RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16979
(114 letters)
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 55.9 bits (135), Expect = 4e-12
Identities = 23/40 (57%), Positives = 26/40 (65%)
Query: 75 QCVICLAPFQPGEEVKELLCHHKFHSECLEPWLRERQHCP 114
+C ICL F+PGEEV L C H FH ECL+ WLR CP
Sbjct: 2 ECPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCP 41
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to chromosome
metabolism and cell cycle control.
Length = 73
Score = 44.7 bits (106), Expect = 1e-07
Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 10/61 (16%)
Query: 64 IAFPADEAPDAQCVICLAPF--------QPGEE--VKELLCHHKFHSECLEPWLRERQHC 113
+A + + D C IC F PG++ V C H FH C+ WL+ R C
Sbjct: 10 VALWSWDIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTC 69
Query: 114 P 114
P
Sbjct: 70 P 70
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain, a
specialized type of Zn-finger of 40 to 60 residues that
binds two atoms of zinc; defined by the 'cross-brace'
motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified in
a proteins with a wide range of functions such as viral
replication, signal transduction, and development; has
two variants, the C3HC4-type and a C3H2C3-type (RING-H2
finger), which have different cysteine/histidine
pattern; a subset of RINGs are associated with B-Boxes
(C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 40.5 bits (95), Expect = 3e-06
Identities = 16/41 (39%), Positives = 22/41 (53%), Gaps = 3/41 (7%)
Query: 75 QCVICLAPFQPGEEVKELLCHHKFHSECLEPWLRERQ-HCP 114
+C ICL F+ E V L C H F C++ WL+ + CP
Sbjct: 1 ECPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCP 39
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 43.8 bits (103), Expect = 3e-06
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 1/41 (2%)
Query: 75 QCVICLAPFQPGEEVKELLCHHKFHSECLEPWLRERQH-CP 114
+C IC++ F + ++ L C H+FH C++ WL + CP
Sbjct: 325 ECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCP 365
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 37.9 bits (88), Expect = 9e-05
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 76 CVICLAPFQPGEEVKEL--LCHHKFHSECLEPWLRERQHCP 114
C C PG+E + +C+H FH C+ WL + CP
Sbjct: 34 CPECQFGMTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCP 74
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 39.6 bits (92), Expect = 1e-04
Identities = 19/52 (36%), Positives = 22/52 (42%), Gaps = 10/52 (19%)
Query: 73 DAQCVICL-APFQPGEEV---------KELLCHHKFHSECLEPWLRERQHCP 114
D C IC+ F P E K L C H H CL+ WL +Q CP
Sbjct: 287 DRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCP 338
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and is
likely to be a general function of this domain; Various
RING fingers exhibit binding activity towards E2
ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 35.2 bits (81), Expect = 3e-04
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 76 CVICLAPFQPGEEVKELLCHHKFHSECLEPWLRER-QHCP 114
C ICL + ++ L C H F C+ WL CP
Sbjct: 1 CPICLEEYL--KDPVILPCGHTFCRSCIRKWLESGNNTCP 38
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11 RING-H2
finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 35.9 bits (83), Expect = 5e-04
Identities = 17/59 (28%), Positives = 22/59 (37%), Gaps = 13/59 (22%)
Query: 69 DEAPDAQCVICLAPFQ--------PGEEVKELL--CHHKFHSECLEPWLRE---RQHCP 114
D D C IC F PG++ + C H FH C+ WL + CP
Sbjct: 17 DTPSDDVCGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKGLCP 75
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 34.8 bits (80), Expect = 6e-04
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 76 CVICLAPFQPGEEVKELLCHHKFHSECLEPWLRERQHCP 114
C ICL + + V C H F EC+ +L+++ CP
Sbjct: 5 CPICLDLLR--DPVVLTPCGHVFCRECILRYLKKKSKCP 41
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 31.7 bits (72), Expect = 0.007
Identities = 15/40 (37%), Positives = 19/40 (47%), Gaps = 3/40 (7%)
Query: 76 CVICLAPFQPGEEVKELLCHHKFHSECLEPWLR-ERQHCP 114
C ICL + + V L C H F S+C+ WL CP
Sbjct: 1 CPICLEEPK--DPVTILPCGHLFCSKCILSWLESGNVTCP 38
>gnl|CDD|204746 pfam11793, FANCL_C, FANCL C-terminal domain. This domain is found
at the C-terminus of the Fancl protein in humans which
is the putative E3 ubiquitin ligase subunit of the FA
complex (Fanconi anaemia). Eight subunits of the Fanconi
anaemia gene products form a multisubunit nuclear
complex which is required for mono-ubiquitination of a
downstream FA protein, FANCD2.
