RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10334
(314 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 58.4 bits (142), Expect = 7e-11
Identities = 20/60 (33%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 103 SKSSLQTYQRLFPNSTLCLNVKNLLSELKLKYGLSIKLVWIPGHMNISGNCAVDLAAKQA 162
S+++L+ + +S L L ++ + EL G+ ++L W+PGH I GN D AK+A
Sbjct: 68 SQAALKALRSPRSSSPLVLRIRKAIRELANH-GVKVRLHWVPGHSGIEGNERADRLAKEA 126
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 49.2 bits (118), Expect = 2e-07
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 98 NLQMNSKSSLQTYQRLFPNSTLCLNVKNLLSELKLKYGLSIKLVWIPGHMNISGNCAVDL 157
N+ +S+ + +P + +KN + EL K + + W+PGH I GN D
Sbjct: 61 NIYTDSQYVIGGITNGWPTKSESKPIKNEIWELLQK-KHKVYIQWVPGHSGIPGNELADK 119
Query: 158 AAKQA 162
AKQ
Sbjct: 120 LAKQG 124
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 40.2 bits (94), Expect = 3e-05
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 33 FRCFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHCRA 76
C IC++ LRD + C + C CI ++L +++S+CP CR
Sbjct: 3 LECPICLDLLRDPVVLTPCGHVFCRECILRYL-KKKSKCPICRT 45
>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 = 39.7 bits (93), Expect = 5e-05
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 35 CFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHCRASL 78
C IC+E+ R+ + C + C +CI ++L ++ CP CR +
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 39.5 bits (92), Expect = 0.001
Identities = 16/53 (30%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 33 FRCFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQ-CPHCRASLHMTDLV 84
++CF+C+E+ C C L CL+C+ T+++ + CP CRA ++ ++
Sbjct: 216 YKCFLCLEEPEVP-SCTPCGHLFCLSCLLISWTKKKYEFCPLCRAKVYPKKVI 267
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 38.4 bits (89), Expect = 0.004
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 33 FRCFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHCRASLHMTDLVNCRWMEEV 92
RC IC + L CS C CIR+ L+ + +CP CRA + L + + E+
Sbjct: 27 LRCHICKDFFDVPVLTS-CSHTFCSLCIRRCLSNQ-PKCPLCRAEDQESKLRSNWLVSEI 84
Query: 93 TQHLDNLQ 100
+ NL+
Sbjct: 85 VESFKNLR 92
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 31.2 bits (71), Expect = 0.052
Identities = 12/46 (26%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 35 CFICIEKLRDTH---LCPHCSKLCCLACIRQFLTEERSQCPHCRAS 77
C IC+++ + P C + C+ ++L + CP CRA
Sbjct: 3 CPICLDEFEPGEEVVVLP-CGHVFHKECLDKWL-RSSNTCPLCRAP 46
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 31.2 bits (71), Expect = 0.061
Identities = 13/45 (28%), Positives = 20/45 (44%), Gaps = 6/45 (13%)
Query: 35 CFICIEKLRDTHLCP--HCSKLCCLACIRQFLTEERSQCPHCRAS 77
C IC+E+ R+ P H C C ++ + +CP CR
Sbjct: 5 CVICLERPRNVVFLPCGHLC--LCEECAKRLR--SKKKCPICRQP 45
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
more complex than their prokaryotic counterparts and
unlike prokaryote, RNase H are essential in higher
eukaryote. Ribonuclease H (RNase H) is classified into
two families, type 1 (prokaryotic RNase HI, eukaryotic
RNase H1 and viral RNase H) and type 2 (prokaryotic
RNase HII and HIII, and eukaryotic RNase H2). RNase H is
an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. RNase
H is involved in DNA replication, repair and
transcription. One of the important functions of RNase H
is to remove Okazaki fragments during DNA replication.
