2 bits (76), Expect = 0.017
Identities = 10/60 (16%), Positives = 19/60 (31%), Gaps = 5/60 (8%)
Query: 7 IVRPSSKGADHLTVTWKVADDLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLDEIIARH 66
+VR SS ++ + D +H + G F L E++ +
Sbjct: 25 LVRESSSEPGDYVLSVRSGDGKVKHYLIERNEGGYYLLGGSGRT-----FPSLPELVEHY 79
Score = 31.3 bits (71), Expect = 0.071
Identities = 18/72 (25%), Positives = 31/72 (43%), Gaps = 9/72 (12%)
Query: 91 RDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYL-PASRSRHEFISVTPEGFRF-- 147
R++AE +LR + + V S + PG ++LS + +H I G+
Sbjct: 9 REEAERLLRGKPDGT-----FLVRESSSEPGDYVLSVRSGDGKVKHYLIERNEGGYYLLG 63
Query: 148 -RGQQFDSVNSL 158
G+ F S+ L
Sbjct: 64 GSGRTFPSLPEL 75
>gnl|CDD|198216 cd10353, SH2_Nterm_RasGAP, N-terminal Src homology 2 (SH2) domain
found in Ras GTPase-activating protein 1 (GAP). RasGAP
is part of the GAP1 family of GTPase-activating
proteins. The protein is located in the cytoplasm and
stimulates the GTPase activity of normal RAS p21, but
not its oncogenic counterpart. Acting as a suppressor of
RAS function, the protein enhances the weak intrinsic
GTPase activity of RAS proteins resulting in RAS
inactivation, thereby allowing control of cellular
proliferation and differentiation. Mutations leading to
changes in the binding sites of either protein are
associated with basal cell carcinomas. Alternative
splicing results in two isoforms. The shorter isoform
which lacks the N-terminal hydrophobic region, has the
same activity, and is expressed in placental tissues. In
general the longer isoform contains 2 SH2 domains, a SH3
domain, a pleckstrin homology (PH) domain, and a
calcium-dependent phospholipid-binding C2 domain. The
C-terminus contains the catalytic domain of RasGap which
catalyzes the activation of Ras by hydrolyzing GTP-bound
active Ras into an inactive GDP-bound form of Ras. This
model contains the N-terminal SH2 domain. 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 = 33.3 bits (76), Expect = 0.027
Identities = 21/72 (29%), Positives = 33/72 (45%), Gaps = 4/72 (5%)
Query: 91 RDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYLPASRSRHEFISVTPEGFRFRGQ 150
R AEE LRQ + Y + S PG F+LS+L + H I + G+
Sbjct: 28 RTIAEERLRQAGKLG----SYLIRESDRRPGSFVLSFLSRTGVNHFRIIAMCGDYYIGGR 83
Query: 151 QFDSVNSLFRWF 162
+F S++ L ++
Sbjct: 84 RFSSLSDLIGYY 95
>gnl|CDD|236184 PRK08203, PRK08203, hydroxydechloroatrazine ethylaminohydrolase;
Reviewed.
Length = 451
Score = 34.1 bits (79), Expect = 0.054
Identities = 17/46 (36%), Positives = 20/46 (43%), Gaps = 10/46 (21%)
Query: 175 VAVGPGGQTPYGGARQTPGGGHLPYHTPGM--TPHH------RGMP 212
V VGPGG P GH+ TPG+ T HH R +P
Sbjct: 34 VEVGPGGALPQPADEVFDARGHVV--TPGLVNTHHHFYQTLTRALP 77
>gnl|CDD|222023 pfam13281, DUF4071, Domain of unknown function (DUF4071). This
domain is found at the N-terminus of many
serine-threonine kinase-like proteins.
