RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4523
(126 letters)
>gnl|CDD|176359 cd01763, Sumo, Small ubiquitin-related modifier (SUMO). Small
ubiquitin-related modifier (SUMO) proteins are
conjugated to numerous intracellular targets and serve
to modulate protein interaction, localization, activity
or stability. SUMO (also known as "Smt3" and "sentrin"
in other organisms) is linked to several different
pathways, including nucleocytoplasmic transport.
Attachment of SUMO to targets proteins is stimulated by
PIAS (Protein inhibitor of activated STATs) proteins
which serve as E3-like ligases.
Length = 87
Score = 126 bits (319), Expect = 3e-39
Identities = 53/98 (54%), Positives = 62/98 (63%), Gaps = 11/98 (11%)
Query: 4 EKKESKSTDEHINLKVLGQDNNVVQFKIKKGTPLRKLMNAYCERCVSILSVLITLQNLSM 63
EK EHINLKV GQD N V FKIK+ TPL+KLM AYC+R Q LSM
Sbjct: 1 EKSGKGEISEHINLKVKGQDGNEVFFKIKRSTPLKKLMEAYCQR-----------QGLSM 49
Query: 64 STVRFRFDGQAINEQDTPSTLEMEEGDTIEIYQQQTGG 101
++VRF FDGQ I + TP L ME+GD IE+ +QTGG
Sbjct: 50 NSVRFLFDGQRIRDNQTPDDLGMEDGDEIEVMLEQTGG 87
>gnl|CDD|227552 COG5227, SMT3, Ubiquitin-like protein (sentrin) [Posttranslational
modification, protein turnover, chaperones].
Length = 103
Score = 85.7 bits (212), Expect = 5e-23
Identities = 42/100 (42%), Positives = 56/100 (56%), Gaps = 11/100 (11%)
Query: 2 TEEKKESKSTDEHINLKVLGQDNNVVQFKIKKGTPLRKLMNAYCERCVSILSVLITLQNL 61
T E K +HINLKV+ QD + FKIKK T +KLM+A+ R Q
Sbjct: 12 TNENPLVKPITKHINLKVVDQDGTELFFKIKKTTTFKKLMDAFSRR-----------QGK 60
Query: 62 SMSTVRFRFDGQAINEQDTPSTLEMEEGDTIEIYQQQTGG 101
+MS++RF FDG+ I+ TP L+ME+ D IE +Q GG
Sbjct: 61 NMSSLRFLFDGKRIDLDQTPGDLDMEDNDEIEAVTEQVGG 100
>gnl|CDD|192903 pfam11976, Rad60-SLD, Ubiquitin-2 like Rad60 SUMO-like. The
small ubiquitin-related modifier SUMO-1 is a Ub/Ubl
family member, and although SUMO-1 shares structural
similarity to Ub, SUMO's cellular functions remain
distinct insomuch as SUMO modification alters protein
function through changes in activity, cellular
localisation, or by protecting substrates from
ubiquitination. Rad60 family members contain
functionally enigmatic, integral SUMO-like domains
(SLDs). Despite their divergence from SUMO, each Rad60
SLD interacts with a subset of SUMO pathway enzymes:
SLD2 specifically binds the SUMO E2 conjugating enzyme
(Ubc9)), whereas SLD1 binds the SUMO E1 (Fub2, also
called Uba2) activating and E3 (Pli1, also called Siz1
and Siz2) specificity enzymes. Structural analysis of
PDB:2uyz reveals a mechanistic basis for the
near-synonymous roles of Rad60 and SUMO in survival of
genotoxic stress and suggest unprecedented
DNA-damage-response functions for SLDs in regulating
SUMOylation. The Rad60 branch of this family is also
known as RENi (Rad60-Esc2-Nip45), and biologically it
should be two distinct families SUMO and RENi
(Rad60-Esc2-Nip45).