RNase H is widely present in various organisms,
including bacteria, archaea and eukaryote and most
prokaryotic and eukaryotic genomes contain multiple
RNase H genes. Despite the lack of amino acid sequence
homology, Type 1 and type 2 RNase H share a main-chain
fold and steric configurations of the four acidic
active-site (DEDD) residues and have the same catalytic
mechanism and functions in cells. Eukaryotic RNase H is
longer and more complex than in prokaryotes. Almost all
eukaryotic RNase HI have highly conserved regions at the
N-terminal called hybrid binding domain (HBD). It is
speculated that the HBD contributes to binding the
RNA/DNA hybrid. Prokaryotes and some single-cell
eukaryotes do not require RNase H for viability, but
RNase H is essential in higher eukaryotes. RNase H
knockout mice lack mitochondrial DNA replication and die
as embryos.
Length = 150
Score = 33.3 bits (77), Expect = 0.062
Identities = 15/38 (39%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 125 NLLSELKLKYGLSIKLVWIPGHMNISGNCAVDLAAKQA 162
LL EL+ + G+ +K +PGH I GN D AK+
Sbjct: 112 KLLEELEER-GIRVKFWHVPGHSGIYGNEEADRLAKKG 148
>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 = 30.6 bits (69), Expect = 0.077
Identities = 13/40 (32%), Positives = 20/40 (50%)
Query: 35 CFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHC 74
C IC+E+ + C C +CIR++L + CP C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 31.3 bits (71), Expect = 0.45
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 8/48 (16%)
Query: 35 CFICIEKLRDTH-------LCPHCSKLCCLACIRQFLTEERSQCPHCR 75
C IC+EK+ D + +C+ + C+ CI + +E++ CP CR
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIW-KKEKNTCPVCR 223
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 30.4 bits (69), Expect = 0.74
Identities = 7/33 (21%), Positives = 12/33 (36%)
Query: 137 SIKLVWIPGHMNISGNCAVDLAAKQAQTSPDAE 169
+ W+ GH N D A++A +
Sbjct: 117 LVFWEWVKGHAGHPENERADQLAREAARAAKKS 149
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated families, type 1
(prokaryotic RNase HI, eukaryotic RNase H1 and viral
RNase H) and type 2 (prokaryotic RNase HII and HIII, and
eukaryotic RNase H2). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is involved in DNA
replication, repair and transcription. RNase H is widely
present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD),
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability.
Length = 139
Score = 29.8 bits (68), Expect = 0.78
Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 3/43 (6%)
Query: 123 VKN--LLSEL-KLKYGLSIKLVWIPGHMNISGNCAVDLAAKQA 162
VKN L EL L + W+ GH GN D A A
Sbjct: 95 VKNVDLWQELDALLAKHQVTWHWVKGHAGHPGNERADELANAA 137
>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 = 27.8 bits (62), Expect = 0.78
Identities = 14/40 (35%), Positives = 18/40 (45%)
Query: 35 CFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHC 74
C IC+E+ +D C L C CI +L CP C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
Ribonuclease H (RNase H) enzymes are divided into two
major families, Type 1 and Type 2, based on amino acid
sequence similarities and biochemical properties. RNase
H is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner in the
presence of divalent cations. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD)
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini of
eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 28.6 bits (65), Expect = 2.3
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 131 KLKYGLSIKLVWIPGHMNISGNCAVDLAAKQA 162
K+K + I V + H N D AK+A
Sbjct: 101 KIKKKIKISFVKVKAHSGDKYNELADKLAKKA 132
>gnl|CDD|227644 COG5339, COG5339, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 479
Score = 29.7 bits (67), Expect = 2.4
Identities = 15/63 (23%), Positives = 22/63 (34%), Gaps = 11/63 (17%)
Query: 90 EEVTQHLDNLQM---------NSKSSLQTYQRLFPNS--TLCLNVKNLLSELKLKYGLSI 138
E + Q + + K S Q Y+R +S L L LK+K G +
Sbjct: 29 ESLEQQVKQANAQGKLTEPSSSVKVSYQNYERGVFSSKVQLLLKADTGADNLKIKPGQPV 88
Query: 139 KLV 141
V
Sbjct: 89 TFV 91
>gnl|CDD|222869 PHA02550, 32, single-stranded DNA binding protein; Provisional.