Length = 365
Score = 32.3 bits (74), Expect = 0.21
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 73 NVRELLSFRYYREECGGMRDKAEEVLRQ--EKRNNP 106
++ +F R G R+KA +VL + EK+ P
Sbjct: 171 LIQFQYAFALNRRNKAGDREKALQVLLEALEKKEGP 206
>gnl|CDD|198179 cd09925, SH2_SHC, Src homology 2 (SH2) domain found in SH2 adaptor
protein C (SHC). SHC is involved in a wide variety of
pathways including regulating proliferation,
angiogenesis, invasion and metastasis, and bone
metabolism. An adapter protein, SHC has been implicated
in Ras activation following the stimulation of a number
of different receptors, including growth factors
[insulin, epidermal growth factor (EGF), nerve growth
factor, and platelet derived growth factor (PDGF)],
cytokines [interleukins 2, 3, and 5], erythropoietin,
and granulocyte/macrophage colony-stimulating factor,
and antigens [T-cell and B-cell receptors]. SHC has been
shown to bind to tyrosine-phosphorylated receptors, and
receptor stimulation leads to tyrosine phosphorylation
of SHC. Upon phosphorylation, SHC interacts with another
adapter protein, Grb2, which binds to the Ras GTP/GDP
exchange factor mSOS which leads to Ras activation. SHC
is composed of an N-terminal domain that interacts with
proteins containing phosphorylated tyrosines, a
(glycine/proline)-rich collagen-homology domain that
contains the phosphorylated binding site, and a
C-terminal SH2 domain. SH2 has been shown to interact
with the tyrosine-phosphorylated receptors of EGF and
PDGF and with the tyrosine-phosphorylated C chain of the
T-cell receptor, providing one of the mechanisms of
T-cell-mediated Ras activation. 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 = 104
Score = 30.4 bits (69), Expect = 0.26
Identities = 20/73 (27%), Positives = 37/73 (50%), Gaps = 10/73 (13%)
Query: 88 GGM-RDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYLPASRSRHEFISVTPEG-F 145
G M R AE +L+ + + V S PG+++L+ + + +H + V PEG
Sbjct: 12 GKMSRRDAESLLQTDG-------DFLVRESTTTPGQYVLTGMQNGQPKH-LLLVDPEGVV 63
Query: 146 RFRGQQFDSVNSL 158
R + + F+S++ L
Sbjct: 64 RTKDRVFESISHL 76
>gnl|CDD|198260 cd10397, SH2_Tec_Btk, Src homology 2 (SH2) domain found in Tec
protein, Bruton's tyrosine kinase (Btk). A member of
the Tec protein tyrosine kinase Btk is expressed in bone
marrow, spleen, all hematopoietic cells except T
lymphocytes and plasma cells where it plays a crucial
role in B cell maturation and mast cell activation. Btk
has been shown to interact with GNAQ, PLCG2, protein
kinase D1, B-cell linker, SH3BP5, caveolin 1, ARID3A,
and GTF2I. Most of the Tec family members have a PH
domain (Txk and the short (type 1) splice variant of
Drosophila Btk29A are exceptions), a Tec homology (TH)
domain, a SH3 domain, a SH2 domain, and a protein kinase
catalytic domain. Btk is implicated in the primary
immunodeficiency disease X-linked agammaglobulinemia
(Bruton's agammaglobulinemia). The TH domain consists
of a Zn2+-binding Btk motif and a proline-rich region.
The Btk motif is found in Tec kinases, Ras GAP, and
IGBP. It is crucial for the function of Tec PH domains
and it's lack of presence in Txk is not surprising since
it lacks a PH domain. The type 1 splice form of the
Drosophila homolog also lacks both the PH domain and the
Btk motif. The proline-rich regions are highly
conserved for the most part with the exception of Bmx
whose residues surrounding the PXXP motif are not
conserved (TH-like) and Btk29A which is entirely unique
with large numbers of glycine residues (TH-extended).
Tec family members all lack a C-terminal tyrosine having
an autoinhibitory function in its phosphorylated state.
