RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11352
(107 letters)
>gnl|CDD|200998 pfam00096, zf-C2H2, Zinc finger, C2H2 type. The C2H2 zinc finger
is the classical zinc finger domain. The two conserved
cysteines and histidines co-ordinate a zinc ion. The
following pattern describes the zinc finger.
#-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C] Where X can
be any amino acid, and numbers in brackets indicate the
number of residues. The positions marked # are those
that are important for the stable fold of the zinc
finger. The final position can be either his or cys.
The C2H2 zinc finger is composed of two short beta
strands followed by an alpha helix. The amino terminal
part of the helix binds the major groove in DNA binding
zinc fingers. The accepted consensus binding sequence
for Sp1 is usually defined by the asymmetric
hexanucleotide core GGGCGG but this sequence does not
include, among others, the GAG (=CTC) repeat that
constitutes a high-affinity site for Sp1 binding to the
wt1 promoter.
Length = 22
Score = 26.5 bits (59), Expect = 0.56
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 53 TCFVCGKQLSNQYNLRVHMETH 74
C CGK S + NL+ H+ TH
Sbjct: 1 KCPDCGKSFSRKSNLKRHLRTH 22
>gnl|CDD|235256 PRK04210, PRK04210, phosphoenolpyruvate carboxykinase;
Provisional.
Length = 601
Score = 27.5 bits (62), Expect = 1.3
Identities = 9/26 (34%), Positives = 15/26 (57%)
Query: 67 LRVHMETHQNAFYACSSCSHVSRSRD 92
++++ E N+F A S S V+R D
Sbjct: 53 IKLNPEKRPNSFLARSDPSDVARVED 78
>gnl|CDD|197676 smart00355, ZnF_C2H2, zinc finger.
Length = 23
Score = 25.1 bits (55), Expect = 1.8
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 53 TCFVCGKQLSNQYNLRVHMETH 74
C CGK ++ LR HM TH
Sbjct: 2 RCPECGKVFKSKSALREHMRTH 23
>gnl|CDD|213357 cd12823, Mrs2_Mfm1p-like, Saccharomyces cerevisiae inner
mitochondrial membrane Mg2+ transporters Mfm1p and
Mrs2p-like family. A eukaryotic subfamily belonging to
the Escherichia coli CorA-Salmonella typhimurium
ZntB_like family (EcCorA_ZntB-like) family of the MIT
superfamily of essential membrane proteins involved in
transporting divalent cations (uptake or efflux) across
membranes. This functionally diverse subfamily includes
the inner mitochondrial membrane Mg2+ transporters
Saccharomyces cerevisiae Mfm1p/Lpe10p, Mrs2p, and human
MRS2/ MRS2L. It also includes a family of Arabidopsis
thaliana proteins (AtMGTs) some of which are localized
to distinct tissues, and not all of which can transport
Mg2+. Structures of the intracellular domain of two
EcCorA_ZntB-like family transporters: Vibrio
parahaemolyticus and Salmonella typhimurium ZntB form
funnel-shaped homopentamers, the tip of the funnel is
formed from two C-terminal transmembrane (TM) helices
from each monomer, and the large opening of the funnel
from the N-terminal cytoplasmic domains. The GMN
signature motif of the MIT superfamily occurs just after
TM1, mutation within this motif is known to abolish Mg2+
transport through Salmonella typhimurium CorA, and
Mrs2p. Natural variants such as GVN and GIN, as in some
ZntB family proteins, may be associated with the
transport of different divalent cations, such as zinc
and cadmium. The functional diversity of MIT
transporters may also be due to minor structural
differences regulating gating, substrate selection, and
transport.
Length = 323
Score = 26.8 bits (60), Expect = 2.5
Identities = 6/20 (30%), Positives = 9/20 (45%)
Query: 66 NLRVHMETHQNAFYACSSCS 85
NL +E AF+ + S
Sbjct: 284 NLPSGLEESPYAFWIVTGGS 303
>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX
protein family. The first LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group are
found in the nucleus and act as transcription factors
or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Is l2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 25.0 bits (55), Expect = 3.1
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 6/41 (14%)
Query: 54 CFVCGKQLSNQYNLRVH--METHQNAFYACSSCSHVSRSRD 92
C CG ++ +QY LRV +E H AC C+ + D
Sbjct: 1 CVGCGGKIHDQYILRVAPDLEWHA----ACLKCAECGQYLD 37
>gnl|CDD|224875 COG1964, COG1964, Predicted Fe-S oxidoreductases [General function
prediction only].
Length = 475
Score = 26.6 bits (59), Expect = 3.1
Identities = 8/32 (25%), Positives = 13/32 (40%), Gaps = 3/32 (9%)
Query: 76 NAFYACSSCSHVSRSRDAL---RKHVSYRHPH 104
+ +Y +SR +AL K+ HP
Sbjct: 276 DDWYPVPIAVPISRFVEALTGDPKYELTSHPA 307
>gnl|CDD|215124 PLN02195, PLN02195, cellulose synthase A.