Length = 304
Score = 29.3 bits (66), Expect = 2.9
Identities = 10/27 (37%), Positives = 12/27 (44%), Gaps = 4/27 (14%)
Query: 194 WSYETCDNKLKNIKQDTKYWASSTRNI 220
Y T + K K+ T YWA NI
Sbjct: 99 DLYNTGKEEYKLRKRKTSYWA----NI 121
>gnl|CDD|234843 PRK00811, PRK00811, spermidine synthase; Provisional.
Length = 283
Score = 29.0 bits (66), Expect = 3.0
Identities = 15/75 (20%), Positives = 25/75 (33%), Gaps = 23/75 (30%)
Query: 162 AQT-SP--DAEILNVTHTDLKSFFKKI----------PSEKWKLTW----------SYET 198
AQ+ SP A+ + H LK F + PS W T+ +
Sbjct: 189 AQSGSPFYQADEIKDMHRKLKEVFPIVRPYQAAIPTYPSGLWSFTFASKNDDLKFLPLDV 248
Query: 199 CDNKLKNIKQDTKYW 213
+ + T+Y+
Sbjct: 249 IEARFAERGIKTRYY 263
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 28.8 bits (64), Expect = 3.6
Identities = 10/41 (24%), Positives = 15/41 (36%)
Query: 35 CFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHCR 75
C IC + P ++C +R + CP CR
Sbjct: 64 CQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCR 104
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 28.9 bits (64), Expect = 3.8
Identities = 13/42 (30%), Positives = 19/42 (45%)
Query: 33 FRCFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQCPHC 74
+C +C LR+ P C C CI L + +CP+C
Sbjct: 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNC 316
>gnl|CDD|235287 PRK04342, PRK04342, DNA topoisomerase VI subunit A; Provisional.
Length = 367
Score = 28.7 bits (65), Expect = 4.3
Identities = 21/86 (24%), Positives = 36/86 (41%), Gaps = 26/86 (30%)
Query: 132 LKYGLSIKLVWIPGHMNISGNCAVDLAAKQAQTSPDAEILNVTHTDLKSFFKKIPSEKWK 191
+KYG SIKL + LA PDA+ + VT +D+ + + +P+ K K
Sbjct: 261 VKYG-SIKLAHLSE----------RLAT------PDAKFIGVTPSDIVEYERDLPTIKLK 303
Query: 192 LTWSYETCDNKLKNIKQD----TKYW 213
++ + K + T +W
Sbjct: 304 -----DSDIKRAKELLNYPWFQTDFW 324
>gnl|CDD|193125 pfam12647, RNHCP, RNHCP domain. This family of proteins is found
in bacteria. Proteins in this family are typically
between 94 and 143 amino acids in length. There is a
conserved RNHCP sequence motif.
Length = 93
Score = 26.9 bits (60), Expect = 5.7
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 3/35 (8%)
Query: 48 CPHCSKLCCLACIRQFLTEERSQCPHCRASLHMTD 82
C HC T R+ CP+C +SLH+
Sbjct: 8 CVHCG---LDVPPLGPGTAHRNHCPNCLSSLHVDI 39
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 27.7 bits (61), Expect = 5.8
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 16/67 (23%)
Query: 33 FRCFICIEKLRDTHLCPHCSKLCCLACIRQFL---------------TEERSQCPHCRAS 77
F C IC++++RD + C L C CI ++ E +CP C++
Sbjct: 19 FDCNICLDQVRDP-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSD 77
Query: 78 LHMTDLV 84
+ LV
Sbjct: 78 VSEATLV 84
>gnl|CDD|225542 COG2995, PqiA, Uncharacterized paraquat-inducible protein A
[Function unknown].