Two tyrosine phosphorylation (pY) sites have been
identified in Btk: one located in the activation loop of
the catalytic domain which regulates the transition
between open (active) and closed (inactive) states and
the other in its SH3 domain. 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 = 106
Score = 30.2 bits (68), Expect = 0.34
Identities = 16/60 (26%), Positives = 26/60 (43%), Gaps = 11/60 (18%)
Query: 91 RDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYL------PASRSRHEFISVTPEG 144
R +AE++L+QE K F+ + GK+ +S P RH + TP+
Sbjct: 15 RSQAEQLLKQE-----GKEGGFIVRDSSKAGKYTVSVFAKSAGDPQGVIRHYVVCSTPQS 69
>gnl|CDD|198180 cd09926, SH2_CRK_like, Src homology 2 domain found in
cancer-related signaling adaptor protein CRK. SH2
domain in the CRK proteins. CRKI (SH2-SH3) and CRKII
(SH2-SH3-SH3) are splicing isoforms of the oncoprotein
CRK. CRKs regulate transcription and cytoskeletal
reorganization for cell growth and motility by linking
tyrosine kinases to small G proteins. The SH2 domain of
CRK associates with tyrosine-phosphorylated receptors or
components of focal adhesions, such as p130Cas and
paxillin. CRK transmits signals to small G proteins
through effectors that bind its SH3 domain, such as C3G,
the guanine-nucleotide exchange factor (GEF) for Rap1
and R-Ras, and DOCK180, the GEF for Rac6. The binding of
p130Cas to the CRK-C3G complex activates Rap1, leading
to regulation of cell adhesion, and activates R-Ras,
leading to JNK-mediated activation of cell
proliferation, whereas the binding of CRK DOCK180
induces Rac1-mediated activation of cellular migration.
The activity of the different splicing isoforms varies
greatly with CRKI displaying substantial transforming
activity, CRKII less so, and phosphorylated CRKII with
no biological activity whatsoever. CRKII has a linker
region with a phosphorylated Tyr and an additional
C-terminal SH3 domain. The phosphorylated Tyr creates a
binding site for its SH2 domain which disrupts the
association between CRK and its SH2 target 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 = 106
Score = 30.1 bits (68), Expect = 0.38
Identities = 22/87 (25%), Positives = 40/87 (45%), Gaps = 11/87 (12%)
Query: 91 RDKAEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYLPASRSRHEFISVTPEG------ 144
R +A+E+L+ ++ + V S PG ++LS SR H I+ +
Sbjct: 16 RQEAQELLQGQRHGV-----FLVRDSSTIPGDYVLSVSENSRVSHYIINSLGQPAPNQSR 70
Query: 145 FRFRGQQFDSVNSLFRWFKEHFRDPIP 171
+R Q+FD + +L ++K H+ D
Sbjct: 71 YRIGDQEFDDLPALLEFYKLHYLDTTT 97
>gnl|CDD|198209 cd10346, SH2_SH2B_family, Src homology 2 (SH2) domain found in SH2B
adapter protein family. The SH2B adapter protein family
has 3 members: SH2B1 (SH2-B, PSM), SH2B2 (APS), and
SH2B3 (Lnk). SH2B family members contain a pleckstrin
homology domain, at least one dimerization domain, and a
C-terminal SH2 domain which binds to phosphorylated
tyrosines in a variety of tyrosine kinases. SH2B1 and
SH2B2 function in signaling pathways found downstream
of growth hormone receptor and receptor tyrosine
kinases, including the insulin, insulin-like growth
factor-I (IGF-I), platelet-derived growth factor (PDGF),
nerve growth factor, hepatocyte growth factor, and
fibroblast growth factor receptors. SH2B2beta, a new
isoform of SH2B2, is an endogenous inhibitor of SH2B1
and/or SH2B2 (SH2B2alpha), negatively regulating insulin
signaling and/or JAK2-mediated cellular responses. SH2B3
negatively regulates lymphopoiesis and early
hematopoiesis. The lnk-deficiency results in enhanced
production of B cells, and expansion as well as enhanced
function of hematopoietic stem cells (HSCs),
demonstrating negative regulatory functions of Sh2b3/Lnk
in cytokine signaling. Sh2b3/Lnk also functions in
responses controlled by cell adhesion and in crosstalk
between integrin- and cytokine-mediated signaling. 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 = 97
Score = 28.9 bits (65), Expect = 0.68
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 8/64 (12%)
Query: 111 YFVSLSKNYPGKFLLSYLPASRSRHEFISVTPEGFRFRGQQ--FDSVNSLFRWFKEHFRD 168
+ V S+ G+F+L++ R++H +++ +G + R Q F S+ + EHFR
Sbjct: 35 FLVRQSETRRGEFVLTFNFQGRAKHLRLTLNEKG-QCRVQHLWFPSIFDML----EHFRQ 89
Query: 169 -PIP 171
PIP
Sbjct: 90 NPIP 93
>gnl|CDD|223065 PHA03378, PHA03378, EBNA-3B; Provisional.
