RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3607
(95 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 = 46.8 bits (112), Expect = 1e-08
Identities = 15/54 (27%), Positives = 36/54 (66%), Gaps = 2/54 (3%)
Query: 25 DDSKRKSRNLSEKKRRDQFNMLINELCTMVSTN--NRKMDKSTVLKSTIAFLKN 76
S+R++ NL E++RR++ N +EL +++ T ++K+ K+ +L+ + ++K+
Sbjct: 1 RKSRREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKS 54
>gnl|CDD|215654 pfam00010, HLH, Helix-loop-helix DNA-binding domain.
Length = 52
Score = 42.8 bits (102), Expect = 3e-07
Identities = 16/49 (32%), Positives = 31/49 (63%), Gaps = 1/49 (2%)
Query: 28 KRKSRNLSEKKRRDQFNMLINELCTMV-STNNRKMDKSTVLKSTIAFLK 75
+RK+ N E++RRD+ N EL ++ + N+K+ K+ +L+ I ++K
Sbjct: 1 RRKAHNERERRRRDRINDAFEELRELLPTPPNKKLSKAEILRLAIEYIK 49
>gnl|CDD|197674 smart00353, HLH, helix loop helix domain.
Length = 53
Score = 41.1 bits (97), Expect = 1e-06
Identities = 14/45 (31%), Positives = 28/45 (62%), Gaps = 2/45 (4%)
Query: 33 NLSEKKRRDQFNMLINELCTMVST--NNRKMDKSTVLKSTIAFLK 75
N E++RR + N +EL +++ T N+K+ K+ +L+ I ++K
Sbjct: 1 NARERRRRRKINEAFDELRSLLPTLPKNKKLSKAEILRLAIEYIK 45
>gnl|CDD|188710 cd08756, RGS_GEF_like, Regulator of G protein signaling (RGS)
domain found in the Rho guanine nucleotide exchange
factor (RhoGEF) protein. The RGS domain found in the
Rho guanine nucleotide exchange factor (RhoGEF) protein
subfamily of the RGS domain containing protein family,
which is a diverse group of multifunctional proteins
that regulate cellular signaling events downstream of
G-protein coupled receptors (GPCRs). The RhoGEFs are
peripheral membrane proteins that regulate essential
cellular processes, including cell shape, cell migration
and cell cycle progression as well as gene transcription
by linking signals from heterotrimeric G-alpha12/13
protein-coupled receptors to Rho GTPase activation,
leading to various cellular responses, such as actin
reorganization and gene expression. The RhoGEF subfamily
includes the leukemia-associated RhoGEF protein (LARG),
p115RhoGEF, PDZ-RhoGEF, and its rat specific splice
variant GTRAP48. The RGS domain of RhoGEFs has very
little sequence similarity with the canonical RGS domain
of the RGS proteins and is often refered to as RH (RGS
Homology) domain. RGS proteins play critical regulatory
role as GTPase activating proteins (GAPs) of the
heterotrimeric G-protein G-alpha-subunits. RGS proteins
play critical regulatory role as GTPase activating
proteins (GAPs) of the heterotrimeric G-protein
G-alpha-subunits. RGS proteins regulate many aspects of
embryonic development such as glial differentiation,
embryonic axis formation, skeletal and muscle
development, cell migration during early embryogenesis,
as well as apoptosis, cell proliferation, and modulation
of cardiac development.
Length = 122
Score = 30.4 bits (69), Expect = 0.057
Identities = 8/49 (16%), Positives = 23/49 (46%)
Query: 1 MSTHQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINE 49
+ +++S + D + + D ++ R+ + +K RD+ N + +
Sbjct: 58 LLWPNIDESLIQEIDKILQNEQDDEEILRRVFLKAREKARDEINDQLAD 106
>gnl|CDD|217203 pfam02724, CDC45, CDC45-like protein. CDC45 is an essential gene
required for initiation of DNA replication in S.
cerevisiae, forming a complex with MCM5/CDC46.
