RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy9147
(236 letters)
>gnl|CDD|216043 pfam00651, BTB, BTB/POZ domain. The BTB (for BR-C, ttk and bab) or
POZ (for Pox virus and Zinc finger) domain is present
near the N-terminus of a fraction of zinc finger
(pfam00096) proteins and in proteins that contain the
pfam01344 motif such as Kelch and a family of pox virus
proteins. The BTB/POZ domain mediates homomeric
dimerisation and in some instances heteromeric
dimerisation. The structure of the dimerised PLZF
BTB/POZ domain has been solved and consists of a tightly
intertwined homodimer. The central scaffolding of the
protein is made up of a cluster of alpha-helices flanked
by short beta-sheets at both the top and bottom of the
molecule. POZ domains from several zinc finger proteins
have been shown to mediate transcriptional repression
and to interact with components of histone deacetylase
co-repressor complexes including N-CoR and SMRT. The POZ
or BTB domain is also known as BR-C/Ttk or ZiN.
Length = 101
Score = 108 bits (273), Expect = 1e-30
Identities = 37/94 (39%), Positives = 59/94 (62%), Gaps = 2/94 (2%)
Query: 21 LDSLRTDGDLVDVTILCDGRKITAHKVILSACSSYFRTIFRENPCQHPVVILKDINYEDI 80
L+ LR +G+L DVT++ ++ AHK +L+ACS YF+ +F N + L+D++ ED
Sbjct: 1 LNELRENGELCDVTLVVGDKEFHAHKAVLAACSPYFKALFTGNKEVE--ITLEDVSPEDF 58
Query: 81 EAVLCFVYQGTVYISKSRMDSFLKTAESLQIKGL 114
EA+L F+Y G + I++ +D L A+ LQI L
Sbjct: 59 EALLEFIYTGKLEITEENVDDLLALADKLQIPAL 92
>gnl|CDD|197585 smart00225, BTB, Broad-Complex, Tramtrack and Bric a brac. Domain
in Broad-Complex, Tramtrack and Bric a brac. Also known
as POZ (poxvirus and zinc finger) domain. Known to be a
protein-protein interaction motif found at the N-termini
of several C2H2-type transcription factors as well as
Shaw-type potassium channels. Known structure reveals a
tightly intertwined dimer formed via interactions
between N-terminal strand and helix structures. However
in a subset of BTB/POZ domains, these two secondary
structures appear to be missing. Be aware SMART predicts
BTB/POZ domains without the beta1- and alpha1-secondary
structures.
Length = 97
Score = 90.1 bits (224), Expect = 2e-23
Identities = 30/86 (34%), Positives = 50/86 (58%), Gaps = 2/86 (2%)
Query: 32 DVTILCDGRKITAHKVILSACSSYFRTIFRENPC--QHPVVILKDINYEDIEAVLCFVYQ 89
DVT++ G+K AHK +L+A S YF+ +F + + L D++ ED A+L F+Y
Sbjct: 1 DVTLVVGGKKFHAHKAVLAAHSPYFKALFSSDFKESDKSEIYLDDVSPEDFRALLNFLYT 60
Query: 90 GTVYISKSRMDSFLKTAESLQIKGLA 115
G + + + ++ L+ A+ LQI GL
Sbjct: 61 GKLDLPEENVEELLELADYLQIPGLV 86
>gnl|CDD|222983 PHA03098, PHA03098, kelch-like protein; Provisional.
Length = 534
Score = 50.5 bits (121), Expect = 2e-07
Identities = 23/84 (27%), Positives = 44/84 (52%), Gaps = 2/84 (2%)
Query: 29 DLVDVTILCDGRKITAHKVILSACSSYFRTIFRENPCQHPVVILKDINYEDIEAVLCFVY 88
+ I+ G I HK+ILS+ S YF+ +F+ N ++ + + +I+Y+ V+ ++Y
Sbjct: 10 CDESIIIVNGGGIIKVHKIILSSSSEYFKKMFKNNFKENEINL--NIDYDSFNEVIKYIY 67
Query: 89 QGTVYISKSRMDSFLKTAESLQIK 112
G + I+ + + L A L I
Sbjct: 68 TGKINITSNNVKDILSIANYLIID 91
>gnl|CDD|165086 PHA02713, PHA02713, hypothetical protein; Provisional.