Length = 991
Score = 30.4 bits (68), Expect = 0.89
Identities = 17/69 (24%), Positives = 19/69 (27%), Gaps = 3/69 (4%)
Query: 169 PIPGAGVAVGPGGQTPYGGARQTPGGGHLPYHTPGMTPHHRGMPTPLGHHSSNMGGPVLM 228
A PG P A PG P PG P ++ G P
Sbjct: 721 TGRARPPAAAPGRARPPAAA---PGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPTPQ 777
Query: 229 HPPTGTPTP 237
PP P P
Sbjct: 778 PPPQAPPAP 786
>gnl|CDD|151242 pfam10786, G6PD_bact, Glucose-6-phosphate 1-dehydrogenase (EC
1.1.1.49). This family is conserved in Firmicutes and
Proteobacteria. Several members are annotated as being
glucose-6-phosphate 1-dehydrogenase (EC:1.1.1.49) but
this could not be confirmed.
Length = 215
Score = 29.7 bits (67), Expect = 0.99
Identities = 16/64 (25%), Positives = 31/64 (48%), Gaps = 4/64 (6%)
Query: 10 PSSKGADHLTVTWKVADDLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLDEIIA---RH 66
S+ DHLT++ + D + + E E+ F +G+ + + D++E IA R
Sbjct: 148 DESEYDDHLTLS-EYLSDTQKQTQLNLEADEDFFCIGKFAFRDDLQIIDVEEFIAETIRE 206
Query: 67 VSPM 70
+ P+
Sbjct: 207 LLPL 210
>gnl|CDD|187589 cd05328, 3alpha_HSD_SDR_c, alpha hydroxysteroid dehydrogenase
(3alpha_HSD), classical (c) SDRs. Bacterial
3-alpha_HSD, which catalyzes the NAD-dependent
oxidoreduction of hydroxysteroids, is a dimeric member
of the classical SDR family. SDRs are a functionally
diverse family of oxidoreductases that have a single
domain with a structurally conserved Rossmann fold
(alpha/beta folding pattern with a central beta-sheet),
an NAD(P)(H)-binding region, and a structurally diverse
C-terminal region. Classical SDRs are typically about
250 residues long, while extended SDRs are approximately
350 residues. Sequence identity between different SDR
enzymes are typically in the 15-30% range, but the
enzymes share the Rossmann fold NAD-binding motif and
characteristic NAD-binding and catalytic sequence
patterns. These enzymes catalyze a wide range of
activities including the metabolism of steroids,
cofactors, carbohydrates, lipids, aromatic compounds,
and amino acids, and act in redox sensing. Classical
SDRs have an TGXXX[AG]XG cofactor binding motif and a
YXXXK active site motif, with the Tyr residue of the
active site motif serving as a critical catalytic
residue (Tyr-151, human 15-hydroxyprostaglandin
dehydrogenase (15-PGDH) numbering). In addition to the
Tyr and Lys, there is often an upstream Ser (Ser-138,
15-PGDH numbering) and/or an Asn (Asn-107, 15-PGDH
numbering) contributing to the active site; while
substrate binding is in the C-terminal region, which
determines specificity. The standard reaction mechanism
is a 4-pro-S hydride transfer and proton relay involving
the conserved Tyr and Lys, a water molecule stabilized
by Asn, and nicotinamide. Extended SDRs have additional
elements in the C-terminal region, and typically have a
TGXXGXXG cofactor binding motif. Complex (multidomain)
SDRs such as ketoreductase domains of fatty acid
synthase have a GGXGXXG NAD(P)-binding motif and an
altered active site motif (YXXXN). Fungal type ketoacyl
reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
Some atypical SDRs have lost catalytic activity and/or
have an unusual NAD(P)-binding motif and missing or
unusual active site residues. Reactions catalyzed within
the SDR family include isomerization, decarboxylation,
epimerization, C=N bond reduction, dehydratase activity,
dehalogenation, Enoyl-CoA reduction, and
carbonyl-alcohol oxidoreduction.