Length = 418
Score = 28.1 bits (63), Expect = 6.0
Identities = 17/69 (24%), Positives = 23/69 (33%), Gaps = 8/69 (11%)
Query: 12 VLFLRLFISTTSHVSRA-LAEVFRCFICIEKLRDTHLCPHCSKLCCLACIRQFLTEERSQ 70
V L T S V+R L E F R+ CL C + +
Sbjct: 185 VALALLTTRTFSCVNRRWLWERFYPQTLATGARE-------GLRSCLCCHYILPHDAEPR 237
Query: 71 CPHCRASLH 79
CP C + L+
Sbjct: 238 CPRCGSKLY 246
>gnl|CDD|184831 PRK14811, PRK14811, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 269
Score = 27.8 bits (62), Expect = 6.6
Identities = 12/25 (48%), Positives = 13/25 (52%), Gaps = 4/25 (16%)
Query: 34 RCFICIEKL----RDTHLCPHCSKL 54
RC IEK+ R TH CP C L
Sbjct: 240 RCGTPIEKIVVGGRGTHFCPQCQPL 264
>gnl|CDD|133455 cd05313, NAD_bind_2_Glu_DH, NAD(P) binding domain of glutamate
dehydrogenase, subgroup 2. Amino acid dehydrogenase
(DH) is a widely distributed family of enzymes that
catalyzes the oxidative deamination of an amino acid to
its keto acid and ammonia with concomitant reduction of
NADP+. Glutamate DH is a multidomain enzyme that
catalyzes the reaction from glutamate to 2-oxyoglutarate
and ammonia in the presence of NAD or NADP. It is
present in all organisms. Enzymes involved in ammonia
asimilation are typically NADP+-dependent, while those
involved in glutamate catabolism are generally
NAD+-dependent. Amino acid DH-like NAD(P)-binding
domains are members of the Rossmann fold superfamily and
include glutamate, leucine, and phenylalanine DHs,
methylene tetrahydrofolate DH,
methylene-tetrahydromethanopterin DH,
methylene-tetrahydropholate DH/cyclohydrolase, Shikimate
DH-like proteins, malate oxidoreductases, and glutamyl
tRNA reductase. Amino acid DHs catalyze the deamination
of amino acids to keto acids with NAD(P)+ as a cofactor.
The NAD(P)-binding Rossmann fold superfamily includes a
wide variety of protein families including NAD(P)-
binding domains of alcohol DHs, tyrosine-dependent
oxidoreductases, glyceraldehyde-3-phosphate DH,
lactate/malate DHs, formate/glycerate DHs, siroheme
synthases, 6-phosphogluconate DH, amino acid DHs,
repressor rex, NAD-binding potassium channel domain,
CoA-binding, and ornithine cyclodeaminase-like domains.
These domains have an alpha -beta-alpha configuration.
NAD binding involves numerous hydrogen and van der Waals
contacts.
Length = 254
Score = 28.0 bits (63), Expect = 6.7
Identities = 8/20 (40%), Positives = 14/20 (70%)
Query: 191 KLTWSYETCDNKLKNIKQDT 210
+L+W+ E D KLK+I ++
Sbjct: 197 RLSWTAEEVDAKLKDIMKNI 216
>gnl|CDD|143650 cd07934, RHD-n_NFkB2, N-terminal sub-domain of the Rel homology
domain (RHD) of nuclear factor kappa B2 (NF-kappa B2).
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 NF-kappa B2 family of
transcription factors, a class I member of the NF-kappa
B family. In class I NF-kappa Bs, the RHD domain
co-occurs with C-terminal ankyrin repeats. NF-kappa B2
is commonly referred to as p100 or p52 (proteolytically
processed form). NF-kappa B proteins are part of a
protein complex that acts as a transcription factor,
which is responsible for regulating a host of cellular
responses to a variety of stimuli. This complex tightly
regulates the expression of a large number of genes, and
is involved in processes such as adaptive and innate
immunity, stress response, inflammation, cell adhesion,
proliferation and apoptosis. The cytosolic NF-kappa B
complex is activated via phosphorylation of the
ankyrin-repeat containing inhibitory protein I-kappa B,
which dissociates from the complex and exposes the
nuclear localization signal of the heterodimer (NF-kappa
B and REL). NF-kappa B2 is involved in the alternative
NF-kappa B signaling pathway which is activated by few
agonists and plays an important role in secondary
lymphoid organogenesis, maturation of B-cells, and
adaptive humoral immunity. p100 may also act as an
I-kappa B due to its C-terminal ankyrin repeats.
