RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4977
(63 letters)
>gnl|CDD|227455 COG5126, FRQ1, Ca2+-binding protein (EF-Hand superfamily) [Signal
transduction mechanisms / Cytoskeleton / Cell division
and chromosome partitioning / General function
prediction only].
Length = 160
Score = 47.3 bits (113), Expect = 1e-08
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 15 KRAQRATSNVFAMFDQAQIQNFKEAFNMIDQNRDGFIDKEDLHDMLASL 63
R++ + F + QIQ KEAF + D++ DG ID+ +L +L SL
Sbjct: 1 MRSKISDLLTFTQLTEEQIQELKEAFQLFDRDSDGLIDRNELGKILRSL 49
Score = 30.0 bits (68), Expect = 0.046
Identities = 11/30 (36%), Positives = 19/30 (63%)
Query: 34 QNFKEAFNMIDQNRDGFIDKEDLHDMLASL 63
+ +EAF + D++ DG+I +L +L SL
Sbjct: 92 EELREAFKLFDKDHDGYISIGELRRVLKSL 121
>gnl|CDD|197492 smart00054, EFh, EF-hand, calcium binding motif. EF-hands are
calcium-binding motifs that occur at least in pairs.
Links between disease states and genes encoding
EF-hands, particularly the S100 subclass, are emerging.
Each motif consists of a 12 residue loop flanked on
either side by a 12 residue alpha-helix. EF-hands
undergo a conformational change unpon binding calcium
ions.
Length = 29
Score = 37.7 bits (89), Expect = 6e-06
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDMLASL 63
KEAF + D++ DG ID E+ D+L +L
Sbjct: 2 LKEAFRLFDKDGDGKIDFEEFKDLLKAL 29
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 36.4 bits (85), Expect = 3e-05
Identities = 12/28 (42%), Positives = 18/28 (64%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDMLASL 63
+EAF + D++ DG+I E+L L SL
Sbjct: 2 LREAFKLFDKDGDGYISAEELRKALRSL 29
>gnl|CDD|200946 pfam00036, efhand, EF hand. The EF-hands can be divided into two
classes: signaling proteins and buffering/transport
proteins. The first group is the largest and includes
the most well-known members of the family such as
calmodulin, troponin C and S100B. These proteins
typically undergo a calcium-dependent conformational
change which opens a target binding site. The latter
group is represented by calbindin D9k and do not
undergo calcium dependent conformational changes.
Length = 29
Score = 35.5 bits (83), Expect = 5e-05
Identities = 11/28 (39%), Positives = 16/28 (57%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDMLASL 63
KEAF D++ DG I E+ ++L L
Sbjct: 2 LKEAFKEFDKDGDGKISFEEFKELLKKL 29
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse
superfamily of calcium sensors and calcium signal
modulators; most examples in this alignment model have
2 active canonical EF hands. Ca2+ binding induces a
conformational change in the EF-hand motif, leading to
the activation or inactivation of target proteins.
EF-hands tend to occur in pairs or higher copy numbers.
Length = 63
Score = 33.3 bits (77), Expect = 9e-04
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDMLASL 63
+EAF + D++ DG I ++L L SL
Sbjct: 2 LREAFRLFDKDGDGTISADELKAALKSL 29
Score = 28.7 bits (65), Expect = 0.046
Identities = 8/26 (30%), Positives = 15/26 (57%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDMLA 61
E +D++ DG ID E+ +++A
Sbjct: 38 IDEMIREVDKDGDGKIDFEEFLELMA 63
>gnl|CDD|205383 pfam13202, EF_hand_3, EF hand.
Length = 25
Score = 31.5 bits (73), Expect = 0.002
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDML 60
K+ F D N DG I KE+L +L
Sbjct: 1 LKDLFRQFDTNGDGKISKEELKRLL 25
>gnl|CDD|185504 PTZ00184, PTZ00184, calmodulin; Provisional.
