RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8078
(105 letters)
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 61.3 bits (150), Expect = 2e-14
Identities = 34/52 (65%), Positives = 38/52 (73%), Gaps = 1/52 (1%)
Query: 48 YRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
R AH RER R + N AF ELR+LLPT PP+KKLSK EILRLAI YI +L
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPT-PPNKKLSKAEILRLAIEYIKHL 51
>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 = 59.1 bits (144), Expect = 2e-13
Identities = 35/58 (60%), Positives = 38/58 (65%)
Query: 47 KYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLE 104
R AH RER R E N AF ELR LLPTLPP KKLSK EILR A+ YI L +L+
Sbjct: 3 SRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELLQ 60
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 58.0 bits (141), Expect = 4e-13
Identities = 32/51 (62%), Positives = 34/51 (66%)
Query: 55 RERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVLET 105
RER R N AF ELR LLPTLP +KKLSK EILRLAI YI L L+
Sbjct: 3 RERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIKSLQEELQK 53
>gnl|CDD|217715 pfam03759, PRONE, PRONE (Plant-specific Rop nucleotide
exchanger). This is a functional guanine exchange
factor (GEF) of plant Rho GTPase.
Length = 360
Score = 28.1 bits (63), Expect = 0.83
Identities = 10/19 (52%), Positives = 13/19 (68%), Gaps = 1/19 (5%)
Query: 65 SAFGELRKLLPTLPPDKKL 83
+ FGEL +L P L P+KK
Sbjct: 44 TVFGELWRLEP-LAPEKKA 61
>gnl|CDD|238911 cd01936, Ntn_CA, Cephalosporin acylase (CA) belongs to a family of
beta-lactam acylases that includes penicillin G acylase
(PGA) and aculeacin A acylase. PGA and CA are crucial
for the production of backbone chemicals like
6-aminopenicillanic acid and 7-aminocephalosporanic acid
(7-ACA), which can be used to synthesize semi-synthetic
penicillins and cephalosporins, respectively. While
both PGA and CA have a conserved Ntn (N-terminal
nucleophile) hydrolase fold and the structural
similarity at their active sites is very high, their
sequence similarity to other Ntn's is low.
Length = 469
Score = 27.6 bits (62), Expect = 1.1
Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 5/63 (7%)
Query: 11 TH---GASRQNLFRL-LDKSDGSTQALSREERR-RRRRATQKYRTAHATRERVRVEAFNS 65
TH +++RL LD D + E R +R T +TA V + S
Sbjct: 128 THTVNTPDHFDVYRLTLDPEDPLGYLVDGEWRPLEKRTVTIPVKTADGGLATVERTVYRS 187
Query: 66 AFG 68
G
Sbjct: 188 VHG 190
>gnl|CDD|223400 COG0323, MutL, DNA mismatch repair enzyme (predicted ATPase) [DNA
replication, recombination, and repair].
Length = 638
Score = 27.7 bits (62), Expect = 1.2
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 52 HATRERVRVEAFNSAFGELRKLLPTLPPDK-KLSKIEILRL 91
HA ER+ E + G + +L P L P + +LS E L
Sbjct: 477 HAAHERILYEKLKNELGNVGELQPLLIPIRLELSPEEADVL 517
>gnl|CDD|162096 TIGR00897, 2A0118, polyol permease family. This family of proteins
includes the ribitol and D-arabinitol transporters from
Klebsiella pneumoniae and the alpha-ketoglutarate
permease from Bacillus subtilis [Transport and binding
proteins, Carbohydrates, organic alcohols, and acids].
Length = 402
Score = 27.5 bits (61), Expect = 1.3
Identities = 9/31 (29%), Positives = 16/31 (51%)
Query: 62 AFNSAFGELRKLLPTLPPDKKLSKIEILRLA 92
F + + L + PTL P K + + +L L+
Sbjct: 328 IFLAGYVPLAAVFPTLAPKHKGAAMSVLNLS 358
>gnl|CDD|188994 cd06455, M3A_TOP, Peptidase M3 Thimet oligopeptidase (TOP) also
includes neurolysin. Peptidase M3 Thimet oligopeptidase
(TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase
24.15; soluble metallo-endopeptidase; EC 3.4.24.15)
family also includes neurolysin (endopeptidase 24.16,
microsomal endopeptidase, mitochondrial oligopeptidase
M, neurotensin endopeptidase, soluble angiotensin
II-binding protein, thimet oligopeptidase II) which
hydrolyzes oligopeptides such as neurotensin, bradykinin
and dynorphin A. TOP and neurolysin are neuropeptidases
expressed abundantly in the testis, but also found in
the liver, lung and kidney. They are involved in the
metabolism of neuropeptides under 20 amino acid residues
long and cleave most bioactive peptides at the same
sites, but recognize different positions on some
naturally occurring and synthetic peptides; they cleave
at distinct sites on the 13-residue bioactive peptide
neurotensin, which modulates central dopaminergic and
cholinergic circuits. TOP has been shown to degrade
peptides released by the proteasome, limiting the extent
of antigen presentation by major histocompatibility
complex class I molecules, and has been associated with
amyloid protein precursor processing.