Length = 977
Score = 26.5 bits (58), Expect = 3.8
Identities = 7/31 (22%), Positives = 15/31 (48%)
Query: 54 CFVCGKQLSNQYNLRVHMETHQNAFYACSSC 84
C CG+++ N + H+ ++ C +C
Sbjct: 9 CATCGEEVGVDSNGEAFVACHECSYPLCKAC 39
>gnl|CDD|215494 PLN02915, PLN02915, cellulose synthase A [UDP-forming], catalytic
subunit.
Length = 1044
Score = 26.4 bits (58), Expect = 3.9
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 47 HSKLFATCFVCGKQLSNQYNLRVHMETHQNAFYACSSCSHVSRS 90
S TC VCG ++ + + + + H F C C RS
Sbjct: 11 QSADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYEYERS 54
>gnl|CDD|224663 COG1749, FlgE, Flagellar hook protein FlgE [Cell motility and
secretion].
Length = 423
Score = 26.2 bits (58), Expect = 4.3
Identities = 8/26 (30%), Positives = 12/26 (46%)
Query: 23 LSSSIPGSSKTKASGSGTTGGSSNHS 48
S S+ G+S A G G + S +
Sbjct: 45 FSQSLVGASTYTALGVGVSSISQIFT 70
>gnl|CDD|220232 pfam09421, FRQ, Frequency clock protein. The frequency clock
protein, is the central component of the frq-based
circadian negative feedback loop, regulates various
aspects of the circadian clock in Neurospora crassa.
This protein has been shown to interact with itself via
a coiled-coil.
Length = 989
Score = 26.1 bits (57), Expect = 4.6
Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 7/46 (15%)
Query: 3 FHYKPSTLHFLISDHCLT-------SPLSSSIPGSSKTKASGSGTT 41
FHYKP +H S + P+ S S+ SGSGTT
Sbjct: 591 FHYKPLFVHQHSSSEETSLEEGSSQGPVEESNNADSRWGFSGSGTT 636
>gnl|CDD|221587 pfam12458, DUF3686, ATPase involved in DNA repair. This domain
family is found in bacteria, and is approximately 450
amino acids in length. There are two conserved sequence
motifs: DVF and SPNGED.
Length = 448
Score = 26.0 bits (58), Expect = 4.9
Identities = 8/10 (80%), Positives = 8/10 (80%)
Query: 97 HVSYRHPHIS 106
HV RHPHIS
Sbjct: 178 HVLGRHPHIS 187
>gnl|CDD|221427 pfam12114, Period_C, Period protein 2/3C-terminal region. This
domain is found in eukaryotes. This domain is typically
between 164 to 200 amino acids in length. This domain
is found associated with pfam08447.
Length = 190
Score = 25.5 bits (56), Expect = 5.3
Identities = 14/35 (40%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 21 SPLSSSIPGSSKTKASGSGTTG-GSSNHSKLFATC 54
S S S S + SGS + GSSN SK F +
Sbjct: 26 SAASGSGSSGSGSLGSGSNGSSSGSSNSSKYFGSI 60
>gnl|CDD|234400 TIGR03924, T7SS_EccC_a, type VII secretion protein EccCa. This
model represents the N-terminal domain or EccCa subunit
of the type VII secretion protein EccC as found in the
Actinobacteria. Type VII secretion is defined more
broadly as including secretion systems for ESAT-6-like
proteins in the Firmicutes as well as in the
Actinobacteria, but this family does not show close
homologs in the Firmicutes [Protein fate, Protein and
peptide secretion and trafficking].
Length = 661
Score = 25.7 bits (57), Expect = 5.5
Identities = 6/18 (33%), Positives = 9/18 (50%)
Query: 87 VSRSRDALRKHVSYRHPH 104
V + A R + +RHP
Sbjct: 82 VRETAAAQRAALLWRHPD 99
>gnl|CDD|190954 pfam04360, Serglycin, Serglycin. Serglycin is the most prevalent
proteoglycan produced in haemopoietic cells. Serglycin
is a proteinase resistant secretory granule
proteoglycan.
Length = 150
Score = 25.3 bits (55), Expect = 5.8
Identities = 11/23 (47%), Positives = 12/23 (52%)
Query: 22 PLSSSIPGSSKTKASGSGTTGGS 44
PLS GS SGSG+ GS
Sbjct: 86 PLSEDYSGSGSGSGSGSGSGSGS 108
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 0.127 0.395
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,891,502
Number of extensions: 351744
Number of successful extensions: 412
Number of sequences better than 10.0: 1
Number of HSP's gapped: 409
Number of HSP's successfully gapped: 36
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
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 (21.8 bits)
S2: 53 (24.2 bits)