RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14919
(339 letters)
>gnl|CDD|200440 cd11284, ADF_Twf-C_like, C-terminal ADF domain of twinfilin and
related proteins. Actin depolymerization
factor/cofilin-like domains (ADF domains) are present in
a family of essential eukaryotic actin regulatory
proteins. Twinfilin contains two ADF domains, and
inhibits the assembly of actin filaments by strongly
interacting with monomeric ADP-actin (ADP-G-actin) in a
1:1 stochiometry (with it's C-terminal ADF domain,
Twf-C) and inhibiting the actin monomer's nucleotide
exchange. Mammalian twinfilin may also cap the barbed
ends of F-actin filaments and prevent further assembly
(or disassembly), in a process which requires both ADF
domains. The N-terminal ADF domain (Twf-N) binds G-actin
with a lower affinity than Twf-C; Twf-C can also bind
F-actin. During capping, Twf-N may interact with the
terminal actin subunit, and Twf-C may bind between two
adjacent subunits at the side of the filament.
Length = 132
Score = 162 bits (413), Expect = 5e-50
Identities = 60/137 (43%), Positives = 79/137 (57%), Gaps = 7/137 (5%)
Query: 170 SGVAFPLLPDAESSVHKLIKAKYNYVQFRIDLQEETINLVQSGE-VTLKQLPSMIPTDSA 228
GVAFP+ +A+ ++ +L N VQ IDL+ ETI LV S L S+IP+D
Sbjct: 1 PGVAFPVSEEAKDALSELASGGVNLVQLSIDLENETIELVSSSSISIPDDLSSLIPSDHP 60
Query: 229 RYHLFNFRHEFEGKIIDSVVFIYSMPGYSLPIKERMLYSSCKAPLLENL-HHLGLTIDKK 287
RYH + + H + SVVFIYS P S +KERMLY+S K+ LL + + IDKK
Sbjct: 61 RYHFYRYPHTYL----SSVVFIYSCPSGS-KVKERMLYASSKSGLLNHAEDEGKIEIDKK 115
Query: 288 LEIDSGSELTEEFLLEE 304
+EI ELTE FL +E
Sbjct: 116 IEIGDPDELTESFLSDE 132
Score = 48.8 bits (117), Expect = 2e-07
Identities = 22/83 (26%), Positives = 35/83 (42%), Gaps = 9/83 (10%)
Query: 18 VFKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQPCYILYRFDSKNETGGHDWLL 77
+ +ENE + L + + LI P Y YR+ + +
Sbjct: 27 QLSIDLENETIELVSSSSISIPDD------LSSLIPSDHPRYHFYRYPHTYLSS---VVF 77
Query: 78 IFWSPDDSPVRQKMLYASTKSTL 100
I+ P S V+++MLYAS+KS L
Sbjct: 78 IYSCPSGSKVKERMLYASSKSGL 100
>gnl|CDD|200441 cd11285, ADF_Twf-N_like, N-terminal ADF domain of twinfilin and
related proteins. Actin depolymerization
factor/cofilin-like domains (ADF domains) are present in
a family of essential eukaryotic actin regulatory
proteins. Twinfilin contains two ADF domains, and
inhibits the assembly of actin filaments by strongly
interacting with monomeric ADP-actin (ADP-G-actin) in a
1:1 stochiometry (with it's C-terminal ADF domain,
Twf-C) and inhibiting the actin monomer's nucleotide
exchange. Mammalian twinfilin may also cap the barbed
ends of F-actin filaments and prevent further assembly
(or disassembly), in a process which requires both ADF
domains. The N-terminal ADF domain (Twf-N) binds G-actin
with a lower affinity than Twf-C; Twf-C can also bind
F-actin. During capping, Twf-N may interact with the
terminal actin subunit, and Twf-C may bind between two
adjacent subunits at the side of the filament.