Length = 70
Score = 31.6 bits (72), Expect = 0.014
Identities = 14/40 (35%), Positives = 19/40 (47%), Gaps = 5/40 (12%)
Query: 75 QCVICLAPFQPGEEVKELLCHH-----KFHSECLEPWLRE 109
+C IC A G E+ ++ C + FH CL WLR
Sbjct: 4 ECGICYAYRLDGGEIPDISCDNPKCGLPFHIACLYEWLRT 43
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 32.1 bits (73), Expect = 0.037
Identities = 15/52 (28%), Positives = 27/52 (51%), Gaps = 7/52 (13%)
Query: 69 DEAPDAQCVICLAPFQPGEEVKELL------CHHKFHSECLEPWLRERQHCP 114
+ + D +C IC+ +E+K + C+H F EC++ W +E+ CP
Sbjct: 170 NRSKDKECAICMEKVY-DKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCP 220
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 30.8 bits (69), Expect = 0.14
Identities = 10/23 (43%), Positives = 13/23 (56%), Gaps = 2/23 (8%)
Query: 94 CHHKFHSECLEPWLRE--RQHCP 114
C +KFH+ CL W R +CP
Sbjct: 1494 CKNKFHTRCLYKWFASSARSNCP 1516
>gnl|CDD|237537 PRK13875, PRK13875, conjugal transfer protein TrbL; Provisional.
Length = 440
Score = 29.9 bits (68), Expect = 0.24
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 20 MGETIIIDRFLNISRRYND 38
M +T +IDRFLN RY D
Sbjct: 1 MNDTGVIDRFLNTFTRYID 19
>gnl|CDD|240008 cd04637, CBS_pair_24, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa
(IMP dehydrogenase-1), and homocystinuria
(cystathionine beta-synthase).
Length = 122
Score = 28.9 bits (65), Expect = 0.30
Identities = 9/23 (39%), Positives = 13/23 (56%)
Query: 77 VICLAPFQPGEEVKELLCHHKFH 99
V+ + EEV+E+ HKFH
Sbjct: 3 VVTVEMDDRLEEVREIFEKHKFH 25
>gnl|CDD|218794 pfam05883, Baculo_RING, Baculovirus U-box/Ring-like domain. This
family consists of several Baculovirus proteins of
around 130 residues in length. The function of this
family is unknown, but it appears to be related to the
U-box and ring finger domain by profile-profile
comparison.
Length = 135
Score = 28.4 bits (64), Expect = 0.61
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 6/45 (13%)
Query: 76 CVICLAPFQPGEEVKELLCH------HKFHSECLEPWLRERQHCP 114
C ICL + V + FH+EC + W RER+ P
Sbjct: 29 CAICLDRINDNDGVVAVTDGGTLNLEKMFHAECDKRWKRERKRDP 73
>gnl|CDD|128983 smart00744, RINGv, The RING-variant domain is a C4HC3 zinc-finger
like motif found in a number of cellular and viral
proteins. Some of these proteins have been shown both
in vivo and in vitro to have ubiquitin E3 ligase
activity. The RING-variant domain is reminiscent of both
the RING and the PHD domains and may represent an
evolutionary intermediate. To describe this domain the
term PHD/LAP domain has been used in the past. Extended
description: The RING-variant (RINGv) domain contains a
C4HC3 zinc-finger-like motif similar to the PHD domain,
while some of the spacing between the Cys/His residues
follow a pattern somewhat closer to that found in the
RING domain. The RINGv domain, similar to the RING, PHD
and LIM domains, is thought to bind two zinc ions
co-ordinated by the highly conserved Cys and His
residues. RING variant domain: C-x (2) -C-x(10-45)-C-x
(1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a
PHD: C-x(1-2) -C-x
(7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C
Classical RING domain: C-x (2) -C-x
(9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
Length = 49
Score = 26.5 bits (59), Expect = 0.77
Identities = 12/42 (28%), Positives = 15/42 (35%), Gaps = 6/42 (14%)
Query: 75 QCVICLAPFQPGEEVKELLCH-----HKFHSECLEPWLRERQ 111
C IC G+ + C H ECLE W+ E
Sbjct: 1 ICRICHDEGDEGDPLV-SPCRCKGSLKYVHQECLERWINESG 41
>gnl|CDD|219116 pfam06636, DUF1157, Protein of unknown function (DUF1157). This
family consists of several uncharacterized proteins
from Melanoplus sanguinipes entomopoxvirus (MsEPV). The
function of this family is unknown.