Length = 250
Score = 29.8 bits (67), Expect = 1.1
Identities = 20/71 (28%), Positives = 26/71 (36%), Gaps = 15/71 (21%)
Query: 154 SVNSLFRWFKEHFRDPIPGAGV---AVGPGG-QTPYGGA-RQTPGGGHLPYHTPGMTPHH 208
S +L W + + GAGV V PG +TP A Q P GG
Sbjct: 154 SKEALTVWTRRRAATWLYGAGVRVNTVAPGPVETPILQAFLQDPRGGESV---------- 203
Query: 209 RGMPTPLGHHS 219
TP+G +
Sbjct: 204 DAFVTPMGRRA 214
>gnl|CDD|198185 cd09931, SH2_C-SH2_SHP_like, C-terminal Src homology 2 (C-SH2)
domain found in SH2 domain Phosphatases (SHP) proteins.
The SH2 domain phosphatases (SHP-1, SHP-2/Syp,
Drosophila corkscrew (csw), and Caenorhabditis elegans
Protein Tyrosine Phosphatase (Ptp-2)) are cytoplasmic
signaling enzymes. They are both targeted and regulated
by interactions of their SH2 domains with
phosphotyrosine docking sites. These proteins contain
two SH2 domains (N-SH2, C-SH2) followed by a tyrosine
phosphatase (PTP) domain, and a C-terminal extension.
Shp1 and Shp2 have two tyrosyl phosphorylation sites in
their C-tails, which are phosphorylated differentially
by receptor and nonreceptor PTKs. Csw retains the
proximal tyrosine and Ptp-2 lacks both sites.
Shp-binding proteins include receptors, scaffolding
adapters, and inhibitory receptors. Some of these bind
both Shp1 and Shp2 while others bind only one. Most
proteins that bind a Shp SH2 domain contain one or more
immuno-receptor tyrosine-based inhibitory motifs
(ITIMs): [SIVL]xpYxx[IVL]. Shp1 N-SH2 domain blocks the
catalytic domain and keeps the enzyme in the inactive
conformation, and is thus believed to regulate the
phosphatase activity of SHP-1. Its C-SH2 domain is
thought to be involved in searching for phosphotyrosine
activators. The SHP2 N-SH2 domain is a conformational
switch; it either binds and inhibits the phosphatase, or
it binds phosphoproteins and activates the enzyme. The
C-SH2 domain contributes binding energy and specificity,
but it does not have a direct role in activation. Csw
SH2 domain function is essential, but either SH2 domain
can fulfill this requirement. The role of the csw SH2
domains during Sevenless receptor tyrosine kinase (SEV)
signaling is to bind Daughter of Sevenless rather than
activated SEV. Ptp-2 acts in oocytes downstream of
sheath/oocyte gap junctions to promote major sperm
protein (MSP)-induced MAP Kinase (MPK-1)
phosphorylation. Ptp-2 functions in the oocyte
cytoplasm, not at the cell surface to inhibit multiple
RasGAPs, resulting in sustained Ras activation. It is
thought that MSP triggers PTP-2/Ras activation and ROS
production to stimulate MPK-1 activity essential for
oocyte maturation and that secreted MSP domains and
Cu/Zn superoxide dismutases function antagonistically to
control ROS and MAPK signaling. 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 = 99
Score = 28.4 bits (64), Expect = 1.2
Identities = 18/74 (24%), Positives = 35/74 (47%), Gaps = 6/74 (8%)
Query: 94 AEEVLRQEKRNNPNKIHYFVSLSKNYPGKFLLSYL-PASRSRHEFISVTPEGFRFRG-QQ 151
AE++L ++ + + V S++ PG F+LS + H I + G ++
Sbjct: 12 AEKLLLEKGKPGS----FLVRESQSKPGDFVLSVRTDDDKVTHIMIRCQGGKYDVGGGEE 67
Query: 152 FDSVNSLFRWFKEH 165
FDS+ L +K++
Sbjct: 68 FDSLTDLVEHYKKN 81
>gnl|CDD|198186 cd09932, SH2_C-SH2_PLC_gamma_like, C-terminal Src homology 2
(C-SH2) domain in Phospholipase C gamma. Phospholipase
C gamma is a signaling molecule that is recruited to
the C-terminal tail of the receptor upon
autophosphorylation of a highly conserved tyrosine.