Length = 139
Score = 161 bits (410), Expect = 2e-49
Identities = 63/135 (46%), Positives = 88/135 (65%), Gaps = 3/135 (2%)
Query: 1 NEALKKFFGSIRD-EKIRVFKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQPCY 59
+E L F S + +R K++IENE LV + G+W QDFD V L++E +PCY
Sbjct: 7 SEELLDAFKSAKSSGSVRAIKITIENEELVPDATIETTGSWEQDFDLLVLPLLEEKEPCY 66
Query: 60 ILYRFDSKNETGGHDWLLIFWSPDDSPVRQKMLYASTKSTLKQDFGSGQIKEEIHATVPV 119
ILYR DSK+ G++W+ I + PD +PVRQKMLYAST++TLK++ GS IK+E+ AT
Sbjct: 67 ILYRLDSKS--AGYEWVFISFVPDSAPVRQKMLYASTRATLKRELGSNHIKDELFATELE 124
Query: 120 DVTLHGYELHKRAVK 134
++TL GYE H +
Sbjct: 125 ELTLEGYEKHLKHEA 139
>gnl|CDD|214516 smart00102, ADF, Actin depolymerisation factor/cofilin -like
domains. Severs actin filaments and binds to actin
monomers.
Length = 127
Score = 88.5 bits (220), Expect = 1e-21
Identities = 39/117 (33%), Positives = 62/117 (52%), Gaps = 8/117 (6%)
Query: 12 RDEKIRVFKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQPCYILYRFDSKNETG 71
R +FK+ +NE +V+ VG+ +D++V + + E + Y LY + E
Sbjct: 14 RKHSAIIFKIDKDNEEIVVEE----VGSTEDSYDEFV-EELPEDECRYALYDYKFTTEES 68
Query: 72 GHD-WLLIFWSPDDSPVRQKMLYASTKSTLKQDFGSGQIKEEIHATVPVDVTLHGYE 127
+ IFWSPD +PV+ KMLYAS+K TLK++ G Q+ E+ AT D+ +
Sbjct: 69 KKSKIVFIFWSPDGAPVKSKMLYASSKDTLKKELGGIQV--EVQATDEDDLDEEALK 123
Score = 87.7 bits (218), Expect = 2e-21
Identities = 33/118 (27%), Positives = 57/118 (48%), Gaps = 7/118 (5%)
Query: 191 KYNYVQFRIDLQEETINLVQSGEV--TLKQLPSMIPTDSARYHLFNFRHEFEGKIIDSVV 248
K++ + F+ID E I + + G + + +P D RY L++++ E +V
Sbjct: 15 KHSAIIFKIDKDNEEIVVEEVGSTEDSYDEFVEELPEDECRYALYDYKFTTEESKKSKIV 74
Query: 249 FIYSMPGYSLPIKERMLYSSCKAPLLENLHHLGLTIDKKLEIDSGSELTEEFLLEELH 306
FI+ P P+K +MLY+S K L + L I +++ +L EE L E+L
Sbjct: 75 FIFWSPD-GAPVKSKMLYASSKDTLKKELG----GIQVEVQATDEDDLDEEALKEKLK 127
>gnl|CDD|200442 cd11286, ADF_cofilin_like, Cofilin, Destrin, and related actin
depolymerizing factors. Actin depolymerization
factor/cofilin-like domains (ADF domains) are present in
a family of essential eukaryotic actin regulatory
proteins. These proteins enhance the turnover rate of
actin, and interact with actin monomers (G-actin) as
well as actin filaments (F-actin), typically with a
preference for ADP-G-actin subunits. The basic function
of cofilin is to promote disassembly of aged actin
filaments. Vertebrates have three isoforms of cofilin:
cofilin-1 (Cfl1, non-muscle cofilin), cofilin-2 (muscle
cofilin), and ADF (destrin). When bound to actin
monomers, cofilins inhibit their spontaneous exchange of
nucleotides. The cooperative binding to (aged)
ADP-F-actin induces a local change in the actin filament
structure and further promotes aging.