Length = 149
Score = 31.3 bits (71), Expect = 0.013
Identities = 14/37 (37%), Positives = 23/37 (62%)
Query: 27 MFDQAQIQNFKEAFNMIDQNRDGFIDKEDLHDMLASL 63
+ QI FKEAF++ D++ DG I ++L ++ SL
Sbjct: 4 QLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSL 40
Score = 24.0 bits (52), Expect = 5.2
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 27 MFDQAQIQNFKEAFNMIDQNRDGFIDKEDLHDMLASL 63
M D + KEAF + D++ +GFI +L ++ +L
Sbjct: 77 MKDTDSEEEIKEAFKVFDRDGNGFISAAELRHVMTNL 113
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 27.3 bits (61), Expect = 0.17
Identities = 9/22 (40%), Positives = 17/22 (77%)
Query: 42 MIDQNRDGFIDKEDLHDMLASL 63
++D++ DG+ID E+L +L +L
Sbjct: 2 LLDKDGDGYIDVEELRKLLKAL 23
Score = 27.3 bits (61), Expect = 0.19
Identities = 8/25 (32%), Positives = 14/25 (56%)
Query: 36 FKEAFNMIDQNRDGFIDKEDLHDML 60
+ FN ID++ DG I E+ + +
Sbjct: 36 IEADFNEIDKDGDGRISFEEFLEAM 60
>gnl|CDD|223014 PHA03231, PHA03231, glycoprotein BALF4; Provisional.
Length = 829
Score = 27.6 bits (62), Expect = 0.31
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 7/53 (13%)
Query: 16 RAQRATSNVF---AMF--DQAQIQNFKEAFNMIDQNRDGFIDKEDLHDMLASL 63
R + SNVF +F Q F + N+ID +R+ F+ L + + L
Sbjct: 621 RDELRDSNVFDLEEIFREYNLYKQRFYDIDNVIDNDRNAFVR--GLAEFMQGL 671
>gnl|CDD|216369 pfam01214, CK_II_beta, Casein kinase II regulatory subunit.
Length = 183
Score = 27.1 bits (61), Expect = 0.42
Identities = 9/29 (31%), Positives = 15/29 (51%), Gaps = 3/29 (10%)
Query: 30 QAQIQNFKEAFNMIDQNRDGFIDKEDLHD 58
++ N+KEA ++I D + E L D
Sbjct: 33 SEEVPNYKEALDLI---LDKEPESESLDD 58
>gnl|CDD|185503 PTZ00183, PTZ00183, centrin; Provisional.
Length = 158
Score = 26.6 bits (59), Expect = 0.75
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 32 QIQNFKEAFNMIDQNRDGFIDKEDLHDMLASL 63
Q + +EAF++ D + G ID ++L + SL
Sbjct: 15 QKKEIREAFDLFDTDGSGTIDPKELKVAMRSL 46
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 25.6 bits (57), Expect = 0.77
Identities = 8/24 (33%), Positives = 11/24 (45%)
Query: 40 FNMIDQNRDGFIDKEDLHDMLASL 63
F D + DG I E+ +L L
Sbjct: 30 FREFDTDGDGKISFEEFCVLLQRL 53
>gnl|CDD|235072 PRK02812, PRK02812, ribose-phosphate pyrophosphokinase;
Provisional.
Length = 330
Score = 26.6 bits (59), Expect = 0.79
Identities = 15/39 (38%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 4 RKTAGRRATTKKR-----AQRATSNVFAM-FDQAQIQNF 36
RKTAGR + T K + V AM AQIQ +
Sbjct: 117 RKTAGRESITAKLVANLITKAGADRVLAMDLHSAQIQGY 155
>gnl|CDD|180947 PRK07366, PRK07366, succinyldiaminopimelate transaminase;
Validated.
Length = 388
Score = 26.2 bits (58), Expect = 1.0
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 15 KRAQRATSNVFAMFDQAQIQNFKEAFNMID 44
+R Q SNVFA D+A+ Q +ID
Sbjct: 5 QRLQPLQSNVFADMDRAKAQARAAGKELID 34
>gnl|CDD|224021 COG1096, COG1096, Predicted RNA-binding protein (consists of S1
domain and a Zn-ribbon domain) [Translation, ribosomal
structure and biogenesis].