Length = 557
Score = 43.1 bits (101), Expect = 7e-05
Identities = 38/116 (32%), Positives = 59/116 (50%), Gaps = 8/116 (6%)
Query: 17 IITELDSLRTDGDLVDVTI-LCDGRKITAHKVILSACSSYFRTIFRENPCQHPVVILKDI 75
+++ + +L D L DV I + DG +I AHK IL+A S YFRT+F +V ++
Sbjct: 12 VVSNISNLLDDDILCDVIITIGDGEEIKAHKTILAAGSKYFRTLFTTPMIIRDLVTRVNL 71
Query: 76 NYEDIEAVLCFV-YQGTVYISKSRMDSFLKTAESLQIKGLAGASNMMGDNESQIQN 130
D +AV V Y +IS + LK A+ L I +++ D ES I++
Sbjct: 72 QMFDKDAVKNIVQYLYNRHISSMNVIDVLKCADYLLI------DDLVTDCESYIKD 121
>gnl|CDD|165153 PHA02790, PHA02790, Kelch-like protein; Provisional.
Length = 480
Score = 31.9 bits (72), Expect = 0.24
Identities = 19/71 (26%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 39 GRKITAHKVILSACSSYFRTIFRENPCQH--PVV-ILKDINYEDIEAVLCFVYQGTVYIS 95
G I + IL S YFRT R+ ++ PV + D++ + +++ + Y G VYI
Sbjct: 30 GGNIIVNSTILKKLSPYFRTHLRQKYTKNKDPVTRVCLDLDIHSLTSIVIYSYTGKVYID 89
Query: 96 KSRMDSFLKTA 106
+ + L+ +
Sbjct: 90 SHNVVNLLRAS 100
>gnl|CDD|223727 COG0654, UbiH, 2-polyprenyl-6-methoxyphenol hydroxylase and related
FAD-dependent oxidoreductases [Coenzyme metabolism /
Energy production and conversion].
Length = 387
Score = 31.2 bits (71), Expect = 0.49
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 19 TELDSLRTDGDLVDVTILCDGRKITAHKVI 48
E++++ DGD V VT+ DG + A ++
Sbjct: 126 AEVEAVEQDGDGVTVTLSFDGETLDADLLV 155
>gnl|CDD|240433 PTZ00482, PTZ00482, membrane-attack complex/perforin (MACPF)
Superfamily; Provisional.
Length = 844
Score = 29.4 bits (66), Expect = 2.0
Identities = 14/90 (15%), Positives = 30/90 (33%), Gaps = 8/90 (8%)
Query: 119 NMMGDNESQIQNEDSRSMDSSLVNQHDRHSLSGVGMDKDSIDPDEESNTYNNTTTYSSTG 178
N Q + D +S +Q + S++ +K + ++ + + G
Sbjct: 130 ADTQANNDQTNDFDQDDSSNSQTDQGLKQSVNLSSAEKLIEEKKGQTENTFKFYNFGNDG 189
Query: 179 EVEDDNQ--------MQYTDDNEEEDDDGD 200
E +D++ + DDGD
Sbjct: 190 EEAAAKDGGKSKSSDPGPLNDSDGQGDDGD 219
>gnl|CDD|220441 pfam09849, DUF2076, Uncharacterized protein conserved in bacteria
(DUF2076). This domain, found in various hypothetical
prokaryotic proteins, has no known function. The domain,
however, is found in various periplasmic ligand-binding
sensor proteins.
