RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15840
(161 letters)
>gnl|CDD|238036 cd00083, HLH, Helix-loop-helix domain, found in specific DNA-
binding proteins that act as transcription factors;
60-100 amino acids long. A DNA-binding basic region is
followed by two alpha-helices separated by a variable
loop region; HLH forms homo- and heterodimers,
dimerization creates a parallel, left-handed, four helix
bundle; the basic region N-terminal to the first
amphipathic helix mediates high-affinity DNA-binding;
there are several groups of HLH proteins: those
(E12/E47) which bind specific hexanucleotide sequences
such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3),
those lacking the basic domain (Emc, Id) function as
negative regulators since they fail to bind DNA, those
(hairy, E(spl), deadpan) which repress transcription
although they can bind specific hexanucleotide sequences
such as N-box (5-CACGc/aG-3), those which have a COE
domain (Collier/Olf-1/EBF) which is involved in both in
dimerization and in DNA binding, and those which bind
pentanucleotides ACGTG or GCGTG and have a PAS domain
which allows the dimerization between PAS proteins, the
binding of small molecules (e.g., dioxin), and
interactions with non-PAS proteins.
Length = 60
Score = 68.4 bits (168), Expect = 2e-16
Identities = 30/58 (51%), Positives = 38/58 (65%)
Query: 96 KKRRLAANARERRRMSGLNEAFDRLREVIPCIGIEHKLSKFETLQMAQTYIHSLRDLL 153
K RR A N RERRR +N+AFD LR ++P + KLSK E L+ A YI SL++LL
Sbjct: 2 KSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 62.5 bits (153), Expect = 4e-14
Identities = 26/53 (49%), Positives = 35/53 (66%), Gaps = 1/53 (1%)
Query: 98 RRLAANARERRRMSGLNEAFDRLREVIPCIGIEHKLSKFETLQMAQTYIHSLR 150
RR A N RERRR +N+AF+ LRE++P + KLSK E L++A YI L+
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPNK-KLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 62.2 bits (152), Expect = 5e-14
Identities = 27/51 (52%), Positives = 35/51 (68%)
Query: 103 NARERRRMSGLNEAFDRLREVIPCIGIEHKLSKFETLQMAQTYIHSLRDLL 153
NARERRR +NEAFD LR ++P + KLSK E L++A YI SL++ L
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEEL 51
>gnl|CDD|178213 PLN02603, PLN02603, asparaginyl-tRNA synthetase.
Length = 565
Score = 33.4 bits (76), Expect = 0.035
Identities = 16/57 (28%), Positives = 23/57 (40%)
Query: 51 SISNEDMLTVPREFKPILISHASSNPRRRRRNSAPSGSVPPPQVMKKRRLAANARER 107
SN L++P ++ S PRRRR +A S S+ P+ K E
Sbjct: 26 PKSNPSALSLPLPPTFHHLAALSGLPRRRRFCAAASASLQSPESAKVEAAKGAFGEA 82
>gnl|CDD|215392 PLN02737, PLN02737, inositol monophosphatase family protein.
Length = 363
Score = 28.6 bits (64), Expect = 1.6
Identities = 17/99 (17%), Positives = 35/99 (35%), Gaps = 9/99 (9%)
Query: 25 FKQTNQDPREEFDTNYDSNYDRQYCDSISNEDMLTVPREFKPILISHASSNPRRRRRNSA 84
+ F + S + S+ + P P ++S + + R +A
Sbjct: 15 LRFPASCIPRTFARQHRSRLAALR--AGSSRSLARRP---TPAVLSETPNQAKYPRVGAA 69
Query: 85 PSGSVPPPQVMKKRRLAANARERRRMSGLNEAFDRLREV 123
+G +P +++ LAA M EA ++ R +
Sbjct: 70 STGPIPAEELLAVAELAAKTGAEVVM----EAVNKPRNI 104
>gnl|CDD|233433 TIGR01482, SPP-subfamily, sucrose-phosphate phosphatase subfamily.
This model includes both the members of the SPP
equivalog model (TIGR01485), encompassing plants and
cyanobacteria, as well as those archaeal sequences which
are the closest relatives (TIGR01487). It remains to be
shown whether these archaeal sequences catalyze the same
reaction as SPP.