Length = 188
Score = 25.4 bits (56), Expect = 1.7
Identities = 11/42 (26%), Positives = 20/42 (47%), Gaps = 1/42 (2%)
Query: 13 TKKRAQRATSNVFAMFDQ-AQIQNFKEAFNMIDQNRDGFIDK 53
T R QRA + + + ++ A + Q RDG+++K
Sbjct: 73 TDVREQRALVRIVGVEGKERELATSGAADIHVSQVRDGYVEK 114
>gnl|CDD|233984 TIGR02722, lp_, uncharacterized proteobacterial lipoprotein.
Members of this protein family are restricted to the
Proteobacteria, and all are predicted lipoproteins. In
genomes that contain the thiK gene for the salvage
enzyme thiamin kinase, the member of this family is
encoded nearby [Cell envelope, Other].
Length = 189
Score = 25.5 bits (56), Expect = 1.9
Identities = 9/45 (20%), Positives = 15/45 (33%), Gaps = 2/45 (4%)
Query: 9 RRATTKKRAQRATSNVFAMFDQAQIQNFKEAFNMIDQNRDGFIDK 53
T K R S F + D + +E Q G +++
Sbjct: 88 ESLTDKIRTALLQSGKFVLTDAQALDRMREQLGY--QAESGLVNQ 130
>gnl|CDD|198175 cd09919, SH2_STAT_family, Src homology 2 (SH2) domain found in
signal transducer and activator of transcription (STAT)
family. STAT proteins mediate the signaling of
cytokines and a number of growth factors from the
receptors of these extracellular signaling molecules to
the cell nucleus. STATs are specifically
phosphorylated by receptor-associated Janus kinases,
receptor tyrosine kinases, or cytoplasmic tyrosine
kinases. The phosphorylated STAT molecules dimerize by
reciprocal binding of their SH2 domains to the
phosphotyrosine residues. These dimeric STATs
translocate into the nucleus, bind to specific DNA
sequences, and regulate the transcription of their
target genes. However there are a number of
unphosphorylated STATs that travel between the
cytoplasm and nucleus and some STATs that exist as
dimers in unstimulated cells that can exert biological
functions independent of being activated by a receptor.
There are seven mammalian STAT family members which
have been identified: STAT1, STAT2, STAT3, STAT4, STAT5
(STAT5A and STAT5B), and STAT6. There are 6 conserved
domains in STAT: N-terminal domain (NTD), coiled-coil
domain (CCD), DNA-binding domain (DBD), alpha-helical
linker domain (LD), SH2 domain, and transactivation
domain (TAD). NTD is involved in dimerization of
unphosphorylated STATs monomers and for the
tetramerization between STAT1, STAT3, STAT4 and STAT5
on promoters with two or more tandem STAT binding
sites. It also plays a role in promoting interactions
with transcriptional co-activators such as CREB binding
protein (CBP)/p300, as well as being important for
nuclear import and deactivation of STATs involving
tyrosine de-phosphorylation. The CCD interacts with
other proteins, such as IFN regulatory protein 9
(IRF-9/p48) with STAT1 and c-JUN with STAT3 and is also
thought to participate in the negative regulation of
these proteins. Distinct genes are bound to STATs via
their DBD domain. This domain is also involved in
nuclear translocation of activated STAT1 and STAT3
phosphorylated dimers upon cytokine stimulation. LD
links the DNA-binding and SH2 domains and is important
for the transcriptional activation of STAT1 in response
to IFN-gamma. It also plays a role in protein-protein
interactions and has also been implicated in the
constitutive nucleocytoplasmic shuttling of
unphosphorylated STATs in resting cells. The SH2
domain is necessary for receptor association and
tyrosine phosphodimer formation. Residues within this
domain may be particularly important for some cellular
functions mediated by the STATs as well as residues
adjacent to this domain. The TAD interacts with
several proteins, namely minichromosome maintenance
complex component 5 (MCM5), breast cancer 1 (BRCA1) and
CBP/p300. TAD also contains a modulatory
phosphorylation site that regulates STAT activity and
is necessary for maximal transcription of a number of
target genes. The conserved tyrosine residue present in
the C-terminus is crucial for dimerization via
interaction with the SH2 domain upon the interaction of
the ligand with the receptor. STAT activation by
tyrosine phosphorylation also determines nuclear import
and retention, DNA binding to specific DNA elements in
the promoters of responsive genes, and transcriptional
activation of STAT dimers. In addition to the SH2
domain there is a coiled-coil domain, a DNA binding
domain, and a transactivation domain in the STAT
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 = 115
Score = 24.5 bits (54), Expect = 3.6
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 49 GFIDKEDLHDMLASL 63
GFI KE+ D+L
Sbjct: 24 GFISKEEAEDLLKKK 38
>gnl|CDD|215863 pfam00332, Glyco_hydro_17, Glycosyl hydrolases family 17.