Length = 234
Score = 28.9 bits (65), Expect = 2.3
Identities = 22/115 (19%), Positives = 38/115 (33%), Gaps = 27/115 (23%)
Query: 97 SRMDSFLKTAESLQIK-GLAGAS-------NMMGDNESQIQNEDSRSMDSSLVNQHDRHS 148
SFL A Q G+AG N+ G + + +V+
Sbjct: 131 PGPGSFLGGA--AQTAAGVAGGMLLGNGLENLFGGHSQP----------AEIVDA----I 174
Query: 149 LSGVGMDKDSIDPDEESNTYNNTTTYSSTGEV---EDDNQMQYTDDNEEEDDDGD 200
G + D N Y + + ++ G+ DD+ + D ++DD D
Sbjct: 175 GEGGDGSGPAPADDTGINNYGDDDSDAAGGDQGSNGDDDDGGFADSGYDDDDMDD 229
>gnl|CDD|145949 pfam03066, Nucleoplasmin, Nucleoplasmin. Nucleoplasmins are also
known as chromatin decondensation proteins. They bind to
core histones and transfer DNA to them in a reaction
that requires ATP. This is thought to play a role in the
assembly of regular nucleosomal arrays.
Length = 146
Score = 28.1 bits (63), Expect = 2.9
Identities = 12/35 (34%), Positives = 21/35 (60%)
Query: 174 YSSTGEVEDDNQMQYTDDNEEEDDDGDASGSISPV 208
S E +DD + + +D+EE+DD+ ++ SPV
Sbjct: 108 ASEEDESDDDEEDEEEEDDEEDDDEDESEEEESPV 142
>gnl|CDD|227693 COG5406, COG5406, Nucleosome binding factor SPN, SPT16 subunit
[Transcription / DNA replication, recombination, and
repair / Chromatin structure and dynamics].
Length = 1001
Score = 28.8 bits (64), Expect = 3.0
Identities = 14/52 (26%), Positives = 28/52 (53%)
Query: 151 GVGMDKDSIDPDEESNTYNNTTTYSSTGEVEDDNQMQYTDDNEEEDDDGDAS 202
VG D +S + +EE + Y ++ S ED+ + ++D E++ + D+S
Sbjct: 924 MVGSDDESDESEEEVSEYEASSDDESDETDEDEESDESSEDLSEDESENDSS 975
>gnl|CDD|213242 cd03275, ABC_SMC1_euk, ATP-binding cassette domain of eukaryotic
SMC1 proteins. The structural maintenance of
chromosomes (SMC) proteins are large (approximately 110
to 170 kDa), and each is arranged into five recognizable
domains. Amino-acid sequence homology of SMC proteins
between species is largely confined to the amino- and
carboxy-terminal globular domains. The amino-terminal
domain contains a 'Walker A' nucleotide-binding domain
(GxxGxGKS/T, in the single-letter amino-acid code),
which by mutational studies has been shown to be
essential in several proteins. The carboxy-terminal
domain contains a sequence (the DA-box) that resembles a
'Walker B' motif, and a motif with homology to the
signature sequence of the ATP-binding cassette (ABC)
family of ATPases. The sequence homology within the
carboxy-terminal domain is relatively high within the
SMC1-SMC4 group, whereas SMC5 and SMC6 show some
divergence in both of these sequences. In eukaryotic
cells, the proteins are found as heterodimers of SMC1
paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6
(formerly known as Rad18).