Length = 225
Score = 28.2 bits (63), Expect = 1.9
Identities = 10/54 (18%), Positives = 17/54 (31%)
Query: 106 ERRRMSGLNEAFDRLREVIPCIGIEHKLSKFETLQMAQTYIHSLRDLLTSANSG 159
+ F RL+ P K+ + + I L L + +SG
Sbjct: 85 FLDIVIAKTFPFSRLKVQYPRRASLVKMRYGIDVDTVREIIKELGLNLVAVDSG 138
>gnl|CDD|188875 cd09769, Luminal_IRE1, The Luminal domain, a dimerization domain,
of the Serine/Threonine protein kinase,
Inositol-requiring protein 1. The Luminal domain is a
dimerization domain present in Inositol-requiring
protein 1 (IRE1), a serine/threonine protein kinase
(STK) and a type I transmembrane protein that is
localized in the endoplasmic reticulum (ER). IRE1, also
called Endoplasmic reticulum (ER)-to-nucleus signaling
protein (or ERN), is a kinase receptor that also
contains an endoribonuclease domain in the cytoplasmic
side. It plays roles in the signaling of the unfolded
protein response (UPR), which is activated when protein
misfolding is detected in the ER in order to decrease
the synthesis of new proteins and increase the capacity
of the ER to cope with the stress. IRE1 acts as an ER
stress sensor and is the oldest and most conserved
component of the UPR in eukaryotes. During ER stress,
IRE1 dimerizes through its luminal domain and forms
oligomers, allowing the kinase domain to undergo
trans-autophosphorylation. This leads to a
conformational change that stimulates its
endoribonuclease activity and results in the cleavage of
its mRNA substrate, HAC1 in yeast and Xbp1 in metazoans,
promoting a splicing event that enables translation into
a transcription factor which activates the UPR. Mammals
contain two IRE1 proteins, IRE1alpha (or ERN1) and
IRE1beta (or ERN2). IRE1alpha is expressed in all cells
and tissues while IRE1beta is found only in intestinal
epithelial cells.
Length = 295
Score = 27.7 bits (62), Expect = 2.4
Identities = 12/54 (22%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 23 FDFKQTNQDPREEFDTNYDSNYDRQYCDSISNEDMLTVPREFKPILISHASSNP 76
D+ + D + + Y YD +Y S S+ ++T R+ +L +P
Sbjct: 170 SDYTPNSNDR--DLQSQYSKTYDLRYIASSSDGSLVTFDRDTGRVLWVQNLPSP 221
>gnl|CDD|235889 PRK06931, PRK06931, diaminobutyrate--2-oxoglutarate
aminotransferase; Provisional.
Length = 459
Score = 27.8 bits (62), Expect = 2.7
Identities = 13/36 (36%), Positives = 19/36 (52%), Gaps = 2/36 (5%)
Query: 93 QVMKKRRLAANARERRRMSGLNEAFDRLREVIPCIG 128
+++K+ LA NA ER L L++ PCIG
Sbjct: 338 KILKEENLAQNAAERGEW--LKAQLAELQKRYPCIG 371
>gnl|CDD|176186 cd05283, CAD1, Cinnamyl alcohol dehydrogenases (CAD). Cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family, reduce
cinnamaldehydes to cinnamyl alcohols in the last step of
monolignal metabolism in plant cells walls. CAD binds 2
zinc ions and is NADPH- dependent. CAD family members
are also found in non-plant species, e.g. in yeast where
they have an aldehyde reductase activity. The medium
chain dehydrogenases/reductase (MDR)/zinc-dependent
alcohol dehydrogenase-like family, which contains the
zinc-dependent alcohol dehydrogenase (ADH-Zn) and
related proteins, is a diverse group of proteins related
to the first identified member, class I mammalian ADH.
MDRs display a broad range of activities and are
distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases
(ADHs) catalyze the NAD(P)(H)-dependent interconversion
of alcohols to aldehydes or ketones. Active site zinc
has a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 337
Score = 26.7 bits (60), Expect = 5.4
Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 9/71 (12%)
Query: 57 MLTVPREFKPILISHASSNPRRRRRNSAPSGSVPPPQVMKKRRLAANAR-----ERRRMS 111
++ P +P+ + R+ + G Q M AA E M
Sbjct: 261 LVGAP--EEPLPVPPFPLIFGRKSVAGSLIGGRKETQEMLD--FAAEHGIKPWVEVIPMD 316
Query: 112 GLNEAFDRLRE 122
G+NEA +RL +
Sbjct: 317 GINEALERLEK 327
>gnl|CDD|180342 PRK05991, PRK05991, precorrin-3B C17-methyltransferase;
Provisional.
