RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy4163
(85 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 = 74.7 bits (184), Expect = 3e-19
Identities = 24/49 (48%), Positives = 32/49 (65%)
Query: 17 QHVGRSVSRHELFPIRANFMALEHCIAPFLNKCDADDDHLITLKEWARC 65
+ +SR EL P+RA + +EHCI PF CDAD D LI+L+EW +C
Sbjct: 64 TNHDGYLSRSELAPLRAPLVPMEHCIKPFFKSCDADKDGLISLREWCKC 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 = 73.9 bits (182), Expect = 7e-19
Identities = 25/61 (40%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 17 QHVGRSVSRHELFPIRANFMALEHCIAPFLNKCDADDDHLITLKEWARCLELNEDEIEDQ 76
+ +S HEL PIR EHCI PF CD D D I+L EW C + ED++ +
Sbjct: 59 GNYDGKLSHHELAPIR--LDPNEHCIKPFFESCDLDKDGSISLDEWCYCF-IKEDDLCEA 115
Query: 77 C 77
C
Sbjct: 116 C 116
>gnl|CDD|223128 COG0050, TufB, GTPases - translation elongation factors
[Translation, ribosomal structure and biogenesis].
Length = 394
Score = 28.8 bits (65), Expect = 0.30
Identities = 13/34 (38%), Positives = 15/34 (44%), Gaps = 8/34 (23%)
Query: 42 IAPFLNKCDADDDHLITLKEWARCLELNEDEIED 75
I FLNK D DD LEL E E+ +
Sbjct: 131 IVVFLNKVDMVDD--------EELLELVEMEVRE 156
>gnl|CDD|132755 cd07070, NR_LBD_SF-1, The ligand binding domain of nuclear
receptor steroidogenic factor 1, a member of nuclear
receptor superfamily. The ligand binding domain of
nuclear receptor steroidogenic factor 1 (SF-1): SF-1, a
member of the nuclear hormone receptor superfamily, is
an essential regulator of endocrine development and
function and is considered a master regulator of
reproduction. Most nuclear receptors function as
homodimer or heterodimers, however SF-1 binds to its
target genes as a monomer, recognizing the variations
of the DNA sequence motif, T/CCA AGGTCA. SF-1 functions
cooperatively with other transcription factors to
modulate gene expression. Phospholipids have been
determined as potential ligands of SF-1. Like other
members of the nuclear receptor (NR) superfamily of
ligand-activated transcription factors, SF-1 has a
central well conserved DNA binding domain (DBD), a
variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 237
Score = 28.4 bits (63), Expect = 0.31
Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 43 APFLNKCDADDDHLITLKEWAR-CLELNEDEIEDQCEDVRN 82
APF C D I++ +WAR C+ E E+ DQ ++N
Sbjct: 38 APFGLLCRMADQTFISIVDWARRCMVFKELEVADQMTLLQN 78
>gnl|CDD|237184 PRK12736, PRK12736, elongation factor Tu; Reviewed.
Length = 394
Score = 27.2 bits (61), Expect = 0.87
Identities = 10/18 (55%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 45 FLNKCDA-DDDHLITLKE 61
FLNK D DD+ L+ L E
Sbjct: 134 FLNKVDLVDDEELLELVE 151
>gnl|CDD|178673 PLN03127, PLN03127, Elongation factor Tu; Provisional.
Length = 447
Score = 27.1 bits (60), Expect = 1.1
Identities = 13/27 (48%), Positives = 16/27 (59%), Gaps = 5/27 (18%)
Query: 45 FLNKCDA-DDDHLITLKEWARCLELNE 70
FLNK D DD+ L+ L E +EL E
Sbjct: 183 FLNKVDVVDDEELLELVE----MELRE 205
>gnl|CDD|234596 PRK00049, PRK00049, elongation factor Tu; Reviewed.
Length = 396
Score = 27.1 bits (61), Expect = 1.1
Identities = 11/18 (61%), Positives = 13/18 (72%), Gaps = 1/18 (5%)
Query: 45 FLNKCD-ADDDHLITLKE 61
FLNKCD DD+ L+ L E
Sbjct: 134 FLNKCDMVDDEELLELVE 151
>gnl|CDD|206671 cd01884, EF_Tu, Elongation Factor Tu (EF-Tu) GTP-binding proteins.
EF-Tu subfamily. This subfamily includes orthologs of
translation elongation factor EF-Tu in bacteria,
mitochondria, and chloroplasts. It is one of several
GTP-binding translation factors found in the larger
family of GTP-binding elongation factors. The eukaryotic
counterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this family. EF-Tu is
one of the most abundant proteins in bacteria, as well
as, one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation.
Length = 195
Score = 26.4 bits (59), Expect = 1.5
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 8/31 (25%)
Query: 45 FLNKCDADDDHLITLKEWARCLELNEDEIED 75
FLNK D DD +E LEL E E+ +
Sbjct: 124 FLNKADMVDD-----EEL---LELVEMEVRE 146
>gnl|CDD|183708 PRK12735, PRK12735, elongation factor Tu; Reviewed.
Length = 396
Score = 26.3 bits (59), Expect = 1.9
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 42 IAPFLNKCD-ADDDHLITLKEWARCLELNE 70
I FLNKCD DD+ L+ L E +E+ E
Sbjct: 131 IVVFLNKCDMVDDEELLELVE----MEVRE 156
>gnl|CDD|237743 PRK14515, PRK14515, aspartate ammonia-lyase; Provisional.