Length = 247
Score = 28.3 bits (64), Expect = 3.4
Identities = 16/63 (25%), Positives = 27/63 (42%), Gaps = 8/63 (12%)
Query: 33 VTILCDGRKITAHKVILSACSSYF---RTIFRENPCQHPVVILKDINYEDIEAVLCFVYQ 89
V DG + T ++I SSY + + + + L+ IN ++A V+Q
Sbjct: 80 VYEDDDGEEKTFRRIITGGSSSYRINGKVVSLKEYNEE----LEKINI-LVKARNFLVFQ 134
Query: 90 GTV 92
G V
Sbjct: 135 GDV 137
>gnl|CDD|211667 TIGR01530, nadN, NAD pyrophosphatase/5'-nucleotidase NadN. This
model describes NadN of Haemophilus influenzae and a
small number of close homologs in pathogenic,
Gram-negative bacteria. NadN is a periplasmic enzyme
that cleaves NAD (nicotinamide adenine dinucleotide) to
NMN (nicotinamide mononucleotide) and AMP. The NMN must
be converted by a 5'-nucleotidase to nicotinamide
riboside for import. NadN belongs a large family of
5'-nucleotidases and has NMN 5'-nucleotidase activity
for NMN, AMP, etc [Transport and binding proteins,
Other, Biosynthesis of cofactors, prosthetic groups, and
carriers, Pyridine nucleotides].
Length = 545
Score = 28.4 bits (63), Expect = 3.6
Identities = 20/89 (22%), Positives = 38/89 (42%), Gaps = 1/89 (1%)
Query: 63 NPCQHPVVILKDINYEDIEAVLCFVYQGTVYISKSR-MDSFLKTAESLQIKGLAGASNMM 121
NP PV +++ Y + L + S +R + L ++ LQ+K G +
Sbjct: 241 NPNGEPVFVMEGWAYSAVVGDLGVKFSPEGIASITRKIPHVLMSSHKLQVKNAEGKWYEL 300
Query: 122 GDNESQIQNEDSRSMDSSLVNQHDRHSLS 150
+E + + +SM S ++ HD + S
Sbjct: 301 TGDERKKALDTLKSMKSISLDDHDAKTDS 329
>gnl|CDD|212530 cd10006, HDAC4, Histone deacetylase 4. Histone deacetylase 4 is a
class IIa Zn-dependent enzyme that catalyzes hydrolysis
of an N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Histone
acetylation/deacetylation process is important for
mediation of transcriptional regulation of many genes.
Histone deacetylases usually act via association with
DNA binding proteins to target specific chromatin
regions. Class IIa histone deacetylases are
signal-dependent co-repressors, having N-terminal
regulatory domain with two or three conserved serine
residues; phosphorylation of these residues is important
for ability to shuttle between the nucleus and cytoplasm
and act as transcriptional co-repressors. HDAC4
participates in regulation of chondrocyte hypertrophy
and skeletogenesis. However, biological substrates for
HDAC4 have not been identified; only low lysine
deacetylation activity has been demonstrated and active
site mutant has enhanced activity toward acetylated
lysines. HDAC4 does not bind DNA directly, but through
transcription factors MEF2C (myocyte enhancer factor-2C)
and MEF2D. Other known interaction partners of the
protein are 14-3-3 proteins, SMRT and N-CoR
co-repressors, BCL6, HP1, SUMO-1 ubiquitin-like protein,
and ANKRA2. It appears to interact in a multiprotein
complex with RbAp48 and HDAC3. Furthermore, HDAC4 is
required for TGFbeta1-induced myofibroblastic
differentiation.
Length = 409
Score = 28.5 bits (63), Expect = 3.8
Identities = 18/55 (32%), Positives = 25/55 (45%)
Query: 105 TAESLQIKGLAGASNMMGDNESQIQNEDSRSMDSSLVNQHDRHSLSGVGMDKDSI 159
T E LQ + + G N Q DS+ + SL + R GVG+D D+I
Sbjct: 59 TLEELQTVHSEAHTLLYGTNPLNRQKLDSKKLLGSLASVFVRLPCGGVGVDSDTI 113
>gnl|CDD|203043 pfam04546, Sigma70_ner, Sigma-70, non-essential region. The domain
is found in the primary vegetative sigma factor. The
function of this domain is unclear and can be removed
without loss of function.