Homologues of CDC45 have been identified in human, mouse
and smut fungus among others.
Length = 583
Score = 29.6 bits (67), Expect = 0.21
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 7 EQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINEL 50
E+S D+ DD DD DD + R+L ++RR ++ EL
Sbjct: 138 EESSKSEDDEDDDDDDDDDDIATRERSLERRRRRREWEEKRAEL 181
>gnl|CDD|183097 PRK11359, PRK11359, cyclic-di-GMP phosphodiesterase; Provisional.
Length = 799
Score = 25.9 bits (57), Expect = 3.8
Identities = 9/47 (19%), Positives = 21/47 (44%)
Query: 1 MSTHQLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLI 47
M + + ++ D ++ + D++ + + L K RDQ L+
Sbjct: 168 MFGYCISEASGMQPDTLLNIPEFPADNRIRLQQLLWKTARDQDEFLL 214
>gnl|CDD|182379 PRK10325, PRK10325, heat shock protein GrpE; Provisional.
Length = 197
Score = 25.0 bits (54), Expect = 6.4
Identities = 12/58 (20%), Positives = 28/58 (48%)
Query: 5 QLEQSFNRNSDDTMDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMD 62
QL ++ R D + + ++ +R++ EK + INEL ++ + +R ++
Sbjct: 50 QLAEAQTRERDGILRVKAEMENLRRRTELDIEKAHKFALEKFINELLPVIDSLDRALE 107
>gnl|CDD|240522 cd13151, DAXX_helical_bundle, Helical bundle domain of the
death-domain associated protein (DAXX). DAXX is a
nuclear protein that modulates transcription of various
genes and is involved in cell death and/or the
suppression of growth. DAXX is also a histone chaperone
conserved in Metazoa that acts specifically on histone
H3.3. This alignment models the N-terminal helical
bundle domain of DAXX, which was shown to interact with
the tumor suppressor Ras-association domain family 1C
(RASSF1C).
Length = 88
Score = 24.4 bits (53), Expect = 6.8
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 31 SRNLSEK-KRRDQFNMLINELCTMVSTNNRKMDKS 64
SR L+ R + + INELCT++ + K +
Sbjct: 54 SRCLARIAARPAKLYVYINELCTVLKAHTPKKKLN 88
>gnl|CDD|225347 COG2733, COG2733, Predicted membrane protein [Function unknown].
Length = 415
Score = 25.0 bits (55), Expect = 8.2
Identities = 12/54 (22%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 4 HQLEQSFNRNSDDTMDDT-DDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVST 56
H++ + F+R D +DD D + R S K + ++ T +S
Sbjct: 251 HKMRKDFDRFLFDLIDDLYHDPGMAARAEAIKSYLKEDEAIATAAGDMWTSLSE 304
>gnl|CDD|119351 cd02872, GH18_chitolectin_chitotriosidase, This conserved domain
family includes a large number of catalytically inactive
chitinase-like lectins (chitolectins) including YKL-39,
YKL-40 (HCGP39), YM1, oviductin, and AMCase (acidic
mammalian chitinase), as well as catalytically active
chitotriosidases. The conserved domain is an
eight-stranded alpha/beta barrel fold belonging to the
family 18 glycosyl hydrolases. The fold has a
pronounced active-site cleft at the C-terminal end of
the beta-barrel. The chitolectins lack a key active
site glutamate (the proton donor required for hydrolytic
activity) but retain highly conserved residues involved
in oligosaccharide binding. Chitotriosidase is a
chitinolytic enzyme expressed in maturing macrophages,
which suggests that it plays a part in antimicrobial
defense. Chitotriosidase hydrolyzes chitotriose, as
well as colloidal chitin to yield chitobiose and is
therefore considered an exochitinase. Chitotriosidase
occurs in two major forms, the large form being
converted to the small form by either RNA or
post-translational processing. Although the small form,
containing the chitinase domain alone, is sufficient for
the chitinolytic activity, the additional C-terminal
chitin-binding domain of the large form plays a role in
processing colloidal chitin. The chitotriosidase gene is
nonessential in humans, as about 35% of the population
are heterozygous and 6% homozygous for an inactivated
form of the gene. HCGP39 is a 39-kDa human cartilage
glycoprotein thought to play a role in connective tissue
remodeling and defense against pathogens.