PLCgamma is composed of a Pleckstrin homology (PH)
domain followed by an elongation factor (EF) domain, 2
catalytic regions of PLC domains that flank 2 tandem
SH2 domains (N-SH2, C-SH2), and ending with a SH3
domain and C2 domain. N-SH2 SH2 domain-mediated
interactions represent a crucial step in transmembrane
signaling by receptor tyrosine kinases. SH2 domains
recognize phosphotyrosine (pY) in the context of
particular sequence motifs in receptor phosphorylation
sites. Both N-SH2 and C-SH2 have a very similar binding
affinity to pY. But in growth factor stimulated cells
these domains bind to different target proteins. N-SH2
binds to pY containing sites in the C-terminal tails of
tyrosine kinases and other receptors. Recently it has
been shown that this interaction is mediated by
phosphorylation-independent interactions between a
secondary binding site found exclusively on the N-SH2
domain and a region of the FGFR1 tyrosine kinase
domain. This secondary site on the SH2 cooperates with
the canonical pY site to regulate selectivity in
mediating a specific cellular process. C-SH2 binds to
an intramolecular site on PLCgamma itself which allows
it to hydrolyze phosphatidylinositol-4,5-bisphosphate
into diacylglycerol and inositol triphosphate. These
then activate protein kinase C and release calcium. 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 = 104
Score = 28.4 bits (64), Expect = 1.3
Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 9/60 (15%)
Query: 4 GEVIVRPSSKGADHLTVTWKVADDLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLDEII 63
G +VRPS + ++++ A+ +H +++EG R IGT +FE L E++
Sbjct: 27 GAFLVRPSETDPNSFAISFR-AEGKIKHCRIKQEG--------RLFVIGTSQFESLVELV 77
>gnl|CDD|184889 PRK14895, gltX, glutamyl-tRNA synthetase; Provisional.
Length = 513
Score = 29.7 bits (66), Expect = 1.5
Identities = 18/69 (26%), Positives = 32/69 (46%)
Query: 58 DLDEIIARHVSPMAANVRELLSFRYYREECGGMRDKAEEVLRQEKRNNPNKIHYFVSLSK 117
D D + ++ V + N +LL YREE GG +++ + + + Y + L+
Sbjct: 318 DNDSLTSKTVEILEQNYNKLLRKLAYREEFGGNTERSTAAYIDIREDASTGLTYKLPLAV 377
Query: 118 NYPGKFLLS 126
P KF +S
Sbjct: 378 ELPKKFKVS 386
>gnl|CDD|220029 pfam08812, YtxC, YtxC-like family. This family includes proteins
similar to B. subtilis YtxC an uncharacterized protein.