Length = 637
Score = 27.1 bits (61), Expect = 1.6
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 15 SRQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTA-----HATRERVR 59
R++++R L D + L E RR R + +R ATRERV+
Sbjct: 81 MREDVYRALKAVDEKNEELDPETRRLLERLLRDFRRNGLDLPEATRERVK 130
>gnl|CDD|219627 pfam07897, DUF1675, Protein of unknown function (DUF1675). The
members of this family are sequences derived from
hypothetical plant proteins of unknown function. One
member of this family is annotated as a putative
RNA-binding protein, but no evidence was found to
support this.
Length = 283
Score = 26.8 bits (59), Expect = 2.5
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 2/39 (5%)
Query: 27 DGSTQALSR--EERRRRRRATQKYRTAHATRERVRVEAF 63
T +L EE R+R+ Q R A R+R E
Sbjct: 58 LMRTTSLPVETEEEWRKRKEMQSLRRLEAKRKRSEKEYN 96
>gnl|CDD|215579 PLN03106, TCP2, Protein TCP2; Provisional.
Length = 447
Score = 26.2 bits (57), Expect = 3.4
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 24 DKSDGSTQALSREERRRRRRATQKYRTAHATRER 57
D S GS +LSR E R + R + RTA +
Sbjct: 192 DTSKGSGLSLSRSELRDKARERARERTAKEKEKE 225
>gnl|CDD|184075 PRK13478, PRK13478, phosphonoacetaldehyde hydrolase; Provisional.
Length = 267
Score = 26.0 bits (58), Expect = 3.7
Identities = 12/24 (50%), Positives = 13/24 (54%), Gaps = 1/24 (4%)
Query: 31 QALSREERRRRR-RATQKYRTAHA 53
QALS E RR RA + R A A
Sbjct: 217 QALSAAELAARRERARARLRAAGA 240
>gnl|CDD|222912 PHA02624, PHA02624, large T antigen; Provisional.
Length = 647
Score = 26.1 bits (58), Expect = 4.4
Identities = 11/61 (18%), Positives = 27/61 (44%), Gaps = 9/61 (14%)
Query: 44 ATQKYRTAHATRERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYLNNVL 103
A ++ + TRE + E F ++ ++ ++IL+ + +A+L+ +L
Sbjct: 360 AKRRVKLLTMTREELLAERFKKLLDKMDEIFK--------GSVDILQY-MAGVAWLHCLL 410
Query: 104 E 104
Sbjct: 411 P 411
>gnl|CDD|112952 pfam04162, Gyro_capsid, Gyrovirus capsid protein (VP1).
Gyroviruses are small circular single stranded viruses.
This family includes the VP1 protein from the chicken
anaemia virus which is the viral capsid protein.
Length = 449
Score = 25.9 bits (56), Expect = 4.8
Identities = 14/44 (31%), Positives = 19/44 (43%)
Query: 28 GSTQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELR 71
G A R +R ++Y+ H R+R R AF AF R
Sbjct: 10 GRFYAFRRGRWHHLKRLRRRYKFRHRRRQRYRRRAFRKAFHNPR 53
>gnl|CDD|132002 TIGR02957, SigX4, RNA polymerase sigma-70 factor, TIGR02957 family.
This group of sigma factors are members of the sigma-70
family (TIGR02937). They and appear by homology, tree
building and bidirectional best hits, to represent a
conserved family. This family is found in a limited
number of bacterial lineages. This family includes
apparent paralogous expansion in Streptomyces coelicolor
A3(2), and multiple copies in Mycobacterium smegmatis
MC2, Streptomyces avermitilis MA-4680 and Nocardia
farcinica IFM10152.