Length = 72
Score = 73.3 bits (181), Expect = 2e-18
Identities = 26/82 (31%), Positives = 44/82 (53%), Gaps = 12/82 (14%)
Query: 15 INLKVLGQDNNVVQFKIKKGTPLRKLMNAYCERCVSILSVLITLQNLSMST-VRFRFDGQ 73
I +K+ G+D V K+K T L KL+NAY ++ + + VR FDG+
Sbjct: 1 IRIKLKGKDGKEVFIKVKPTTTLSKLINAYRKK-----------RGIPADQQVRLIFDGE 49
Query: 74 AINEQDTPSTLEMEEGDTIEIY 95
++ DT + ++E+GDTI++
Sbjct: 50 RLDPNDTVADYDIEDGDTIDVV 71
>gnl|CDD|214563 smart00213, UBQ, Ubiquitin homologues. Ubiquitin-mediated
proteolysis is involved in the regulated turnover of
proteins required for controlling cell cycle
progression.
Length = 72
Score = 41.5 bits (98), Expect = 4e-06
Identities = 13/81 (16%), Positives = 28/81 (34%), Gaps = 11/81 (13%)
Query: 15 INLKVLGQDNNVVQFKIKKGTPLRKLMNAYCERCVSILSVLITLQNLSMSTVRFRFDGQA 74
I L V D + ++K + +L E + R + G+
Sbjct: 1 IELTVKTLDGKTITLEVKPSDTVSELKEKIAEL-----------TGIPPEQQRLIYKGKV 49
Query: 75 INEQDTPSTLEMEEGDTIEIY 95
+ + T + +++G TI +
Sbjct: 50 LEDDRTLADYGIQDGSTIHLV 70
>gnl|CDD|215813 pfam00240, ubiquitin, Ubiquitin family. This family contains a
number of ubiquitin-like proteins: SUMO (smt3
homologue), Nedd8, Elongin B, Rub1, and Parkin. A
number of them are thought to carry a distinctive
five-residue motif termed the proteasome-interacting
motif (PIM), which may have a biologically significant
role in protein delivery to proteasomes and recruitment
of proteasomes to transcription sites.
Length = 69
Score = 33.0 bits (76), Expect = 0.005
Identities = 9/77 (11%), Positives = 28/77 (36%), Gaps = 11/77 (14%)
Query: 23 DNNVVQFKIKKGTPLRKLMNAYCERCVSILSVLITLQNLSMSTVRFRFDGQAINEQDTPS 82
D + ++ + +L ++ + + + R F G+ + + T S
Sbjct: 4 DGKTITLEVDPSDTVSELKEKIEDK-----------EGIPVDQQRLIFSGKVLEDDTTLS 52
Query: 83 TLEMEEGDTIEIYQQQT 99
+++G T+ + +
Sbjct: 53 EYGIQDGSTLHLVLRLR 69
>gnl|CDD|176352 cd00196, UBQ, Ubiquitin-like proteins. Ubiquitin homologs;
Includes ubiquitin and ubiquitin-like proteins.
Ubiquitin-mediated proteolysis is part of the regulated
turnover of proteins required for controlling cell
cycle progression. Other family members are protein
modifiers that perform a wide range of functions.
Ubiquitination usually results in a covalent bond
between the C-terminus of ubiquitin and the
epsilon-amino group of a substrate lysine. The
three-step mechanism requires an activating enzyme (E1)
that forms a thiol ester with the C-terminal carboxy
group, a conjugating enzyme (E2) that transiently
carries the activated ubiquitin molecule as a thiol
ester, and a ligase (E3) that transfers the activated
ubiquitin from the E2 to the substrate lysine residue.
In poly-ubiquitination, ubiquitin itself is the
substrate.
Length = 69
Score = 30.2 bits (68), Expect = 0.075
Identities = 13/80 (16%), Positives = 28/80 (35%), Gaps = 11/80 (13%)
Query: 18 KVLGQDNNVVQFKIKKGTPLRKLMNAYCERCVSILSVLITLQNLSMSTVRFRFDGQAINE 77
KV D V+ + GT + L ++ L R +G+ + +
Sbjct: 1 KVKLNDGKTVELLVPSGTTVADLKEKLAKK-----------LGLPPEQQRLLVNGKILPD 49
Query: 78 QDTPSTLEMEEGDTIEIYQQ 97
T +++GD + + +
Sbjct: 50 SLTLEDYGLQDGDELVLVPR 69
>gnl|CDD|219382 pfam07346, DUF1477, Protein of unknown function (DUF1477). This
family consists of several hypothetical
Nucleopolyhedrovirus proteins of around 100 resides in
length. The function of this family is unknown.