Length = 211
Score = 27.9 bits (63), Expect = 3.9
Identities = 12/49 (24%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 159 IDPDEESNTYNNTTTYSSTGEVEDDNQMQYTDDNEEEDDDGDASGSISP 207
IDP+ + S E + ++ DD+E+ED+D + + P
Sbjct: 30 IDPNAAAAAATAAAIESELDEEDLEDDD---DDDEDEDEDDEEEADLGP 75
>gnl|CDD|238202 cd00329, TopoII_MutL_Trans, MutL_Trans: transducer domain, having
a ribosomal S5 domain 2-like fold, conserved in the
C-terminal domain of type II DNA topoisomerases (Topo
II) and DNA mismatch repair (MutL/MLH1/PMS2) proteins.
This transducer domain is homologous to the second
domain of the DNA gyrase B subunit, which is known to
be important in nucleotide hydrolysis and the
transduction of structural signals from ATP-binding
site to the DNA breakage/reunion regions of the
enzymes. The GyrB dimerizes in response to ATP binding,
and is homologous to the N-terminal half of eukaryotic
Topo II and the ATPase fragment of MutL. Type II DNA
topoisomerases catalyze the ATP-dependent transport of
one DNA duplex through another, in the process
generating transient double strand breaks via covalent
attachments to both DNA strands at the 5' positions.
Included in this group are proteins similar to human
MLH1 and PMS2. MLH1 forms a heterodimer with PMS2
which functions in meiosis and in DNA mismatch repair
(MMR). Cells lacking either hMLH1 or hPMS2 have a
strong mutator phenotype and display microsatellite
instability (MSI). Mutation in hMLH1 accounts for a
large fraction of Lynch syndrome (HNPCC) families.
Length = 107
Score = 26.8 bits (60), Expect = 4.3
Identities = 8/37 (21%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 37 CDGRKITAHKVILSACSS-YFRTIFRENPCQHPVVIL 72
+GR + + A Y R + ++ ++PV +L
Sbjct: 50 VNGRPVREGGTHVKAVREAYTRALNGDDVRRYPVAVL 86
>gnl|CDD|191696 pfam07168, Ureide_permease, Ureide permease. Heterocyclic nitrogen
compounds may serve as nitrogen sources or nitrogen
transport compounds in plants that are not able to fix
nitrogen. This family represents ureide permease, a
transporter of a wide spectrum of oxo derivatives of
heterocyclic nitrogen compounds, including allantoin,
uric acid and xanthine; it has 10 putative transmembrane
domains with a large cytosolic central domain containing
a 'Walker A' motif. Ureide permease is likely to
transport other purine degradation products when
nitrogen sources are low. Transport is dependent on
glucose and a proton gradient. The family is found in
bacteria, plants and yeast.
Length = 336
Score = 27.9 bits (62), Expect = 4.4
Identities = 12/42 (28%), Positives = 18/42 (42%)
Query: 160 DPDEESNTYNNTTTYSSTGEVEDDNQMQYTDDNEEEDDDGDA 201
D E+ N + N + S +E ++M D E DD A
Sbjct: 154 DNKEKLNAFENYQSEFSISSLELMSRMNSEDLENGEADDAKA 195
>gnl|CDD|223052 PHA03346, PHA03346, US22 family homolog; Provisional.
Length = 520
Score = 28.2 bits (63), Expect = 4.8
Identities = 12/41 (29%), Positives = 18/41 (43%)
Query: 69 VVILKDINYEDIEAVLCFVYQGTVYISKSRMDSFLKTAESL 109
V+ YE+ E VLC + +YI + D + A L
Sbjct: 103 CVVRVTDRYEETELVLCMGAETRLYIYEPSQDILILVAPHL 143
>gnl|CDD|182858 PRK10947, PRK10947, global DNA-binding transcriptional dual
regulator H-NS; Provisional.
Length = 135
Score = 27.2 bits (60), Expect = 4.9
Identities = 10/38 (26%), Positives = 16/38 (42%)
Query: 157 DSIDPDEESNTYNNTTTYSSTGEVEDDNQMQYTDDNEE 194
D IDP+E N+ + + + Y D+N E
Sbjct: 68 DGIDPNELLNSLAAVKSGTKAKRAARPAKYSYVDENGE 105
>gnl|CDD|222141 pfam13454, NAD_binding_9, FAD-NAD(P)-binding.
