RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16163
(85 letters)
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic
epithelial cells. 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 = 54
Score = 30.8 bits (69), Expect = 0.015
Identities = 10/12 (83%), Positives = 10/12 (83%)
Query: 12 HKGVPYCHVPCY 23
H G PYCHVPCY
Sbjct: 43 HDGSPYCHVPCY 54
>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein
(TLP). The first LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic
epithelial cells. 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 = 54
Score = 27.2 bits (60), Expect = 0.29
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 12 HKGVPYCHVPCY 23
H G PYCH PCY
Sbjct: 43 HDGKPYCHKPCY 54
>gnl|CDD|188122 TIGR01264, tyr_amTase_E, tyrosine aminotransferase, eukaryotic.
This model describes tyrosine aminotransferase as found
in animals and Trypanosoma cruzi. It is the first enzyme
of a pathway of tyrosine degradation via homogentisate.
Several plant enzyme designated as probable tyrosine
aminotransferases are very closely related to an
experimentally demonstrated nicotianamine
aminotransferase, an enzyme in a siderophore (iron
uptake chelator) biosynthesis pathway. These plant
sequences are excluded from the model seed and score
between the trusted an noise cutoffs [Energy metabolism,
Amino acids and amines].
Length = 401
Score = 27.4 bits (61), Expect = 0.68
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 51 PCGSNMPRSHLESKLNLYNQYY 72
PCGS R HLE L + +
Sbjct: 180 PCGSVFSRQHLEEILAVAERQC 201
>gnl|CDD|234621 PRK00082, hrcA, heat-inducible transcription repressor;
Provisional.
Length = 339
Score = 26.7 bits (60), Expect = 1.4
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 3/44 (6%)
Query: 42 TSFGKVENK--PCGSNMPRSHLESKLNLYNQYYDGKS-GEIRSR 82
T G+VEN+ + S LE N N+ G + EIRS+
Sbjct: 155 TDSGRVENRVIELPEGISPSDLEEASNFLNERLVGLTLSEIRSK 198
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short protein with
only one LIM domain. CRIP gene is developmentally
regulated and can be induced by glucocorticoid hormones
during the first three postnatal weeks. The domain
shows close sequence homology to LIM domain of thymus
LIM protein. However, unlike the TLP proteins which
have two LIM domains, the members of this family have
only one LIM domain. 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 = 54
Score = 25.2 bits (55), Expect = 1.9
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 12 HKGVPYCHVPCY 23
H G PYC+ PCY
Sbjct: 43 HDGKPYCNHPCY 54
>gnl|CDD|191652 pfam06961, DUF1294, Protein of unknown function (DUF1294). This
family includes a number of hypothetical bacterial and
archaeal proteins of unknown function.
Length = 55
Score = 24.7 bits (55), Expect = 3.0
Identities = 11/21 (52%), Positives = 11/21 (52%), Gaps = 3/21 (14%)
Query: 24 GALFGPQLFGHGTRVESHTSF 44
GAL QLF H TR SF
Sbjct: 38 GALLAQQLFRHKTR---KQSF 55
>gnl|CDD|215468 PLN02870, PLN02870, Probable galacturonosyltransferase.
Length = 533
Score = 25.7 bits (56), Expect = 3.0
Identities = 22/74 (29%), Positives = 32/74 (43%), Gaps = 8/74 (10%)
Query: 11 THKGVPYCH-VPCYGALFGPQLFGHGTRVESHT-SFGKVENK------PCGSNMPRSHLE 62
T +GV C C G GP+L G E F K+ N+ P G +P S +
Sbjct: 60 TLEGVNKCSSFDCLGRRLGPRLLGRVDDSERLVRDFYKILNEVNTEEIPDGLKLPDSFSQ 119
Query: 63 SKLNLYNQYYDGKS 76
++ N +YD K+
Sbjct: 120 LVSDMKNNHYDAKT 133
>gnl|CDD|173823 cd00314, plant_peroxidase_like, Heme-dependent peroxidases similar
to plant peroxidases. Along with animal peroxidases,
these enzymes belong to a group of peroxidases
containing a heme prosthetic group (ferriprotoporphyrin
IX), which catalyzes a multistep oxidative reaction
involving hydrogen peroxide as the electron acceptor.
