RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14654
(122 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 = 56.8 bits (138), Expect = 2e-12
Identities = 19/60 (31%), Positives = 28/60 (46%), Gaps = 5/60 (8%)
Query: 13 VMKPMLERKRRARINRCLDELKEIMVTSLQAEGENVSKLEKADILELTVRHLHKLRRQQS 72
+ ER+RR RIN DEL+ ++ T KL KA+IL V ++ L+
Sbjct: 6 EAHNLRERRRRERINDAFDELRSLLPTL-----PPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 55.9 bits (136), Expect = 5e-12
Identities = 19/56 (33%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 13 VMKPMLERKRRARINRCLDELKEIMVTSLQAEGENVSKLEKADILELTVRHLHKLR 68
ER+RR RIN +EL+E++ T KL KA+IL L + ++ L+
Sbjct: 3 KAHNERERRRRDRINDAFEELRELLPTP------PNKKLSKAEILRLAIEYIKHLQ 52
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 53.8 bits (130), Expect = 4e-11
Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 5/56 (8%)
Query: 16 PMLERKRRARINRCLDELKEIMVTSLQAEGENVSKLEKADILELTVRHLHKLRRQQ 71
ER+RR +IN DEL+ ++ T KL KA+IL L + ++ L+ +
Sbjct: 1 NARERRRRRKINEAFDELRSLLPT-----LPKNKKLSKAEILRLAIEYIKSLQEEL 51
>gnl|CDD|219453 pfam07527, Hairy_orange, Hairy Orange. The Orange domain is found
in the Drosophila proteins Hesr-1, Hairy, and Enhancer
of Split. The Orange domain is proposed to mediate
specific protein-protein interaction between Hairy and
Scute.
Length = 42
Score = 36.0 bits (84), Expect = 3e-04
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 84 RFKAGFTHCAAEVSQYLASS 103
+F+AGF C EV+++L+S
Sbjct: 1 KFRAGFRECLNEVARFLSSV 20
>gnl|CDD|128787 smart00511, ORANGE, Orange domain. This domain confers specificity
among members of the Hairy/E(SPL) family.
Length = 45
Score = 32.5 bits (75), Expect = 0.004
Identities = 9/25 (36%), Positives = 15/25 (60%), Gaps = 1/25 (4%)
Query: 85 FKAGFTHCAAEVSQYLASSMQQHQQ 109
F++G+ CA EVS++L S +
Sbjct: 3 FRSGYRECANEVSRFL-SQLPGTDP 26
>gnl|CDD|153250 cd07988, LPLAT_ABO13168-like, Lysophospholipid Acyltransferases
(LPLATs) of Glycerophospholipid Biosynthesis: Unknown
ABO13168. Lysophospholipid acyltransferase (LPLAT)
superfamily member: acyltransferases of de novo and
remodeling pathways of glycerophospholipid biosynthesis
which catalyze the incorporation of an acyl group from
either acylCoAs or acyl-acyl carrier proteins (acylACPs)
into acceptors such as glycerol 3-phosphate,
dihydroxyacetone phosphate or lyso-phosphatidic acid.
Included in this subgroup are uncharacterized
phospholipid/glycerol acyltransferases such as the
Acinetobacter baumannii ATCC 17978 locus ABO13168
putative acyltransferase, and similar proteins.
Length = 163
Score = 27.6 bits (62), Expect = 1.2
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 2/26 (7%)
Query: 72 SLGLTPEA--AYADRFKAGFTHCAAE 95
L + PE + D++K GF H A
Sbjct: 97 VLAIAPEGTRSKVDKWKTGFYHIARG 122
>gnl|CDD|131679 TIGR02631, xylA_Arthro, xylose isomerase, Arthrobacter type. This
model describes a D-xylose isomerase that is also active
as a D-glucose isomerase. It is tetrameric and dependent
on a divalent cation Mg2+, Co2+ or Mn2+ as characterized
in Arthrobacter. Members of this family differ
substantially from the D-xylose isomerases of family
TIGR02630.