Length = 133
Score = 73.4 bits (181), Expect = 5e-16
Identities = 31/108 (28%), Positives = 57/108 (52%), Gaps = 9/108 (8%)
Query: 18 VFKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQPCYILYRFDSKNETGGH--DW 75
+FK+S + + +V+ + VG +D ++ L + + Y +Y F+ + + GG
Sbjct: 26 IFKISDDKKEIVV----EKVGERDASYDDFLEKLPEN-ECRYAVYDFEYETKDGGKRSKL 80
Query: 76 LLIFWSPDDSPVRQKMLYASTKSTLKQDFGSGQIKEEIHATVPVDVTL 123
+ I W PD +P++ KMLYAS+K LK+ + EI AT +++
Sbjct: 81 VFISWCPDTAPIKSKMLYASSKDALKKKLNGIKK--EIQATDLSELSE 126
Score = 45.2 bits (108), Expect = 4e-06
Identities = 39/123 (31%), Positives = 66/123 (53%), Gaps = 12/123 (9%)
Query: 188 IKAKYNYVQFRIDLQEETINLVQSGEV--TLKQLPSMIPTDSARYHLFNFRHEFEGK--- 242
+K K+ Y+ F+I ++ I + + GE + +P + RY +++F E+E K
Sbjct: 18 LKKKHKYIIFKISDDKKEIVVEKVGERDASYDDFLEKLPENECRYAVYDF--EYETKDGG 75
Query: 243 IIDSVVFIYSMPGYSLPIKERMLYSSCKAPLLENLHHLGLTIDKKLEIDSGSELTEEFLL 302
+VFI P + PIK +MLY+S K L + L+ I K+++ SEL+EE +L
Sbjct: 76 KRSKLVFISWCPDTA-PIKSKMLYASSKDALKKKLNG----IKKEIQATDLSELSEEEIL 130
Query: 303 EEL 305
E+L
Sbjct: 131 EKL 133
>gnl|CDD|200435 cd00013, ADF_gelsolin, Actin depolymerization factor/cofilin- and
gelsolin-like domains. Actin depolymerization
factor/cofilin-like domains are present in a family of
essential eukaryotic actin regulatory proteins; these
proteins enhance the turnover rate of actin and interact
with actin monomers as well as actin filaments.
Length = 97
Score = 67.1 bits (164), Expect = 4e-14
Identities = 26/102 (25%), Positives = 48/102 (47%), Gaps = 5/102 (4%)
Query: 193 NYVQFRIDLQEETINLVQSGEVTLKQLPSMIPTDSARYHLFNFRHEFEGKIIDSVVFIYS 252
++V F++D ++E I + +G L + +P D RY + F++ VFI
Sbjct: 1 DWVLFKVDAKKEEIVVGSTGAGFLDEFLEELPEDDPRYAFYRFKYPHSDDKRSKFVFISW 60
Query: 253 MPGYSLPIKERMLYSSCKAPLLENLHHLGLTIDKKLEIDSGS 294
+P IK++M+Y++ K L E L + ++I G
Sbjct: 61 IPDGV-SIKQKMVYATNKQTLKEALFG----LAVPVQIRDGD 97
Score = 64.8 bits (158), Expect = 2e-13
Identities = 25/102 (24%), Positives = 41/102 (40%), Gaps = 10/102 (9%)
Query: 17 RVFKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQPCYILYRFDSKNETGG-HDW 75
+FKV + E +V+ F + + E P Y YRF + +
Sbjct: 3 VLFKVDAKKEEIVVGSTG-------AGFLDEFLEELPEDDPRYAFYRFKYPHSDDKRSKF 55
Query: 76 LLIFWSPDDSPVRQKMLYASTKSTLKQDFGSGQIKEEIHATV 117
+ I W PD ++QKM+YA+ K TLK+ + +
Sbjct: 56 VFISWIPDGVSIKQKMVYATNKQTLKEALFG--LAVPVQIRD 95
>gnl|CDD|143992 pfam00241, Cofilin_ADF, Cofilin/tropomyosin-type actin-binding
protein. Severs actin filaments and binds to actin
monomers.