Length = 479
Score = 25.7 bits (56), Expect = 3.1
Identities = 11/36 (30%), Positives = 15/36 (41%)
Query: 5 MVKGTAFTASPAQHVGRSVSRHELFPIRANFMALEH 40
M KG SP HV + S ++ FP + L
Sbjct: 127 MEKGDYHYISPNSHVNMAQSTNDAFPTAIHIATLNA 162
>gnl|CDD|234657 PRK00135, scpB, segregation and condensation protein B; Reviewed.
Length = 188
Score = 25.6 bits (57), Expect = 3.2
Identities = 7/23 (30%), Positives = 14/23 (60%)
Query: 57 ITLKEWARCLELNEDEIEDQCED 79
++L++ A LEL E++ E+
Sbjct: 21 LSLEQLAEILELEPTEVQQLLEE 43
>gnl|CDD|129576 TIGR00485, EF-Tu, translation elongation factor TU. This model
models orthologs of translation elongation factor EF-Tu
in bacteria, mitochondria, and chloroplasts, one of
several GTP-binding translation factors found by the
more general pfam model GTP_EFTU. The eukaryotic
conterpart, eukaryotic translation elongation factor 1
(eEF-1 alpha), is excluded from this model. EF-Tu is one
of the most abundant proteins in bacteria, as well as
one of the most highly conserved, and in a number of
species the gene is duplicated with identical function.
When bound to GTP, EF-Tu can form a complex with any
(correctly) aminoacylated tRNA except those for
initiation and for selenocysteine, in which case EF-Tu
is replaced by other factors. Transfer RNA is carried to
the ribosome in these complexes for protein translation
[Protein synthesis, Translation factors].
Length = 394
Score = 25.5 bits (56), Expect = 3.7
Identities = 14/30 (46%), Positives = 18/30 (60%), Gaps = 5/30 (16%)
Query: 42 IAPFLNKCD-ADDDHLITLKEWARCLELNE 70
I FLNKCD DD+ L+ L E +E+ E
Sbjct: 131 IVVFLNKCDMVDDEELLELVE----MEVRE 156
>gnl|CDD|132741 cd06943, NR_LBD_RXR_like, The ligand binding domain of the
retinoid X receptor and Ultraspiracle, members of
nuclear receptor superfamily. The ligand binding
domain of the retinoid X receptor (RXR) and
Ultraspiracle (USP): This family includes two
evolutionary related nuclear receptors: retinoid X
receptor (RXR) and Ultraspiracle (USP). RXR is a
nuclear receptor in mammalian and USP is its
counterpart in invertebrates. The native ligand of
retinoid X receptor is 9-cis retinoic acid (RA). RXR
functions as a DNA binding partner by forming
heterodimers with other nuclear receptors including
CAR, FXR, LXR, PPAR, PXR, RAR, TR, and VDR. RXRs can
play different roles in these heterodimers. It acts
either as a structural component of the heterodimer
complex, required for DNA binding but not acting as a
receptor or as both a structural and a functional
component of the heterodimer, allowing 9-cis RA to
signal through the corresponding heterodimer. In
addition, RXR can also form homodimers, functioning as
a receptor for 9-cis RA, independently of other nuclear
receptors. Ultraspiracle (USP) plays similar roles as
DNA binding partner of other nuclear rec eptors in
invertebrates. USP has no known high-affinity ligand
and is thought to be a silent component in the
heterodimeric complex with partner receptors. Like
other members of the nuclear receptor (NR) superfamily
of ligand-activated transcription factors, RXR and USP
have a central well conserved DNA binding domain (DBD),
a variable N-terminal domain, a flexible hinge and a
C-terminal ligand binding domain (LBD).
Length = 207
Score = 25.3 bits (56), Expect = 4.3
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 43 APFLNKCDADDDHLITLKEWARCL-ELNEDEIEDQ 76
P N C A D L L EWA+ + +E ++DQ
Sbjct: 30 DPVSNICQAADKQLFQLVEWAKRIPHFSELPLDDQ 64
>gnl|CDD|187843 cd09712, Cas10d_I-D, CRISPR/Cas system-associated protein Cas10d.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Large proteins, some contain Zn-finger domain. Fused to
N-terminal HD domain; signature gene for I-D subtype;
also known as Csc3 family.
Length = 900
Score = 24.9 bits (54), Expect = 6.5
Identities = 12/69 (17%), Positives = 18/69 (26%), Gaps = 17/69 (24%)
Query: 15 PAQHVGRSVSRHELFPIRANFMALEHCIAPF----LNK-CDADDDHLITLKEWARCLELN 69
++ + + L IA F +K C A D +LN
Sbjct: 16 TLWNLLQQLEFTVLNVKE-----RRLLIAGFTLHDYHKHCHAQDM-------PNDEFDLN 63
Query: 70 EDEIEDQCE 78
EI
Sbjct: 64 IQEIIPIIL 72
>gnl|CDD|233825 TIGR02344, chap_CCT_gamma, T-complex protein 1, gamma subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
gamma chain (part of a paralogous family) from animals,
plants, fungi, and other eukaryotes.
Length = 525
Score = 24.7 bits (54), Expect = 7.6
Identities = 7/21 (33%), Positives = 15/21 (71%)
Query: 60 KEWARCLELNEDEIEDQCEDV 80
++W R L++ E+ ++ CED+
Sbjct: 258 EDWNRILQMEEEYVQLMCEDI 278
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
0.321 0.134 0.416
Gapped
Lambda K H
0.267 0.0708 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,217,768
Number of extensions: 327160
Number of successful extensions: 275
Number of sequences better than 10.0: 1
Number of HSP's gapped: 274
Number of HSP's successfully gapped: 16
Length of query: 85
Length of database: 10,937,602
Length adjustment: 53
Effective length of query: 32
Effective length of database: 8,586,840
Effective search space: 274778880
Effective search space used: 274778880
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 (24.2 bits)