Length = 185
Score = 27.6 bits (61), Expect = 6.9
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 4/69 (5%)
Query: 146 HMNISGNCAVDLAAKQ--AQTSPDAEILNVTHTDLKSFFK-KIPSEKWKLTWSYETCDNK 202
H N SGNC+VD+ K AQ S + IL+VT ++ K K+ +K + T Y+ + +
Sbjct: 76 HCNESGNCSVDVGPKDMTAQFS-NLGILHVTKKNMMEILKEKLKRQKLRNTGPYKLTEAE 134
Query: 203 LKNIKQDTK 211
+ ++Q+ K
Sbjct: 135 ERELEQEAK 143
>gnl|CDD|239123 cd02658, Peptidase_C19B, 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 = 311
Score = 27.7 bits (62), Expect = 7.5
Identities = 7/37 (18%), Positives = 15/37 (40%)
Query: 231 RIGHSLLTHKFLLDRQEPPMCNDCQVQITIKQFKHIL 267
++ LL+ ++ + QV I FK ++
Sbjct: 52 KLADGLLSGRYSKPASLKSENDPYQVGIKPSMFKALI 88
>gnl|CDD|221890 pfam13005, HTH_Tnp_IS66, putative Helix-turn-helix domain of
transposase IS66. This is a putative helix-turn-helix
region of the N-terminus of the insertion element IS66
transposase.
Length = 59
Score = 25.3 bits (56), Expect = 8.1
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 7/34 (20%)
Query: 64 LTEERSQCPHCRASLHMTDLVNCRWMEEVTQHLD 97
L E CP C +LH EEV++ LD
Sbjct: 1 LEPEEKACPCCGGALH-------EIGEEVSEELD 27
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting
signal (K/R-K/R-Y-G-P-K), which supports the fact that
these proteins function not only in the cytoplasm but
also in the nucleus. CRPs control regulatory pathways
during cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 25.2 bits (56), Expect = 8.8
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 33 FRCFICIEKLRDTHLCPHCSKLCCLAC 59
F C +C ++L T L H ++ C +C
Sbjct: 26 FTCAVCNKRLDSTTLAEHDGEIYCKSC 52
>gnl|CDD|203513 pfam06750, DiS_P_DiS, Bacterial Peptidase A24 N-terminal domain.
This family is found at the N-terminus of the pre-pilin
peptidases (pfam01478). It's function has not been
specifically determined; however some of the family
have been characterized as bifunctional, and this
domain may contain the N-methylation activity
(EC:2.1.1.-). It consists of an intracellular region
between a pair of transmembrane. This region contains
an invariant proline and two almost fully conserved
disulphide bridges - hence the name DiS-P-DiS. The
cysteines have been shown to be essential to the
overall function of the enzyme in, but their role was
incorrectly ascribed.
Length = 86
Score = 25.9 bits (58), Expect = 8.8
Identities = 8/17 (47%), Positives = 9/17 (52%)
Query: 68 RSQCPHCRASLHMTDLV 84
RS CPHC L D +
Sbjct: 27 RSHCPHCGHKLRWYDNI 43
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
0.325 0.135 0.420
Gapped
Lambda K H
0.267 0.0635 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,891,637
Number of extensions: 1324270
Number of successful extensions: 1634
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1625
Number of HSP's successfully gapped: 49
Length of query: 314
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 217
Effective length of database: 6,635,264
Effective search space: 1439852288
Effective search space used: 1439852288
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 59 (26.7 bits)