Length = 153
Score = 27.2 bits (61), Expect = 5.8
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 17 IITELDSLRTDGDLVDVTILCDGRKITAHKVILS 50
E+ LR G VT L DG + A V+L+
Sbjct: 117 HRAEVVDLRPRGGGYTVT-LADGATLRADAVVLA 149
>gnl|CDD|204125 pfam09078, CheY-binding, CheY binding. Members of this family
adopt a secondary structure consisting of an open-face
beta/alpha sandwich, with four antiparallel
beta-strands and two alpha-helices. They bind to a
corresponding domain on CheY, with subsequent
phosphorylation of the CheY Asp57 residue, and
activation of CheY, which then affects flagellar
rotation.
Length = 64
Score = 25.7 bits (57), Expect = 5.9
Identities = 7/10 (70%), Positives = 8/10 (80%)
Query: 78 EDIEAVLCFV 87
+DI AV CFV
Sbjct: 46 DDIVAVCCFV 55
>gnl|CDD|227596 COG5271, MDN1, AAA ATPase containing von Willebrand factor type A
(vWA) domain [General function prediction only].
Length = 4600
Score = 28.0 bits (62), Expect = 5.9
Identities = 23/108 (21%), Positives = 42/108 (38%), Gaps = 3/108 (2%)
Query: 105 TAESLQIKGLAGASNMMGDNESQIQNEDSRSMDSSLVNQHDRHSLSGVGMDKDSIDPDEE 164
E LQ G A + + + N++ SM+S+ + + D G +D D +
Sbjct: 4211 EEEDLQALGNAEKDQIKSIDRDESANQNPDSMNSTNIAE-DEADEVGDKQLQDGQDISDI 4269
Query: 165 SNTYNNT-TTYSSTGEVEDDNQMQYTDDNEEEDDDGDASGSISPVNSI 211
T +T T + + D++ E D+ D + I+P I
Sbjct: 4270 KQTGEDTLPTEFGSINQSEKVFELSEDEDIE-DELPDYNVKITPAMPI 4316
>gnl|CDD|235298 PRK04439, PRK04439, S-adenosylmethionine synthetase; Provisional.
Length = 399
Score = 27.4 bits (62), Expect = 6.5
Identities = 11/40 (27%), Positives = 18/40 (45%), Gaps = 2/40 (5%)
Query: 33 VTILCDGRKITAHKVILSACSSYFRTIFRE-NPCQHPVVI 71
T G +I ++ + A Y R R +P +H V+I
Sbjct: 92 ATKEVGGEEIPVGEIAIEAAKEYLRENLRNLDPERH-VII 130
>gnl|CDD|227492 COG5163, NOP7, Protein required for biogenesis of the 60S ribosomal
subunit [Translation, ribosomal structure and
biogenesis].
Length = 591
Score = 27.3 bits (60), Expect = 7.3
Identities = 15/49 (30%), Positives = 19/49 (38%), Gaps = 6/49 (12%)
Query: 155 DKDSIDPDEESNTYNNTTTYSSTGEVEDDNQMQYTDD---NEEEDDDGD 200
DS DP T T +S E + N+ + EEDDD D
Sbjct: 452 SVDSYDPRASLMTMEETQRHS---EEDLVNRFEDVRYEHVAGEEDDDDD 497
>gnl|CDD|131396 TIGR02343, chap_CCT_epsi, T-complex protein 1, epsilon subunit.
Members of this family, all eukaryotic, are part of the
group II chaperonin complex called CCT (chaperonin
containing TCP-1) or TRiC. The archaeal equivalent group
II chaperonin is often called the thermosome. Both are
somewhat related to the group I chaperonin of bacterial,
GroEL/GroES. This family consists exclusively of the CCT
epsilon chain (part of a paralogous family) from
animals, plants, fungi, and other eukaryotes.