The plant peroxidase-like superfamily is found in all
three kingdoms of life and carries out a variety of
biosynthetic and degradative functions. Several
sub-families can be identified. Class I includes
intracellular peroxidases present in fungi, plants,
archaea and bacteria, called catalase-peroxidases, that
can exhibit both catalase and broad-spectrum peroxidase
activities depending on the steady-state concentration
of hydrogen peroxide. Catalase-peroxidases are typically
comprised of two homologous domains that probably arose
via a single gene duplication event. Class II includes
ligninase and other extracellular fungal peroxidases,
while class III is comprised of classic extracellular
plant peroxidases, like horseradish peroxidase.
Length = 255
Score = 25.6 bits (56), Expect = 3.8
Identities = 6/33 (18%), Positives = 9/33 (27%)
Query: 40 SHTSFGKVENKPCGSNMPRSHLESKLNLYNQYY 72
+HT GK + N Y+
Sbjct: 158 AHTLGGKNHGDLLNYEGSGLWTSTPFTFDNAYF 190
>gnl|CDD|188123 TIGR01265, tyr_nico_aTase, tyrosine/nicotianamine family
aminotransferase. This subfamily of pyridoxal
phosphate-dependent enzymes includes known examples of
both tyrosine aminotransferase from animals and
nicotianamine aminotransferase from barley.
Length = 403
Score = 25.4 bits (56), Expect = 4.3
Identities = 7/24 (29%), Positives = 11/24 (45%)
Query: 49 NKPCGSNMPRSHLESKLNLYNQYY 72
+ PCGS R HL+ + +
Sbjct: 179 SNPCGSVFSRDHLQKIAEVAEKLG 202
>gnl|CDD|185613 PTZ00433, PTZ00433, tyrosine aminotransferase; Provisional.
Length = 412
Score = 25.1 bits (55), Expect = 4.5
Identities = 11/27 (40%), Positives = 14/27 (51%), Gaps = 2/27 (7%)
Query: 38 VESHTSFGKVEN--KPCGSNMPRSHLE 62
V+ T + N PCGSN R H+E
Sbjct: 174 VDDRTKALIMTNPSNPCGSNFSRKHVE 200
>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein
(TLP). The LIM domain of thymus LIM protein (TLP) like
proteins: This family includes the LIM domains of TLP
and CRIP (Cysteine-Rich Intestinal Protein). TLP is the
distant member of the CRP family of proteins. TLP has
two isomers (TLP-A and TLP-B) and sharing approximately
30% with each of the three other CRPs. Like CRP1, CRP2
and CRP3/MLP, TLP has two LIM domains, connected by a
flexible linker region. Unlike the CRPs, TLP lacks the
nuclear targeting signal (K/R-K/R-Y-G-P-K) and is
localized solely in the cytoplasm. TLP is specifically
expressed in the thymus in a subset of cortical
epithelial cells. TLP has a role in development of
normal thymus and in controlling the development and
differentiation of thymic epithelial cells. CRIP is a
short LIM protein with only one LIM domain. CRIP gene
is developmentally regulated and can be induced by
glucocorticoid hormones during the first three
postnatal weeks. The domain shows close sequence
homology to LIM domain of thymus LIM protein. However,
unlike the TLP proteins which have two LIM domains, the
members of this family have only one LIM domain. 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 = 53
Score = 23.5 bits (51), Expect = 7.6
Identities = 9/22 (40%), Positives = 13/22 (59%), Gaps = 2/22 (9%)
Query: 2 TVTNTSVTYTHKGVPYCHVPCY 23
T+T + H+G PYC+ CY
Sbjct: 34 TLTPGQHS-EHEGKPYCNK-CY 53
>gnl|CDD|149273 pfam08123, DOT1, Histone methylation protein DOT1. The DOT1 domain
regulates gene expression by methylating histone H3. H3
methylation by DOT1 has been shown to be required for
the DNA damage checkpoint in yeast.
Length = 205
Score = 24.2 bits (53), Expect = 9.3
Identities = 6/17 (35%), Positives = 10/17 (58%)
Query: 2 TVTNTSVTYTHKGVPYC 18
+ SV++T +GV Y
Sbjct: 185 KLPEGSVSWTSRGVEYY 201
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
0.316 0.133 0.417
Gapped
Lambda K H
0.267 0.0734 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,988,330
Number of extensions: 286276
Number of successful extensions: 230
Number of sequences better than 10.0: 1
Number of HSP's gapped: 230
Number of HSP's successfully gapped: 13
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 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (24.2 bits)