Length = 220
Score = 29.0 bits (66), Expect = 1.6
Identities = 20/100 (20%), Positives = 45/100 (45%), Gaps = 22/100 (22%)
Query: 63 IARHVSPMAANV----------RELLSFRYY---REECGGMRDKAEEVLRQEKRNNPNKI 109
+++ A+ R+++ Y+ +EE + + A +L+ E+++ P++I
Sbjct: 1 FRHYIANALADFIVEHKEKELIRKIIEENYFFLDQEEKEQILEIAHSILKGERKDLPSEI 60
Query: 110 HYFVSLSKNYPGKFLLSYLPASRSRHEFISVTPEGF-RFR 148
+ KN K +L +L + I++ +GF FR
Sbjct: 61 YKLN--RKNLIIKKILEFLEENNE----INI--DGFVTFR 92
>gnl|CDD|215658 pfam00017, SH2, SH2 domain.
Length = 77
Score = 27.5 bits (62), Expect = 1.6
Identities = 11/60 (18%), Positives = 21/60 (35%), Gaps = 7/60 (11%)
Query: 4 GEVIVRPSSKGADHLTVTWKVADDLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLDEII 63
G +VR S T++ + D +H ++ + G F L E++
Sbjct: 22 GTFLVRESESKPGDYTLSVR-DDGRVKHYRIQSLDNGGYYISGG------VTFNSLPELV 74
>gnl|CDD|180659 PRK06690, PRK06690, acetyl-CoA acetyltransferase; Provisional.
Length = 361
Score = 29.3 bits (66), Expect = 1.8
Identities = 13/32 (40%), Positives = 15/32 (46%), Gaps = 4/32 (12%)
Query: 174 GVAVGPGGQTPYGGARQTPGGGHLPYHTPGMT 205
G VGPGG AR + L H PG+T
Sbjct: 50 GNVVGPGGNV----ARLSALEAGLGLHIPGVT 77
>gnl|CDD|233652 TIGR01951, nusB, transcription antitermination factor NusB. A
transcription antitermination complex active in many
bacteria was designated N-utilization substance (Nus)
in E. coli because of its interaction with phage lambda
protein N. This model represents NusB. Other components
are NusA and NusG. NusE is, in fact, ribosomal protein
S10 [Transcription, Transcription factors].
Length = 129
Score = 27.1 bits (61), Expect = 5.3
Identities = 12/45 (26%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 25 ADDLYQHIDVREEGKENSFSLGRSLWIGT-EEFEDLDEIIARHVS 68
+++ + EE E R L G E E++DE+I+ H+
Sbjct: 22 LEEIIEEFLEEEELDEEDREYFRELVRGVLENQEEIDELISPHLE 66
>gnl|CDD|237695 PRK14376, PRK14376, hypothetical protein; Provisional.
Length = 176
Score = 27.2 bits (60), Expect = 5.6
Identities = 18/58 (31%), Positives = 21/58 (36%), Gaps = 14/58 (24%)
Query: 168 DPIPGA--GVAVGPGGQTPYGGARQTPGGG------------HLPYHTPGMTPHHRGM 211
DP+PG G +VGPG G +T GG P G HRG
Sbjct: 106 DPVPGEAPGTSVGPGTVRKPRGRTRTAGGPVGAVDAGTPHRSRRPTGGHGTASLHRGT 163
>gnl|CDD|236561 PRK09550, mtnK, methylthioribose kinase; Reviewed.
Length = 401
Score = 27.9 bits (63), Expect = 5.7
Identities = 12/44 (27%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 23 KVAD-DLYQHIDVREEGKENSFSLGRSLWIGTEEFEDLDEIIAR 65
VAD D + ++R E + ++ LGR L + ++ ++++IA
Sbjct: 350 HVADLDTIEDPELRAEAERHALKLGRELILNRDKIASIEDLIAL 393
>gnl|CDD|198395 cd10448, GIY-YIG_unchar_3, GIY-YIG domain of uncharacterized
hypothetical protein found in bacteria. The family
includes a group of uncharacterized bacterial proteins
with a GIY-YIG domain that shows statistically
significant similarity to the N-terminal catalytic
domains of GIY-YIG family of intron-encoded homing
endonuclease I-TevI and catalytic GIY-YIG domain of
nucleotide excision repair endonuclease UvrC.