Length = 115
Score = 28.8 bits (65), Expect = 0.38
Identities = 8/29 (27%), Positives = 17/29 (58%)
Query: 44 YCERCVSILSVLITLQNLSMSTVRFRFDG 72
+ E C+S ++ T +L++ T++ FD
Sbjct: 39 FYELCISFITSASTGNSLALPTLKNLFDT 67
>gnl|CDD|212690 cd00174, SH3, Src Homology 3 domain superfamily. Src Homology 3
(SH3) domains are protein interaction domains that bind
proline-rich ligands with moderate affinity and
selectivity, preferentially to PxxP motifs. Thus, they
are referred to as proline-recognition domains (PRDs).
SH3 domains are less selective and show more diverse
specificity compared to other PRDs. They have been shown
to bind peptide sequences that lack the PxxP motif;
examples include the PxxDY motif of Eps8 and the
RKxxYxxY sequence in SKAP55. SH3 domain containing
proteins 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, among others. Many members of this
superfamily are adaptor proteins that associate with a
number of protein partners, facilitating complex
formation and signal transduction.
Length = 51
Score = 25.9 bits (58), Expect = 1.4
Identities = 7/37 (18%), Positives = 16/37 (43%), Gaps = 6/37 (16%)
Query: 65 TVRFRFDGQAINEQDTPSTLEMEEGDTIEIYQQQTGG 101
+ ++ Q +E L ++GD I + ++ G
Sbjct: 3 RALYDYEAQDDDE------LSFKKGDIITVLEKDDDG 33
>gnl|CDD|212810 cd11877, SH3_PIX, Src Homology 3 domain of Pak Interactive eXchange
factors. PIX proteins are Rho guanine nucleotide
exchange factors (GEFs), which activate small GTPases by
exchanging bound GDP for free GTP. They act as GEFs for
both Cdc42 and Rac 1, and have been implicated in cell
motility, adhesion, neurite outgrowth, and cell
polarity. Vertebrates contain two proteins from the PIX
subfamily, alpha-PIX and beta-PIX. Alpha-PIX, also
called ARHGEF6, is localized in dendritic spines where
it regulates spine morphogenesis. Mutations in the
ARHGEF6 gene cause X-linked intellectual disability in
humans. Beta-PIX play roles in regulating neuroendocrine
exocytosis, focal adhesion maturation, cell migration,
synaptic vesicle localization, and insulin secretion.
PIX proteins contain an N-terminal SH3 domain followed
by RhoGEF (also called Dbl-homologous or DH) and
Pleckstrin Homology (PH) domains, and a C-terminal
leucine-zipper domain for dimerization. The SH3 domain
of PIX binds to an atypical PxxxPR motif in
p21-activated kinases (PAKs) with high affinity. The
binding of PAKs to PIX facilitate the localization of
PAKs to focal complexes and also localizes PAKs to PIX
targets Cdc43 and Rac, leading to the activation of
PAKs. 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 = 1.5
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 4/37 (10%)
Query: 65 TVRFRFDGQAINEQDTPSTLEMEEGDTIEIYQQQTGG 101
VR +F+ + NE + L ++GD I + Q GG
Sbjct: 1 LVRAKFNFEGTNEDE----LSFDKGDIITVTQVVEGG 33
>gnl|CDD|212778 cd11844, SH3_CAS, Src homology 3 domain of CAS (Crk-Associated
Substrate) scaffolding proteins. CAS proteins function
as molecular scaffolds to regulate protein complexes
that are involved in many cellular processes including
migration, chemotaxis, apoptosis, differentiation, and
progenitor cell function. They mediate the signaling of
integrins at focal adhesions where they localize, and
thus, regulate cell invasion and survival.
Over-expression of these proteins is implicated in poor
prognosis, increased metastasis, and resistance to
chemotherapeutics in many cancers such as breast, lung,
melanoma, and glioblastoma. CAS proteins have also been
linked to the pathogenesis of inflammatory disorders,
Alzheimer's, Parkinson's, and developmental defects.