Length = 370
Score = 28.2 bits (63), Expect = 0.91
Identities = 10/19 (52%), Positives = 15/19 (78%)
Query: 13 FIIYHGAMGETIIIDRFLN 31
F+I +G+M E +IIDRF +
Sbjct: 51 FMIINGSMYENVIIDRFFD 69
>gnl|CDD|235106 PRK03158, PRK03158, histidinol-phosphate aminotransferase;
Provisional.
Length = 359
Score = 27.6 bits (62), Expect = 1.3
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 45 ELSPPRAPFSTRRFGQIPSIAFPADEAPDAQCV 77
+L+ R PF+T R Q +IA D+A +CV
Sbjct: 243 KLNIARPPFNTTRIAQYAAIAALEDQAFLKECV 275
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain.
Length = 47
Score = 25.8 bits (57), Expect = 1.4
Identities = 14/47 (29%), Positives = 18/47 (38%), Gaps = 12/47 (25%)
Query: 76 CVICLAPFQPGEEVKELL--CH-----HKFHSECLEPWLRER--QHC 113
C IC + EE + L+ C H CLE WL+ C
Sbjct: 1 CRIC---LEGEEEDEPLIRPCRCRGSLKYVHQSCLERWLKTSGNTTC 44
>gnl|CDD|177362 PHA02415, PHA02415, DNA primase domain-containing protein.
Length = 930
Score = 27.7 bits (61), Expect = 1.5
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 5/52 (9%)
Query: 38 DALSLDSELSPPRAPFSTRRFGQIPSIAFPADEAPDAQCVICL---APFQPG 86
+ALS+D+ P A + R + +I F + Q VICL PF+ G
Sbjct: 231 NALSIDTCAMPGAAALALRGLANVDAIDFSSLRG--KQVVICLDNDEPFEDG 280
>gnl|CDD|241027 cd12583, RRM2_hnRNPD, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D0 (hnRNP D0) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP D0, also termed AU-rich element RNA-binding
protein 1, a UUAG-specific nuclear RNA binding protein
that may be involved in pre-mRNA splicing and telomere
elongation. hnRNP D0 contains two RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), in the middle and an RGG
box rich in glycine and arginine residues in the
C-terminal part. Each of RRMs can bind solely to the
UUAG sequence specifically. .