Length = 281
Score = 25.8 bits (57), Expect = 4.8
Identities = 22/82 (26%), Positives = 33/82 (40%), Gaps = 9/82 (10%)
Query: 2 FLQREKFSETHGASRQNLFRLLDKSDGST-QALSREERRRRRRATQKYRTAHATRERVRV 60
F+ RE F + + ++ KS+ + Q +SR RR A + R +
Sbjct: 117 FVLREVF----DYPYEEIASIVGKSEANCRQLVSRA--RRHLDARRPRFEVSREESRQLL 170
Query: 61 EAFNSAF--GELRKLLPTLPPD 80
E F A G+L LL L D
Sbjct: 171 ERFVEAAQTGDLDGLLELLAED 192
>gnl|CDD|216865 pfam02074, Peptidase_M32, Carboxypeptidase Taq (M32)
metallopeptidase.
Length = 494
Score = 25.6 bits (56), Expect = 5.5
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 22 LLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVRVE 61
LL+K +GS + L + R + Y A A ER+ E
Sbjct: 66 LLEKVEGSFEDLLEDAAVNVRVWRRAYERARAIPERLAKE 105
>gnl|CDD|219795 pfam08324, PUL, PUL domain. The PUL (PLAP, Ufd3p and Lub1p)
domain is a novel alpha-helical Ub-associated domain.
It directly binds to Cdc48, a chaperone-like AAA ATPase
that collects ubiquitylated substrates.
Length = 263
Score = 25.4 bits (56), Expect = 5.9
Identities = 7/33 (21%), Positives = 15/33 (45%)
Query: 61 EAFNSAFGELRKLLPTLPPDKKLSKIEILRLAI 93
+ L K+L + P + +++LRL +
Sbjct: 58 ALLEALTIYLLKILKSWPEANRFPALDLLRLLV 90
>gnl|CDD|236766 PRK10811, rne, ribonuclease E; Reviewed.
Length = 1068
Score = 25.8 bits (57), Expect = 6.0
Identities = 12/28 (42%), Positives = 15/28 (53%), Gaps = 2/28 (7%)
Query: 34 SREERRRRRRATQKYRTAHATRERVRVE 61
+REE RR RR Q+ TRE + E
Sbjct: 635 NREENRRNRRQAQQ--QTAETRESQQAE 660
>gnl|CDD|181362 PRK08296, PRK08296, hypothetical protein; Provisional.
Length = 603
Score = 25.4 bits (56), Expect = 6.3
Identities = 12/42 (28%), Positives = 18/42 (42%), Gaps = 3/42 (7%)
Query: 34 SREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKLLP 75
+ R R R ++YR ER +AF+ G R + P
Sbjct: 331 TEALRAERDRIVEEYRDLLDGDER---KAFDELLGLARTVYP 369
>gnl|CDD|143647 cd07887, RHD-n_Dorsal_Dif, N-terminal sub-domain of the Rel
homology domain (RHD) of the arthropod protein Dorsal.
Proteins containing the Rel homology domain (RHD) are
metazoan transcription factors. The RHD is composed of
two structural sub-domains; this model characterizes the
N-terminal RHD sub-domain of the arthropod Dorsal and
Dif (Dorsal-related immunity factor), and similar
proteins. Dorsal and Dif are Rel-like transcription
factors, which play roles in mediating innate immunity
in Drosophila. They are activated via the Toll pathway.
Cytoplasmic Dorsal/Dif are inactivated via forming a
complex with Cactus, the Drosophila homologue of
mammalian I-kappa B proteins. In response to signals,
Cactus is degraded and Dorsal/Dif can be transported
into the nucleus, where they act as transcription
factors. Dorsal is also an essential gene in
establishing the proper dorsal/ventral polarity in the
developing embryo.
Length = 173
Score = 25.1 bits (55), Expect = 6.9
Identities = 8/45 (17%), Positives = 20/45 (44%), Gaps = 10/45 (22%)
Query: 55 RERVRVEAFNSAFGELRKLLPTLPPDKKLSKIEILRLAICYIAYL 99
RE + V+ F + F +++ I++ + +C+ +L
Sbjct: 116 REEINVDPFRTGFDHK----------DQINSIDLNVVRLCFQVFL 150
>gnl|CDD|227496 COG5167, VID27, Protein involved in vacuole import and degradation
[Intracellular trafficking and secretion].
Length = 776
Score = 25.3 bits (55), Expect = 6.9
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 60 VEAFNSAFGELRKLLPTLPPDKKLSKIEILR 90
V A N FGE ++ LP D + + L+
Sbjct: 728 VVADNFEFGEDSNVIVALPDDVRKVNVRSLK 758
>gnl|CDD|239134 cd02669, Peptidase_C19M, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 440
Score = 25.4 bits (56), Expect = 7.1
Identities = 8/25 (32%), Positives = 13/25 (52%)
Query: 18 NLFRLLDKSDGSTQALSREERRRRR 42
L +LL K DG T+ ++ +R
Sbjct: 304 PLKQLLKKYDGKTETELKDSLKRYL 328
>gnl|CDD|235628 PRK05855, PRK05855, short chain dehydrogenase; Validated.
