RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2690
(125 letters)
>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 = 55.8 bits (135), Expect = 3e-11
Identities = 28/113 (24%), Positives = 39/113 (34%), Gaps = 11/113 (9%)
Query: 4 CPGHKKREFLKGLMEYFMNTMLSQKNTTTSATEEGTFSTGDEQ--------VATWNFGTL 55
C + EF + L ++F N DEQ W F L
Sbjct: 3 CTDSELAEFPRRLRDWFKNLHEDLYERRELVDHYSELLKRDEQKNYPMCKDPLGWMFNQL 62
Query: 56 DLDKNKVLEQEEWKNFRNLISQQKQLRRCGKKLPRHCDANNDKKISLSEWLNC 108
D + + L + E R + + C K + CDA+ D ISL EW C
Sbjct: 63 DTNHDGYLSRSELAPLR---APLVPMEHCIKPFFKSCDADKDGLISLREWCKC 112
>gnl|CDD|238155 cd00252, SPARC_EC, SPARC_EC; extracellular Ca2+ binding domain
(containing 2 EF-hand motifs) of SPARC and related
proteins (QR1, SC1/hevin, testican and tsc-36/FRP).
SPARC (BM-40) is a multifunctional glycoprotein, a
matricellular protein, that functions to regulate
cell-matrix interactions; binds to such proteins as
collagen and vitronectin and binds to endothelial cells
thus inhibiting cellular proliferation. The EC domain
interacts with a follistatin-like (FS) domain which
appears to stabilize Ca2+ binding. The two EF-hands
interact canonically but their conserved disulfide bonds
confer a tight association between the EF-hand pair and
an acid/amphiphilic N-terminal helix. Proposed active
form involves a Ca2+ dependent symmetric
homodimerization of EC-FS modules.
Length = 116
Score = 38.9 bits (91), Expect = 9e-05
Identities = 19/62 (30%), Positives = 22/62 (35%), Gaps = 5/62 (8%)
Query: 48 ATWNFGTLDLDKNKVLEQEEWKNFRNLISQQKQLRRCGKKLPRHCDANNDKKISLSEWLN 107
W F LD + + L E R L C K CD + D ISL EW
Sbjct: 50 VGWMFNQLDGNYDGKLSHHELAPIR-LD----PNEHCIKPFFESCDLDKDGSISLDEWCY 104
Query: 108 CL 109
C
Sbjct: 105 CF 106
>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 = 34.8 bits (81), Expect = 0.001
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 52 FGTLDLDKNKVLEQEEWKNFRNLISQQKQLRRCGKKLPRHCDANNDKKISLSEWL 106
F D D + + +E K + + ++ R D + D KI E+L
Sbjct: 6 FRLFDKDGDGTISADELKAALKSLGEGLSEEEI-DEMIREVDKDGDGKIDFEEFL 59
Score = 24.0 bits (53), Expect = 8.9
Identities = 7/22 (31%), Positives = 8/22 (36%)
Query: 90 RHCDANNDKKISLSEWLNCLNV 111
R D + D IS E L
Sbjct: 7 RLFDKDGDGTISADELKAALKS 28
>gnl|CDD|222177 pfam13499, EF_hand_5, EF-hand domain pair.
Length = 60
Score = 30.0 bits (68), Expect = 0.061
Identities = 12/59 (20%), Positives = 24/59 (40%), Gaps = 3/59 (5%)
Query: 54 TLDLDKNKVLEQEEWKNF---RNLISQQKQLRRCGKKLPRHCDANNDKKISLSEWLNCL 109
LD D + ++ EE + L +++ + D + D +IS E+L +
Sbjct: 2 LLDKDGDGYIDVEELRKLLKALGLKLTDEEVEELIEADFNEIDKDGDGRISFEEFLEAM 60
>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 = 25.0 bits (56), Expect = 2.6
Identities = 7/20 (35%), Positives = 10/20 (50%)
Query: 90 RHCDANNDKKISLSEWLNCL 109
R D + D KI E+ + L
Sbjct: 7 RLFDKDGDGKIDFEEFKDLL 26
>gnl|CDD|213327 cd12119, ttLC_FACS_AlkK_like, Fatty acyl-CoA synthetases similar to
LC-FACS from Thermus thermophiles. This family includes
fatty acyl-CoA synthetases that can activate
medium-chain to long-chain fatty acids. They catalyze
the ATP-dependent acylation of fatty acids in a two-step
reaction. The carboxylate substrate first reacts with
ATP to form an acyl-adenylate intermediate, which then
reacts with CoA to produce an acyl-CoA ester. The fatty
acyl-CoA synthetases are responsible for fatty acid
degradation as well as physiological regulation of
cellular functions via the production of fatty acyl-CoA
esters. The fatty acyl-CoA synthetase from Thermus
thermophiles in this family was shown catalyzing the
long-chain fatty acid, myristoyl acid, while another
member in this family, the AlkK protein identified from
Pseudomonas oleovorans, targets medium chain fatty
acids. This family also includes uncharacterized FACS
proteins.