Length = 532
Score = 27.5 bits (61), Expect = 7.4
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 7/59 (11%)
Query: 146 RHSLSGVGMDKDSIDPDEESNTYNNTTTYSSTGEVEDDNQM-----QYTDDNEEEDDDG 199
R SL GMDK I PD + N+ T S +++ DN + + + ++E DG
Sbjct: 44 RTSLGPKGMDKMLISPDGDITVTNDGATILS--QMDVDNPIAKLMVELSKSQDDEIGDG 100
>gnl|CDD|227519 COG5192, BMS1, GTP-binding protein required for 40S ribosome
biogenesis [Translation, ribosomal structure and
biogenesis].
Length = 1077
Score = 27.4 bits (60), Expect = 7.7
Identities = 26/164 (15%), Positives = 62/164 (37%), Gaps = 16/164 (9%)
Query: 69 VVILKDINYEDIEAVLCFVYQGTVYISKSRMDSFLKTAESLQIKGLAGASNMMGDNESQI 128
++ KD Y ++ + + +M L+ E Q G+ G + N I
Sbjct: 335 ILKDKDRVYIEVPTSNFSKDENSEAGEGEKMKMQLQEIE--QDPGVDGVGLQLFSNSDAI 392
Query: 129 QNEDSRSMDSSLVNQHDRHSLSGVGMDKDSIDPDEESNTYNNTTTYSSTGEVE------- 181
D S + V + R +G + +++ DE S ++ +T +V+
Sbjct: 393 DTVDRESSEIDNVGRKTRRQPTGKAIAEETSREDELSFDDSDVSTSDENEDVDFTGKKGA 452
Query: 182 -------DDNQMQYTDDNEEEDDDGDASGSISPVNSISTQSSGQ 218
D+ ++ + D++ ++ +G+ + ++ SG+
Sbjct: 453 INNEDESDNEEVAFDSDSQFDESEGNLRWKEGLASKLAYSQSGK 496
>gnl|CDD|114337 pfam05609, LAP1C, Lamina-associated polypeptide 1C (LAP1C). This
family contains rat LAP1C proteins and several
uncharacterized highly related sequences from both mice
and humans. LAP1s (lamina-associated polypeptide 1s) are
type 2 integral membrane proteins with a single
membrane-spanning region of the inner nuclear membrane.
LAP1s bind to both A- and B-type lamins and have a
putative role in the membrane attachment and assembly of
the nuclear lamina.
Length = 465
Score = 27.3 bits (60), Expect = 8.9
Identities = 26/115 (22%), Positives = 44/115 (38%), Gaps = 10/115 (8%)
Query: 116 GASNMMGDNESQIQNEDSRSMDSSLVNQHDRHSLSGVGMDKDSIDPDEESNTYNNTTTYS 175
G S ++E+ Q E S++ V D ++S +D D Y
Sbjct: 34 GLSKDHQEDETSSQPESSQTGSKKTVRSPDEANVS-----EDPKD-----KLRRPPLRYP 83
Query: 176 STGEVEDDNQMQYTDDNEEEDDDGDASGSISPVNSISTQSSGQVPKVGRASSRVI 230
E N+ + ++ E EDD +S +++ S S KVGRA + +
Sbjct: 84 RYEATEVQNKQSFLEEGETEDDHHSSSSNVTKEPLRSRDSHESSDKVGRADAHLG 138
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
0.311 0.128 0.361
Gapped
Lambda K H
0.267 0.0732 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,343,118
Number of extensions: 1019200
Number of successful extensions: 826
Number of sequences better than 10.0: 1
Number of HSP's gapped: 795
Number of HSP's successfully gapped: 56
Length of query: 236
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 142
Effective length of database: 6,768,326
Effective search space: 961102292
Effective search space used: 961102292
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 57 (25.7 bits)