Length = 75
Score = 26.1 bits (57), Expect = 1.7
Identities = 18/62 (29%), Positives = 29/62 (46%), Gaps = 3/62 (4%)
Query: 39 ALSLDSELSPPRAPFSTRRFGQIPSIAFPADEAPDAQCVICLAPFQPGEEVKELLCHHKF 98
LS D+ R F FG++ SI P D + + C F+ E VK+++ K+
Sbjct: 6 GLSPDTPEEKIREYFGA--FGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIM-EKKY 62
Query: 99 HS 100
H+
Sbjct: 63 HN 64
>gnl|CDD|241029 cd12585, RRM2_hnRPDL, RNA recognition motif 2 in heterogeneous
nuclear ribonucleoprotein D-like (hnRNP DL) and similar
proteins. This subgroup corresponds to the RRM2 of
hnRNP DL (or hnRNP D-like), also termed AU-rich element
RNA-binding factor, or JKT41-binding protein (protein
laAUF1 or JKTBP), is a dual functional protein that
possesses DNA- and RNA-binding properties. It has been
implicated in mRNA biogenesis at the transcriptional
and post-transcriptional levels. hnRNP DL binds
single-stranded DNA (ssDNA) or double-stranded DNA
(dsDNA) in a non-sequencespecific manner, and interacts
with poly(G) and poly(A) tenaciously. It contains two
putative two RNA recognition motifs (RRMs), also termed
RBDs (RNA binding domains) or RNPs (ribonucleoprotein
domains), and a glycine- and tyrosine-rich C-terminus.
.
Length = 75
Score = 26.1 bits (57), Expect = 1.8
Identities = 12/42 (28%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 58 FGQIPSIAFPADEAPDAQCVICLAPFQPGEEVKELLCHHKFH 99
FG+I +I P D + + C + E V++LL ++H
Sbjct: 23 FGEIENIELPMDTKTNERRGFCFVTYTDEEPVQKLL-ESRYH 63
>gnl|CDD|177904 PLN02263, PLN02263, serine decarboxylase.
Length = 470
Score = 27.1 bits (60), Expect = 2.6
Identities = 7/43 (16%), Positives = 14/43 (32%)
Query: 62 PSIAFPADEAPDAQCVICLAPFQPGEEVKELLCHHKFHSECLE 104
P + V +A + +E++ H+ CL
Sbjct: 15 PDLLVSDPLPVATYNVAVVAEYGDLGGEREIVLGRNVHTTCLA 57
>gnl|CDD|132807 cd06897, PX_SNARE, The phosphoinositide binding Phox Homology
domain of SNARE proteins from fungi. The PX domain is
a phosphoinositide (PI) binding module present in many
proteins with diverse functions such as cell signaling,
vesicular trafficking, protein sorting, and lipid
modification, among others. This subfamily is composed
of fungal proteins similar to Saccharomyces cerevisiae
Vam7p. They contain an N-terminal PX domain and a
C-terminal SNARE domain. The SNARE (Soluble NSF
attachment protein receptor) family of proteins are
integral membrane proteins that serve as key factors
for vesicular trafficking. Vam7p is anchored at the
vacuolar membrane through the specific interaction of
its PX domain with phosphatidylinositol-3-phosphate
(PI3P) present in bilayers. It plays an essential role
in vacuole fusion. The PX domain is involved in
targeting of proteins to PI-enriched membranes, and may
also be involved in protein-protein interaction.
Length = 108
Score = 26.1 bits (58), Expect = 3.3
Identities = 8/33 (24%), Positives = 16/33 (48%), Gaps = 5/33 (15%)
Query: 32 ISRRYNDALSLDSEL-----SPPRAPFSTRRFG 59
+SRRY++ ++L +L P P + +
Sbjct: 31 VSRRYSEFVALHKQLESEVGIEPPYPLPPKSWF 63
>gnl|CDD|240775 cd12329, RRM2_hnRNPD_like, RNA recognition motif 2 in
heterogeneous nuclear ribonucleoprotein hnRNP D0, hnRNP
A/B, hnRNP DL and similar proteins. This subfamily
corresponds to the RRM2 of hnRNP D0, hnRNP A/B, hnRNP
DL and similar proteins. hnRNP D0, a UUAG-specific
nuclear RNA binding protein that may be involved in
pre-mRNA splicing and telomere elongation. hnRNP A/B is
an RNA unwinding protein with a high affinity for G-
followed by U-rich regions. It has also been identified
as an APOBEC1-binding protein that interacts with
apolipoprotein B (apoB) mRNA transcripts around the
editing site and thus plays an important role in apoB
mRNA editing. hnRNP DL (or hnRNP D-like) is a dual
functional protein that possesses DNA- and RNA-binding
properties. It has been implicated in mRNA biogenesis
at the transcriptional and post-transcriptional levels.