Length = 127
Score = 65.4 bits (160), Expect = 3e-13
Identities = 32/107 (29%), Positives = 56/107 (52%), Gaps = 8/107 (7%)
Query: 18 VFKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQPCYILYRFDSKNETGG-HDWL 76
+FK+ + + +V+ VG +D++V +L E + Y +Y + + +
Sbjct: 20 IFKIDKDKDQIVVEQ----VGDTGDSYDEFVEEL-PERECRYAVYDVEYTTDGSKKSKIV 74
Query: 77 LIFWSPDDSPVRQKMLYASTKSTLKQDFGSGQIKEEIHATVPVDVTL 123
+ WSPD +PV+ KMLYAS+K LK+ G I+ E+ AT D++
Sbjct: 75 FVSWSPDGAPVKSKMLYASSKDALKRALGG--IQVEVQATDADDLSE 119
Score = 47.3 bits (113), Expect = 6e-07
Identities = 37/132 (28%), Positives = 69/132 (52%), Gaps = 10/132 (7%)
Query: 178 PDAESSVHKLIKA-KYNYVQFRIDLQEETINLVQSGEV--TLKQLPSMIPTDSARYHLFN 234
+ ++S ++L K K+NY+ F+ID ++ I + Q G+ + + +P RY +++
Sbjct: 1 DNLKASFNELKKRKKHNYIIFKIDKDKDQIVVEQVGDTGDSYDEFVEELPERECRYAVYD 60
Query: 235 FRHEFEGKIIDSVVFI-YSMPGYSLPIKERMLYSSCKAPLLENLHHLGLTIDKKLEIDSG 293
+ +G +VF+ +S G P+K +MLY+S K L L I +++
Sbjct: 61 VEYTTDGSKKSKIVFVSWSPDG--APVKSKMLYASSKDALKRALG----GIQVEVQATDA 114
Query: 294 SELTEEFLLEEL 305
+L+EE LLE+L
Sbjct: 115 DDLSEEELLEKL 126
>gnl|CDD|200439 cd11283, ADF_GMF-beta_like, ADF-homology domain of glia maturation
factor beta and related proteins. Actin
depolymerization factor/cofilin-like domains (ADF
domains) are present in a family of essential eukaryotic
actin regulatory proteins. Most of these proteins
enhance the turnover rate of actin and interact with
actin monomers as well as actin filaments. The glia
maturation factor (GMF), however, does not bind actin
but interacts with the Arp2/3 complex (which contains
actin-related proteins, amongst others) and suppresses
Arp2/3 activity, inducing the dissociation of branched
daughter filaments from their mother filaments. This
family includes both mammalian GMF isoforms, GMF-beta
and GMF-gamma. GMF-beta regulates cellular growth,
fission, differentiation and apoptosis. GMF-gamma is
important in myeloid cell development and is an
important regulator for cell migration and polarity in
neutrophils.
Length = 122
Score = 37.6 bits (88), Expect = 0.001
Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 50 DLIQEAQPCYIL--YRFDSKNETGGHDWLLIFWSPDDSPVRQKMLYASTKSTLKQDFG 105
+ + E P ++L Y+ + + +LI+WSP +MLYA K L ++
Sbjct: 51 EELPEHSPRFVLYSYKMKHDDGRISYPLVLIYWSPQGCSPELQMLYAGAKELLVKEAE 108
>gnl|CDD|173441 PTZ00152, PTZ00152, cofilin/actin-depolymerizing factor 1-like
protein; Provisional.
Length = 122
Score = 35.3 bits (81), Expect = 0.010
Identities = 26/110 (23%), Positives = 46/110 (41%), Gaps = 23/110 (20%)
Query: 15 KIR------VFKVSIENEALVLAGYKKVVGTWTQDFDKYVP--DLIQEAQPCYILYRFDS 66
KIR +F IEN +++ + K T + + D IQ A Y+++ +
Sbjct: 19 KIRKTCRWIIFV--IENCEIII--HSKGATTTLTELVGSIDKNDKIQCA---YVVFDAVN 71
Query: 67 KNETGGHDWLLIFWSPDDSPVRQKMLYASTK-STLKQDFGSGQIKEEIHA 115
K ++ + S R +M YAS+K + LK+ G + I +
Sbjct: 72 KIH-------FFMYARESSNSRDRMTYASSKQALLKKIEGVNVLTSVIES 114
>gnl|CDD|178755 PLN03216, PLN03216, actin depolymerizing factor; Provisional.