Length = 517
Score = 27.2 bits (61), Expect = 2.9
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 2/22 (9%)
Query: 30 TTTSATEEGTFSTGDEQVATWN 51
T T +G F TGD VA +
Sbjct: 389 KTEELTRDGWFRTGD--VAVID 408
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 26.4 bits (59), Expect = 4.2
Identities = 11/40 (27%), Positives = 19/40 (47%), Gaps = 2/40 (5%)
Query: 5 PGHKKREFLKGLMEYFMNT-MLSQKNTTTSATEEGTFSTG 43
PG K E + LMEY+ ++ +L +K E+ +
Sbjct: 227 PGLSKEEA-RSLMEYYADSGILLKKVDEELVDEKLSLLGN 265
>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 = 23.9 bits (53), Expect = 5.1
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 90 RHCDANNDKKISLSEWLNCLN 110
+ D + D KIS E+ L
Sbjct: 7 KEFDKDGDGKISFEEFKELLK 27
>gnl|CDD|205583 pfam13405, EF_hand_4, EF-hand domain.
Length = 30
Score = 24.1 bits (53), Expect = 6.1
Identities = 6/21 (28%), Positives = 8/21 (38%)
Query: 90 RHCDANNDKKISLSEWLNCLN 110
+ D + D IS E L
Sbjct: 7 KLFDKDGDGYISAEELRKALR 27
>gnl|CDD|191952 pfam08155, NOGCT, NOGCT (NUC087) domain. This C terminal domain
is found in the NOG subfamily of nucleolar GTP-binding
proteins.
Length = 55
Score = 24.2 bits (53), Expect = 7.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 54 TLDLDKNKVLEQEEWKN 70
++DL KN +L EEWK
Sbjct: 19 SVDLRKNYILANEEWKY 35
>gnl|CDD|182093 PRK09819, PRK09819, alpha-mannosidase; Provisional.
Length = 875
Score = 25.7 bits (57), Expect = 8.9
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 9/36 (25%)
Query: 38 GTFSTGDEQVATWNFGTLD----LDKNKVLEQEEWK 69
FS D+Q FG++ V EQE W+
Sbjct: 627 SKFSLADQQ-----FGSITRPVNDPAMDVWEQEGWQ 657
>gnl|CDD|234340 TIGR03744, traC_PFL_4706, conjugative transfer ATPase, PFL_4706
family. Members of this protein family are predicted
ATP-binding proteins apparently associated with DNA
conjugal transfer. Members are found both in plasmids
and in bacterial chromosomal regions that appear to
derive from integrative elements such as conjugative
transposons. More distant homologs, outside the scope of
this family, include type IV secretion/conjugal transfer
proteins such as TraC, VirB4 and TrsE. The granularity
of this protein family definition is chosen so as to
represent one distinctive clade and act as a marker
through which to define and recognize the class of
mobile element it serves [Mobile and extrachromosomal
element functions, Plasmid functions].
Length = 893
Score = 25.8 bits (57), Expect = 9.3
Identities = 10/36 (27%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 55 LDLDKNKVLEQEEWKNFRNLISQQKQLRRCGKKLPR 90
L++ ++V E+ FR L +QK + +K P
Sbjct: 796 LNMPPDEV---EQIARFRELTEEQKAMLLSARKEPG 828
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 0.128 0.389
Gapped
Lambda K H
0.267 0.0908 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,912,214
Number of extensions: 467185
Number of successful extensions: 313
Number of sequences better than 10.0: 1
Number of HSP's gapped: 308
Number of HSP's successfully gapped: 22
Length of query: 125
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 40
Effective length of database: 7,167,512
Effective search space: 286700480
Effective search space used: 286700480
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 (23.9 bits)