Length = 582
Score = 25.3 bits (56), Expect = 7.2
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 36 EERRRRRRATQKYRTAHATRERV 58
+E RRR RA + Y+ E+V
Sbjct: 515 DEARRRGRADKLYQRRGYGPEKV 537
>gnl|CDD|225290 COG2441, COG2441, Predicted butyrate kinase [Energy production and
conversion].
Length = 374
Score = 25.3 bits (55), Expect = 8.1
Identities = 6/15 (40%), Positives = 13/15 (86%)
Query: 74 LPTLPPDKKLSKIEI 88
LPT+P +K+++I++
Sbjct: 122 LPTVPEWRKVNRIDL 136
>gnl|CDD|189762 pfam00901, Orbi_VP5, Orbivirus outer capsid protein VP5.
cryoelectron microscopy indicates that VP5 is a trimer
implying that there are 360 copies of VP5 per virion.
Length = 507
Score = 25.0 bits (55), Expect = 8.5
Identities = 12/56 (21%), Positives = 22/56 (39%), Gaps = 3/56 (5%)
Query: 20 FRLLDKSDGSTQALSREER---RRRRRATQKYRTAHATRERVRVEAFNSAFGELRK 72
+L+K+ S + +EE +R +A QK E +E + L+
Sbjct: 142 MEILEKALKSYLKIVKEENKSLQRLAKALQKESEERTQDETKMIEEYRDKIDALKN 197
>gnl|CDD|236942 PRK11637, PRK11637, AmiB activator; Provisional.
Length = 428
Score = 25.0 bits (55), Expect = 8.6
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 16 RQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHATRER 57
R N RL D ++R ER + RA ++ R A R++
Sbjct: 239 RANESRLRDS-------IARAEREAKARAEREAREAARVRDK 273
>gnl|CDD|234317 TIGR03703, plsB, glycerol-3-phosphate O-acyltransferase. Members
of this protein family are PlsB, glycerol-3-phosphate
O-acyltransferase, present in E. coli and numerous
related species. In many bacteria, PlsB is not found,
and appears to be replaced by a two enzyme system for
1-acyl-glycerol-3-phosphate biosynthesis, the PlsX/Y
system [Fatty acid and phospholipid metabolism,
Biosynthesis].
Length = 799
Score = 25.3 bits (56), Expect = 8.8
Identities = 8/38 (21%), Positives = 16/38 (42%)
Query: 16 RQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHA 53
R+ LF L S +A+ E + ++ + + A
Sbjct: 207 RRTLFNKLLASPSVRKAIRDEAKSKKISEEKARKRALK 244
>gnl|CDD|227278 COG4942, COG4942, Membrane-bound metallopeptidase [Cell division
and chromosome partitioning].
Length = 420
Score = 25.1 bits (55), Expect = 8.9
Identities = 12/56 (21%), Positives = 19/56 (33%), Gaps = 1/56 (1%)
Query: 4 QREKFSETHGASRQNLFRLLDKSDGSTQALSREERRRRRRATQKYRTAHATRERVR 59
+K E A+ L + ++ A +RE A + R A A R
Sbjct: 221 ADQKKLEELRANESRLKNEIASAEA-AAAKAREAAAAAEAAAARARAAEAKRTGET 275
>gnl|CDD|227282 COG4946, COG4946, Uncharacterized protein related to the
periplasmic component of the Tol biopolymer transport
system [Function unknown].
Length = 668
Score = 25.2 bits (55), Expect = 9.5
Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 2/64 (3%)
Query: 15 SRQNLFRLLDKSDG-STQALSREERRRRRRATQKYRTAHATRERVRVEAFNSAFGELRKL 73
SR F ++ DG S Q + R RR T + ++ ++ GE++++
Sbjct: 339 SRGKAF-IMRPWDGYSIQVGKKGGVRYRRIQVDPEGDVIGTNDGDKLGIYDKDGGEVKRI 397
Query: 74 LPTL 77
L
Sbjct: 398 EKDL 401
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
0.322 0.134 0.368
Gapped
Lambda K H
0.267 0.0707 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,463,969
Number of extensions: 471507
Number of successful extensions: 891
Number of sequences better than 10.0: 1
Number of HSP's gapped: 883
Number of HSP's successfully gapped: 73
Length of query: 105
Length of database: 10,937,602
Length adjustment: 70
Effective length of query: 35
Effective length of database: 7,832,822
Effective search space: 274148770
Effective search space used: 274148770
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)