Length = 141
Score = 35.7 bits (82), Expect = 0.010
Identities = 17/46 (36%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 76 LLIFWSPDDSPVRQKMLYASTKSTLKQDFGSGQIKEEIHATVPVDV 121
I WSP+ S +R KMLYA++K L++ + E+ AT P ++
Sbjct: 88 FFIAWSPEASRIRAKMLYATSKDGLRRVLDG--VHYELQATDPTEM 131
Score = 33.7 bits (77), Expect = 0.043
Identities = 25/96 (26%), Positives = 46/96 (47%), Gaps = 5/96 (5%)
Query: 189 KAKYNYVQFRIDLQEE--TINLVQSGEVTLKQLPSMIPTDSARYHLFNFRHEFEGKIIDS 246
K + Y+ F+ID + T++ V + L + +PTD RY +F+F S
Sbjct: 26 KKVHRYIVFKIDEKSRKVTVDKVGGPGESYDDLAASLPTDDCRYAVFDFDFVTVDNCRKS 85
Query: 247 VVFIYSMPGYSLPIKERMLYSSCKAPL---LENLHH 279
+F + + I+ +MLY++ K L L+ +H+
Sbjct: 86 KIFFIAWSPEASRIRAKMLYATSKDGLRRVLDGVHY 121
>gnl|CDD|240762 cd12316, RRM3_RBM19_RRM2_MRD1, RNA recognition motif 3 in
RNA-binding protein 19 (RBM19) and RNA recognition motif
2 found in multiple RNA-binding domain-containing
protein 1 (MRD1). This subfamily corresponds to the
RRM3 of RBM19 and RRM2 of MRD1. RBM19, also termed
RNA-binding domain-1 (RBD-1), is a nucleolar protein
conserved in eukaryotes involved in ribosome biogenesis
by processing rRNA and is essential for preimplantation
development. It has a unique domain organization
containing 6 conserved RNA recognition motifs (RRMs),
also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). MRD1 is encoded by a novel
yeast gene MRD1 (multiple RNA-binding domain). It is
well conserved in yeast and its homologs exist in all
eukaryotes. MRD1 is present in the nucleolus and the
nucleoplasm. It interacts with the 35 S precursor rRNA
(pre-rRNA) and U3 small nucleolar RNAs (snoRNAs). It is
essential for the initial processing at the A0-A2
cleavage sites in the 35 S pre-rRNA. MRD1 contains 5
conserved RRMs, which may play an important structural
role in organizing specific rRNA processing events. .
Length = 74
Score = 28.8 bits (65), Expect = 0.77
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 138 PLTSQEEERAELRKFESSG---QCQISIDTRTQTLSGVAFPLLPDAESSV 184
P T+ EEE EL FE+ G + + +D T+ G AF E +V
Sbjct: 8 PFTTTEEELREL--FEAFGEISEVHLPLDKETKRSKGFAFVSFMFPEHAV 55
>gnl|CDD|217228 pfam02781, G6PD_C, Glucose-6-phosphate dehydrogenase, C-terminal
domain.