Length = 87
Score = 26.3 bits (59), Expect = 5.8
Identities = 17/46 (36%), Positives = 26/46 (56%), Gaps = 6/46 (13%)
Query: 24 VADDLYQHIDVREEGKENSFS----LGRSLWIGTEEFEDLDEIIAR 65
V DL + I +EG + F+ + R ++ EEFED++E IAR
Sbjct: 18 VTSDLIRRIYEHKEGLGSGFTSKYNVTRLVYY--EEFEDIEEAIAR 61
>gnl|CDD|221787 pfam12815, CTD, Spt5 C-terminal nonapeptide repeat binding Spt4.
The C-terminal domain of the transcription elongation
factor protein Spt5 is necessary for binding to Spt4 to
form the functional complex that regulates early
transcription elongation by RNA polymerase II. The
complex may be involved in pre-mRNA processing through
its association with mRNA capping enzymes. This CTD
domain carries a regular nonapeptide repeat that can be
present in up to 18 copies, as in S. pombe. The repeat
has a characteristic TPA motif.
Length = 112
Score = 26.6 bits (59), Expect = 6.3
Identities = 14/41 (34%), Positives = 15/41 (36%), Gaps = 1/41 (2%)
Query: 180 GGQTPYGGARQTPGGGHLPYHTPGMTPHHRGMPTPLGHHSS 220
GG Y GA TPG P + G PTP S
Sbjct: 69 GGSGSYLGAS-TPGAAPTPAKSAPTPGAWGGAPTPGYSADS 108
>gnl|CDD|233383 TIGR01373, soxB, sarcosine oxidase, beta subunit family,
heterotetrameric form. This model describes the beta
subunit of a family of known and putative
heterotetrameric sarcosine oxidases. Five operons of
such oxidases are found in Mesorhizobium loti and three
in Agrobacterium tumefaciens, a high enough copy number
to suggest that not all members are share the same
function. The model is designated as subfamily rather
than equivalog for this reason. Sarcosine oxidase
catalyzes the oxidative demethylation of sarcosine to
glycine. The reaction converts tetrahydrofolate to
5,10-methylene-tetrahydrofolate. The enzyme is known in
monomeric and heterotetrameric (alpha,beta,gamma,delta)
forms [Energy metabolism, Amino acids and amines].
Length = 407
Score = 27.1 bits (60), Expect = 8.2
Identities = 12/42 (28%), Positives = 17/42 (40%), Gaps = 4/42 (9%)
Query: 167 RDPIPGAGVAVGPGGQTPYGGARQTPGGGHLPYHTPGMTPHH 208
+ P+P + G G GG + TP G + HT H
Sbjct: 351 KTPLPNLYLNCGWG----TGGFKATPASGTVFAHTLARGEPH 388
>gnl|CDD|165528 PHA03270, PHA03270, envelope glycoprotein C; Provisional.
Length = 466
Score = 27.2 bits (60), Expect = 9.9
Identities = 16/67 (23%), Positives = 17/67 (25%), Gaps = 8/67 (11%)
Query: 171 PGAGVAVGPGGQTPYGGARQTPGGGHLPYHTPGMTPHHRGMPTPLGHHSSNMGGPVLMHP 230
GAG G +PG P TP T P P P
Sbjct: 21 AGAGAPRGAVSNASEAPTSGSPGSAEGPRTTPTPTRGKGTPTGP--------ASPPKSGP 72
Query: 231 PTGTPTP 237
P P P
Sbjct: 73 PKSPPAP 79
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
0.318 0.138 0.435
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,094,690
Number of extensions: 1285222
Number of successful extensions: 1329
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1317
Number of HSP's successfully gapped: 54
Length of query: 238
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 144
Effective length of database: 6,768,326
Effective search space: 974638944
Effective search space used: 974638944
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 (21.7 bits)
S2: 57 (25.7 bits)