Length = 310
Score = 24.6 bits (54), Expect = 4.1
Identities = 9/24 (37%), Positives = 14/24 (58%)
Query: 9 RRATTKKRAQRATSNVFAMFDQAQ 32
++ T K+ + VFAMFD+ Q
Sbjct: 262 KKGTPKRPGWAIETYVFAMFDENQ 285
>gnl|CDD|219018 pfam06419, COG6, Conserved oligomeric complex COG6. COG6 is a
component of the conserved oligomeric golgi complex,
which is composed of eight different subunits and is
required for normal golgi morphology and localisation.
Length = 615
Score = 24.6 bits (54), Expect = 4.5
Identities = 6/50 (12%), Positives = 18/50 (36%)
Query: 10 RATTKKRAQRATSNVFAMFDQAQIQNFKEAFNMIDQNRDGFIDKEDLHDM 59
+ + + +++ + + A NMI + D + +L +
Sbjct: 488 EQIDELVDELTELQASYLLEESGLGDLYNALNMIFFDYDDYEPLSELPLL 537
>gnl|CDD|235589 PRK05749, PRK05749, 3-deoxy-D-manno-octulosonic-acid transferase;
Reviewed.
Length = 425
Score = 24.4 bits (54), Expect = 4.9
Identities = 11/33 (33%), Positives = 13/33 (39%), Gaps = 2/33 (6%)
Query: 33 IQNFKEAFNMIDQNRDGFI--DKEDLHDMLASL 63
NFKE F + Q D EDL + L
Sbjct: 353 TFNFKEIFERLLQAGAAIQVEDAEDLAKAVTYL 385
>gnl|CDD|204523 pfam10591, SPARC_Ca_bdg, Secreted protein acidic and rich in
cysteine Ca binding region. The SPARC_Ca_bdg domain of
Secreted Protein Acidic and Rich in Cysteine is
responsible for the anti-spreading activity of human
urothelial cells. It is rich in alpha-helices. This
extracellular calcium-binding domain contains two
EF-hands that each coordinates one Ca2+ ion, forming a
helix-loop-helix structure that not only drives the
conformation of the protein but is also necessary for
biological activity. The anti-spreading activity was
dependent on the coordination of Ca2+ by a Glu residue
at the Z position of EF-hand 2.
Length = 112
Score = 23.9 bits (52), Expect = 6.1
Identities = 9/24 (37%), Positives = 15/24 (62%)
Query: 40 FNMIDQNRDGFIDKEDLHDMLASL 63
FN +D N DG++ + +L + A L
Sbjct: 59 FNQLDTNHDGYLSRSELAPLRAPL 82
>gnl|CDD|183550 PRK12480, PRK12480, D-lactate dehydrogenase; Provisional.
Length = 330
Score = 24.1 bits (52), Expect = 6.7
Identities = 9/39 (23%), Positives = 18/39 (46%)
Query: 20 ATSNVFAMFDQAQIQNFKEAFNMIDQNRDGFIDKEDLHD 58
A + +FD+A + K+ +++ R I+ DL
Sbjct: 208 ANKESYHLFDKAMFDHVKKGAILVNAARGAVINTPDLIA 246
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
0.320 0.128 0.343
Gapped
Lambda K H
0.267 0.0699 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 2,988,241
Number of extensions: 201689
Number of successful extensions: 272
Number of sequences better than 10.0: 1
Number of HSP's gapped: 272
Number of HSP's successfully gapped: 28
Length of query: 63
Length of database: 10,937,602
Length adjustment: 34
Effective length of query: 29
Effective length of database: 9,429,566
Effective search space: 273457414
Effective search space used: 273457414
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 53 (24.3 bits)