All memembers in this family contain two putative RNA
recognition motifs (RRMs), also termed RBDs (RNA
binding domains) or RNPs (ribonucleoprotein domains),
and a glycine- and tyrosine-rich C-terminus. .
Length = 75
Score = 25.0 bits (55), Expect = 4.8
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 57 RFGQIPSIAFPADEAPDAQCVICLAPFQPGEEVKELLCHHKFH 99
+FG I I P D+ + + C F E VK+ + +FH
Sbjct: 22 KFGNIVEIELPMDKKTNKRRGFCFITFDSEEPVKK-ILETQFH 63
>gnl|CDD|235039 PRK02458, PRK02458, ribose-phosphate pyrophosphokinase;
Provisional.
Length = 323
Score = 25.9 bits (57), Expect = 5.5
Identities = 12/36 (33%), Positives = 19/36 (52%)
Query: 4 EDDGFNTSGFIIYHGAMGETIIIDRFLNISRRYNDA 39
+DD G+II A + I+ID LN + + +A
Sbjct: 202 QDDSEREEGYIIGDVAGKKAILIDDILNTGKTFAEA 237
>gnl|CDD|226909 COG4533, COG4533, ABC-type uncharacterized transport system,
periplasmic component [General function prediction
only].
Length = 564
Score = 25.4 bits (56), Expect = 8.1
Identities = 13/65 (20%), Positives = 21/65 (32%), Gaps = 4/65 (6%)
Query: 38 DALSLDSELSPPRAPFSTRRFGQIPSIAFPADEAPDAQCVICLAPFQPGEEVKELL---C 94
+L+ L P P+ +P++ P D D I PF+ E L
Sbjct: 230 HPYTLEIHLHRP-DPWLPLLLASVPAMILPRDVPTDPDHPIGTGPFKVQENTDNRLVLEA 288
Query: 95 HHKFH 99
+
Sbjct: 289 FDHYF 293
>gnl|CDD|222444 pfam13901, DUF4206, Domain of unknown function (DUF4206). This is
a family of cysteine-rich proteins. Many members also
carry a pleckstrin-homology domain, pfam00169.
Length = 202
Score = 25.3 bits (56), Expect = 8.1
Identities = 13/44 (29%), Positives = 15/44 (34%), Gaps = 10/44 (22%)
Query: 76 CVIC-----LAPFQPGEEVKELLCHHKFHSECLEPWLRERQHCP 114
C C + PFQ + C FH EC E CP
Sbjct: 155 CEFCDNDEVIFPFQTDTTSRCEGCGAVFHKECY-----ESSPCP 193
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 23.7 bits (51), Expect = 8.6
Identities = 10/30 (33%), Positives = 14/30 (46%)
Query: 76 CVICLAPFQPGEEVKELLCHHKFHSECLEP 105
C +C P GE ++ C +H CL P
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGP 31
>gnl|CDD|192013 pfam08356, EF_assoc_2, EF hand associated. This region
predominantly appears near EF-hands (pfam00036) in
GTP-binding proteins. It is found in all three
eukaryotic kingdoms.
Length = 89
Score = 24.4 bits (54), Expect = 9.3
Identities = 14/60 (23%), Positives = 21/60 (35%), Gaps = 13/60 (21%)
Query: 5 DDGFNTSGFIIYH------GAMGETIIIDRFLNISRRYNDALSLDSELSPPR---APFST 55
+ G GF+ + G T I R Y D+LSL + P+ P +
Sbjct: 26 EKGLTLKGFLFLNKLFIERGRHETTWTILRKFG----YTDSLSLRDDFLHPKFDVPPDQS 81
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
0.323 0.140 0.450
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,037,496
Number of extensions: 515330
Number of successful extensions: 468
Number of sequences better than 10.0: 1
Number of HSP's gapped: 465
Number of HSP's successfully gapped: 42
Length of query: 114
Length of database: 10,937,602
Length adjustment: 78
Effective length of query: 36
Effective length of database: 7,477,990
Effective search space: 269207640
Effective search space used: 269207640
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)