Length = 382
Score = 27.1 bits (60), Expect = 2.6
Identities = 16/47 (34%), Positives = 21/47 (44%), Gaps = 4/47 (8%)
Query: 53 KADILELTVRH----LHKLRRQQSLGLTPEAAYADRFKAGFTHCAAE 95
+ DIL TV H + L R + GL PE + FTH A+
Sbjct: 186 RGDILLPTVGHALAFIETLERPELFGLNPETGHEQMAGLNFTHGIAQ 232
>gnl|CDD|173915 cd02164, PPAT_CoAS, phosphopantetheine adenylyltransferase domain
of eukaryotic and archaeal bifunctional enzymes. The
PPAT domain of the bifunctional enzyme with PPAT and
DPCK functions. The final two steps of the CoA
biosynthesis pathway are catalyzed by phosphopantetheine
adenylyltransferase (PPAT) and dephospho-CoA (dPCoA)
kinase (DPCK). The PPAT reaction involves the reversible
adenylation of 4'-phosphopantetheine to form 3'-dPCoA
and PPi, and DPCK catalyses phosphorylation of the
3'-hydroxy group of the ribose moiety of dPCoA. In
eukaryotes the two enzymes are part of a large
multienzyme complex . Studies in Corynebacterium
ammoniagenes suggested that separate enzymes were
present, and this was confirmed through identification
of the bacterial PPAT/CoAD.
Length = 143
Score = 26.5 bits (59), Expect = 2.9
Identities = 11/41 (26%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 8 VVYPEVMKPMLERKRRARINRCLDELKEIMVTSLQAEGENV 48
VV PE P + R R L L+ ++V ++A+ +
Sbjct: 94 VVSPETY-PGALKINRKREENGLSPLEIVVVPLVKADEDGE 133
>gnl|CDD|240159 cd05120, APH_ChoK_like, Aminoglycoside 3'-phosphotransferase (APH)
and Choline Kinase (ChoK) family. The APH/ChoK family is
part of a larger superfamily that includes the catalytic
domains of other kinases, such as the typical
serine/threonine/tyrosine protein kinases (PKs), RIO
kinases, actin-fragmin kinase (AFK), and
phosphoinositide 3-kinase (PI3K). The family is composed
of APH, ChoK, ethanolamine kinase (ETNK), macrolide
2'-phosphotransferase (MPH2'), an unusual homoserine
kinase, and uncharacterized proteins with similarity to
the N-terminal domain of acyl-CoA dehydrogenase 10
(ACAD10). The members of this family catalyze the
transfer of the gamma-phosphoryl group from ATP (or CTP)
to small molecule substrates such as aminoglycosides,
macrolides, choline, ethanolamine, and homoserine.
Phosphorylation of the antibiotics, aminoglycosides and
macrolides, leads to their inactivation and to bacterial
antibiotic resistance. Phosphorylation of choline,
ethanolamine, and homoserine serves as precursors to the
synthesis of important biological compounds, such as the
major phospholipids, phosphatidylcholine and
phosphatidylethanolamine and the amino acids, threonine,
methionine, and isoleucine.
Length = 155
Score = 26.2 bits (58), Expect = 3.6
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 46 ENVSKLEKADILELTVRHLHKLRRQQSLGLT 76
+ VS+ EK DI E L KL + L L
Sbjct: 81 DEVSEEEKEDIAEQLAELLAKLHQLPLLVLC 111
>gnl|CDD|178104 PLN02486, PLN02486, aminoacyl-tRNA ligase.
Length = 383
Score = 26.6 bits (59), Expect = 4.2
Identities = 10/37 (27%), Positives = 18/37 (48%)
Query: 1 MSTLSIEVVYPEVMKPMLERKRRARINRCLDELKEIM 37
M T ++ EV+ ++ER +RAR + + M
Sbjct: 341 MLTGEVKKRLIEVLTEIVERHQRARAAVTDEMVDAFM 377
>gnl|CDD|218128 pfam04523, Herpes_U30, Herpes virus tegument protein U30. This
family is named after the human herpesvirus protein, but
has been characterized in cytomegalovirus as UL47.