They share a common domain structure that includes an
N-terminal SH3 domain, an unstructured substrate domain
that contains many YxxP motifs, a serine-rich four-helix
bundle, and a FAT-like C-terminal domain. Vertebrates
contain four CAS proteins: BCAR1 (or p130Cas), NEDD9 (or
HEF1), EFS (or SIN), and CASS4 (or HEPL). The SH3 domain
of CAS proteins binds to diverse partners including FAK,
FRNK, Pyk2, PTP-PEST, DOCK180, among others. 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 = 56
Score = 26.2 bits (58), Expect = 1.7
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 76 NEQDTPSTLEMEEGDTIEIYQQQTGGF 102
N ++P L GD + + +Q T G
Sbjct: 8 NVAESPDELAFRRGDILTVLEQNTAGL 34
>gnl|CDD|205688 pfam13510, Fer2_4, 2Fe-2S iron-sulfur cluster binding domain.
The 2Fe-2S ferredoxin family have a general core
structure consisting of beta(2)-alpha-beta(2) which a
beta-grasp type fold. The domain is around one hundred
amino acids with four conserved cysteine residues to
which the 2Fe-2S cluster is ligated. This cluster
appears within sarcosine oxidase proteins.
Length = 82
Score = 26.3 bits (59), Expect = 1.9
Identities = 9/28 (32%), Positives = 12/28 (42%), Gaps = 9/28 (32%)
Query: 65 TVRFRFDGQAINEQDTPSTLEMEEGDTI 92
V F FDG+ + EGDT+
Sbjct: 3 PVTFTFDGRPV---------TAPEGDTV 21
>gnl|CDD|212994 cd12061, SH3_betaPIX, Src Homology 3 domain of beta-Pak Interactive
eXchange factor. Beta-PIX, also called Rho guanine
nucleotide exchange factor 7 (ARHGEF7) or Cool (Cloned
out of Library)-1, activates small GTPases by exchanging
bound GDP for free GTP. It acts as a GEF for both Cdc42
and Rac 1, and plays important roles in regulating
neuroendocrine exocytosis, focal adhesion maturation,
cell migration, synaptic vesicle localization, and
insulin secretion. PIX proteins contain an N-terminal
SH3 domain followed by RhoGEF (also called
Dbl-homologous or DH) and Pleckstrin Homology (PH)
domains, and a C-terminal leucine-zipper domain for
dimerization. The SH3 domain of PIX binds to an atypical
PxxxPR motif in p21-activated kinases (PAKs) with high
affinity. The binding of PAKs to PIX facilitate the
localization of PAKs to focal complexes and also
localizes PAKs to PIX targets Cdc43 and Rac, leading to
the activation of PAKs. 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 = 54
Score = 25.4 bits (55), Expect = 2.8
Identities = 12/37 (32%), Positives = 20/37 (54%), Gaps = 4/37 (10%)
Query: 66 VRFRFDGQAINEQDTPSTLEMEEGDTIEIYQQQTGGF 102
VR +F+ Q NE + L +GD I + + + GG+
Sbjct: 2 VRAKFNFQQTNEDE----LSFSKGDVIHVTRVEEGGW 34
>gnl|CDD|233039 TIGR00594, polc, DNA-directed DNA polymerase III (polc). All
proteins in this family for which functions are known
are DNA polymerases. This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1022
Score = 27.0 bits (60), Expect = 3.3
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 52 LSVLITLQNLSMSTVRFRFDGQAINEQDTPSTLEM-EEGDTIEIYQQQTGGFKQ 104
L+++ L D +I D T + +EGDT ++Q ++ G +
Sbjct: 563 LTLIQDATELIRKRRGIDLDIASIPLDD-KKTFSLLQEGDTTGVFQLESRGMQD 615
>gnl|CDD|226440 COG3930, COG3930, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 434
Score = 26.8 bits (59), Expect = 3.4
Identities = 9/34 (26%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 71 DGQAINE-QDTPSTLEMEEGDTIEIYQQQTGGFK 103
+ + Q +T+ EE + I +Y+ T GF
Sbjct: 187 AKEVVPILQADLNTVFKEEEEMIRVYESDTAGFV 220
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
0.313 0.129 0.358
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,878,875
Number of extensions: 483986
Number of successful extensions: 345
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 24
Length of query: 126
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 41
Effective length of database: 7,167,512
Effective search space: 293867992
Effective search space used: 293867992
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)