Length = 362
Score = 24.8 bits (55), Expect = 8.6
Identities = 12/28 (42%), Positives = 16/28 (57%), Gaps = 5/28 (17%)
Query: 52 TMVST-NNRKMDKSTVLKSTIAFLKNYN 78
M ++ NRK T +KS IAFL+ Y
Sbjct: 89 AMAASPENRK----TFIKSAIAFLRKYG 112
>gnl|CDD|218270 pfam04795, PAPA-1, PAPA-1-like conserved region. Family of
proteins with a conserved region found in PAPA-1, a
PAP-1 binding protein.
Length = 89
Score = 24.2 bits (53), Expect = 9.2
Identities = 8/22 (36%), Positives = 14/22 (63%)
Query: 29 RKSRNLSEKKRRDQFNMLINEL 50
R+ +N SEK+ ++ IN+L
Sbjct: 11 RRRKNQSEKRAEEEKMETINKL 32
>gnl|CDD|217050 pfam02460, Patched, Patched family. The transmembrane protein
Patched is a receptor for the morphogene Sonic Hedgehog.
This protein associates with the smoothened protein to
transduce hedgehog signals.
Length = 801
Score = 24.6 bits (54), Expect = 9.6
Identities = 10/50 (20%), Positives = 21/50 (42%), Gaps = 8/50 (16%)
Query: 33 NLSEKKRRDQFNMLINELCTMVSTNNRKMDKSTVLKSTIAFLKNYNGTYY 82
+L+ + RD+ N +++E + + ST +L+ Y Y
Sbjct: 504 DLTIPENRDRLNEMVDEFESTPYSMGP--------NSTSFWLREYENFYK 545
>gnl|CDD|217503 pfam03344, Daxx, Daxx Family. The Daxx protein (also known as the
Fas-binding protein) is thought to play a role in
apoptosis, but precise role played by Daxx remains to be
determined. Daxx forms a complex with Axin.
Length = 715
Score = 24.9 bits (54), Expect = 9.6
Identities = 12/37 (32%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 31 SRNLSE-KKRRDQFNMLINELCTMVSTNNRKMDKSTV 66
R L+ + RR + + INELCT++ ++ K + T+
Sbjct: 115 GRCLTRAQARRTKTFVYINELCTVLKQHSAKKRQVTL 151
>gnl|CDD|151173 pfam10669, Phage_Gp23, Protein gp23 (Bacteriophage A118). This
is the highly conserved family of the major tail
subunit protein.
Length = 121
Score = 24.3 bits (52), Expect = 9.9
Identities = 13/46 (28%), Positives = 25/46 (54%)
Query: 18 MDDTDDKDDSKRKSRNLSEKKRRDQFNMLINELCTMVSTNNRKMDK 63
M + DK +++R+ R+ K+ RD+F +NE ++ N M +
Sbjct: 48 MKEERDKMETEREKRDKESKEERDKFISTMNEQQRLMDKQNDMMGQ 93
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 0.355
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: 4,336,856
Number of extensions: 322634
Number of successful extensions: 429
Number of sequences better than 10.0: 1
Number of HSP's gapped: 424
Number of HSP's successfully gapped: 29
Length of query: 95
Length of database: 10,937,602
Length adjustment: 62
Effective length of query: 33
Effective length of database: 8,187,654
Effective search space: 270192582
Effective search space used: 270192582
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)