Cytomegalovirus UL47 is a component of the tegument,
which is a protein layer surrounding the viral capsid.
UL47 co-precipitates with UL48 and UL69 tegument
proteins, and the major capsid protein UL86. A
UL47-containing complex is thought to be involved in the
release of viral DNA from the disassembling virus
particle.
Length = 883
Score = 26.1 bits (58), Expect = 5.3
Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 8/62 (12%)
Query: 19 ERKRRARINRCLDELKEIMVTSLQAEGENVSKLEKADILELTVRHLHKLRRQQSLGLTPE 78
+ +++ D + + + LQ + +L +DILE R L LGLT E
Sbjct: 298 QAAVEQFLDKINDFMTTL-GSYLQIACSSKKQLSLSDILE-IKRRLL------RLGLTEE 349
Query: 79 AA 80
Sbjct: 350 TC 351
>gnl|CDD|233137 TIGR00811, sit, silicon transporter. Marine diatoms such as
Cylindrotheca fusiformis encode at least six silicon
transport protein homologues which exhibit similar size
and topology. One characterized member of the family
(Sit1) functions in the energy-dependent uptake of
either Silicic acid [Si(OH)4] or Silicate [Si(OH)3O-] by
a Na+ symport mechanism. The system is found in marine
diatoms which make their "glass houses" out of silicon
[Transport and binding proteins, Other].
Length = 545
Score = 26.1 bits (57), Expect = 6.1
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 22 RRARINRCLDELKEIMVTSLQAEGENVSKLEKADILELTVRHLHKLRRQQSLGLTPEAAY 81
RR R+ + + EL+E++ ++ E + E A L + V+ L KL ++ T +
Sbjct: 483 RRERMLKNIRELREMINNAISDEEKTT--FEAA--LAIEVKALDKLNAEEEEEATNKKEG 538
Query: 82 AD 83
D
Sbjct: 539 KD 540
>gnl|CDD|201526 pfam00957, Synaptobrevin, Synaptobrevin.
Length = 89
Score = 24.8 bits (55), Expect = 7.3
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 11/39 (28%)
Query: 24 ARINRCLDELKEIMVTSLQAEGENVSKL----EKADILE 58
+I +DE+K+IM EN+ K+ EK D+L
Sbjct: 6 NKIQAQVDEVKDIMT-------ENIDKVLERGEKLDLLV 37
>gnl|CDD|237382 PRK13420, PRK13420, F0F1 ATP synthase subunit A; Provisional.
Length = 226
Score = 25.5 bits (56), Expect = 7.4
Identities = 5/17 (29%), Positives = 9/17 (52%)
Query: 99 YLASSMQQHQQQPSTEP 115
Y+A +Q H+ + E
Sbjct: 209 YIAGGIQAHELKSQGES 225
>gnl|CDD|233879 TIGR02468, sucrsPsyn_pln, sucrose phosphate synthase/possible
sucrose phosphate phosphatase, plant. Members of this
family are sucrose-phosphate synthases of plants. This
enzyme is known to exist in multigene families in
several species of both monocots and dicots. The
N-terminal domain is the glucosyltransferase domain.
Members of this family also have a variable linker
region and a C-terminal domain that resembles sucrose
phosphate phosphatase (SPP) (EC 3.1.3.24) (see
TIGR01485), the next and final enzyme of sucrose
biosynthesis. The SPP-like domain likely serves a
binding and not a catalytic function, as the reported
SPP is always encoded by a distinct protein.
Length = 1050
Score = 25.5 bits (56), Expect = 9.1
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 16 PMLERKRRARINR 28
+LERK RAR R
Sbjct: 405 VILERKLRARARR 417
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
0.315 0.127 0.349
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,085,004
Number of extensions: 518752
Number of successful extensions: 637
Number of sequences better than 10.0: 1
Number of HSP's gapped: 633
Number of HSP's successfully gapped: 39
Length of query: 122
Length of database: 10,937,602
Length adjustment: 84
Effective length of query: 38
Effective length of database: 7,211,866
Effective search space: 274050908
Effective search space used: 274050908
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 (24.1 bits)