Length = 250
Score = 26.2 bits (58), Expect = 8.5
Identities = 20/50 (40%), Positives = 27/50 (54%), Gaps = 10/50 (20%)
Query: 86 SGSVPPPQVMKKR-RLAA---------NARERRRMSGLNEAFDRLREVIP 125
S ++ P ++++KR RLAA N R R L EAFD LRE +P
Sbjct: 138 SDNLKPWELIEKRLRLAAEAGFVIALYNPISRARPWQLGEAFDLLREHLP 187
>gnl|CDD|176533 cd08591, PI-PLCc_beta, Catalytic domain of metazoan
phosphoinositide-specific phospholipase C-beta. This
subfamily corresponds to the catalytic domain present in
metazoan phosphoinositide-specific phospholipase C
(PI-PLC, EC 3.1.4.11)-beta isozymes. PI-PLC is a
signaling enzyme that hydrolyzes the membrane
phospholipids phosphatidylinositol-4,5-bisphosphate
(PIP2) to generate two important second messengers in
eukaryotic signal transduction cascades, Inositol
1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG).
InsP3 triggers inflow of calcium from intracellular
stores, while DAG, together with calcium, activates
protein kinase C, which goes on to phosphorylate other
molecules, leading to altered cellular activity. Calcium
is required for the catalysis. PLC-beta represents a
class of mammalian PI-PLC that has an N-terminal
pleckstrin homology (PH) domain, an array of EF hands, a
PLC catalytic core domain, a C2 domain, and a unique
C-terminal coiled-coil (CT) domain necessary for
homodimerization. The PLC catalytic core domain is a TIM
barrel with two highly conserved regions (X and Y) split
by a highly degenerate linker sequence. There are four
PLC-beta isozymes (1-4). They are activated by the
heterotrimeric G protein alpha q subunits through their
C2 domain and long C-terminal extension. The beta-gamma
subunits of heterotrimeric G proteins are known to
activate the PLC-beta2 and -beta3 isozymes only. Aside
from four PLC-beta isozymes identified in mammals, some
eukaryotic PLC-beta homologs have been classified into
this subfamily, such as NorpA and PLC-21 from Drosophila
and PLC-beta from turkey, Xenopus, sponge, and hydra.
Length = 257
Score = 26.1 bits (58), Expect = 8.9
Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 20/67 (29%)
Query: 47 QYCDSISNEDMLTVPREFKPILISHASSNPRRRRRNSAPSGSVPPPQVMKKRRLAANARE 106
+YC I + +LT P E P+ P +P P +K++ L N
Sbjct: 111 EYCREIFGDLLLTEPLEKYPLE----------------PGVPLPSPNDLKRKILIKN--- 151
Query: 107 RRRMSGL 113
+++S L
Sbjct: 152 -KKLSSL 157
>gnl|CDD|129792 TIGR00709, dat, 2,4-diaminobutyrate 4-transaminases. This family
consists of L-diaminobutyric acid transaminases. This
general designation covers both 2.6.1.76
(diaminobutyrate-2-oxoglutarate transaminase, which uses
glutamate as the amino donor in DABA biosynthesis), and
2.6.1.46 (diaminobutyrate--pyruvate transaminase, which
uses alanine as the amino donor). Most members with
known function are 2.6.1.76, and at least some
annotations as 2.6.1.46 in current databases at time of
model revision are incorrect. A distinct branch of this
family contains examples of 2.6.1.76 nearly all of which
are involved in ectoine biosynthesis. A related enzyme
is 4-aminobutyrate aminotransferase (EC 2.6.1.19), also
called GABA transaminase. These enzymes all are
pyridoxal phosphate-containing class III
aminotransferase [Central intermediary metabolism,
Other].
Length = 442
Score = 26.5 bits (58), Expect = 9.0
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 93 QVMKKRRLAANARERRRMSGLNEAFDRLREVIPCIG 128
K LA NA+ER + D + + PCIG
Sbjct: 319 NYWKDDNLAQNAQERGER--ITSFLDDMIKEHPCIG 352
>gnl|CDD|178210 PLN02600, PLN02600, enoyl-CoA hydratase.
Length = 251
Score = 25.9 bits (57), Expect = 9.9
Identities = 19/72 (26%), Positives = 31/72 (43%), Gaps = 14/72 (19%)
Query: 98 RRLAANARERRRMSGLNEAFDR-----------LREVIP---CIGIEHKLSKFETLQMAQ 143
R A NA + + GL AF++ LR +P C G + K + + Q
Sbjct: 12 RPEAKNAIGKEMLRGLRSAFEKIQADASARVVMLRSSVPGVFCAGADLKERRKMSPSEVQ 71
Query: 144 TYIHSLRDLLTS 155
+++SLR +S
Sbjct: 72 KFVNSLRSTFSS 83
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 0.132 0.379
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,338,005
Number of extensions: 761165
Number of successful extensions: 867
Number of sequences better than 10.0: 1
Number of HSP's gapped: 861
Number of HSP's successfully gapped: 26
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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 (21.7 bits)
S2: 55 (24.9 bits)