Length = 294
Score = 30.4 bits (69), Expect = 1.2
Identities = 16/65 (24%), Positives = 25/65 (38%), Gaps = 6/65 (9%)
Query: 10 SIRDEKIRVFKV--SIENEALVLAGYKKVVGTWTQDFDKYVPDLIQEAQ---PCYILYRF 64
IRDEK++V K I+ + +VL Y ++ Y+ D A +
Sbjct: 72 DIRDEKVKVLKALRPIDEDDVVLGQYGAGEDG-GKEKPGYLEDPTVPADSNTETFAAGVL 130
Query: 65 DSKNE 69
NE
Sbjct: 131 HIDNE 135
>gnl|CDD|233162 TIGR00871, zwf, glucose-6-phosphate 1-dehydrogenase. This enzyme
(EC 1.1.1.49) acts on glucose 6-phospate and reduces
NADP(+). An alternate name appearing in the literature
for the human enzyme, based on a slower activity with
beta-D-glucose, is glucose 1-dehydrogenase (EC
1.1.1.47), but that name more properly describes a
subfamily of the short chain dehydrogenases/reductases
family. This is a well-studied enzyme family, with
sequences available from well over 50 species. The
trusted cutoff is set above the score for the Drosophila
melanogaster CG7140 gene product, a homolog of unknown
function. G6PD homologs from the bacteria Aquifex
aeolicus and Helicobacter pylori lack several motifs
well conserved most other members, were omitted from the
seed alignment, and score well below the trusted cutoff
[Energy metabolism, Pentose phosphate pathway].
Length = 482
Score = 30.0 bits (68), Expect = 1.8
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 10 SIRDEKIRVFK----VSIENEALVLAGYKK 35
SIRDEK++V K + ++ +V Y
Sbjct: 258 SIRDEKVKVLKALRPIDPDDNNVVRGQYGA 287
>gnl|CDD|176131 cd08440, PBP2_LTTR_like_4, TThe C-terminal substrate binding domain
of an uncharacterized LysR-type transcriptional
regulator, contains the type 2 periplasmic binding fold.
LysR-transcriptional regulators comprise the largest
family of prokaryotic transcription factor. Homologs of
some of LTTRs with similar domain organizations are also
found in the archaea and eukaryotic organisms. The LTTRs
are composed of two functional domains joined by a
linker helix involved in oligomerization: an N-terminal
HTH (helix-turn-helix) domain, which is responsible for
the DNA-binding specificity, and a C-terminal
substrate-binding domain, which is structurally
homologous to the type 2 periplasmic binding proteins.
As also observed in the periplasmic binding proteins,
the C-terminal domain of the bacterial transcriptional
repressor undergoes a conformational change upon
substrate binding which in turn changes the DNA binding
affinity of the repressor. The genes controlled by the
LTTRs have diverse functional roles including amino acid
biosynthesis, CO2 fixation, antibiotic resistance,
degradation of aromatic compounds, nodule formation of
nitrogen-fixing bacteria, and synthesis of virulence
factors, to a name a few. This substrate-binding domain
shows significant homology to the type 2 periplasmic
binding proteins (PBP2), which are responsible for the
uptake of a variety of substrates such as phosphate,
sulfate, polysaccharides, lysine/arginine/ornithine, and
histidine. The PBP2 bind their ligand in the cleft
between these domains in a manner resembling a Venus
flytrap. After binding their specific ligand with high
affinity, they can interact with a cognate membrane
transport complex comprised of two integral membrane
domains and two cytoplasmically located ATPase domains.
This interaction triggers the ligand translocation
across the cytoplasmic membrane energized by ATP
hydrolysis.
Length = 197
Score = 28.6 bits (65), Expect = 3.5
Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 6/49 (12%)
Query: 168 TLSGVAFPLLPDAESSVHKLIKAKYNYVQFRI--DLQEETINLVQSGEV 214
L +A LLP ++ ++ ++ R+ E+ I V+SGEV
Sbjct: 6 ALPSLAATLLPPVLAAFR----RRHPGIRVRLRDVSAEQVIEAVRSGEV 50
>gnl|CDD|241010 cd12566, RRM2_MRD1, RNA recognition motif 2 in yeast multiple
RNA-binding domain-containing protein 1 (MRD1) and
similar proteins. This subgroup corresponds to the RRM2
of MRD1 which is encoded by a novel yeast gene MRD1
(multiple RNA-binding domain). It is well-conserved in
yeast and its homologs exist in all eukaryotes. MRD1 is
present in the nucleolus and the nucleoplasm. It
interacts with the 35 S precursor rRNA (pre-rRNA) and U3
small nucleolar RNAs (snoRNAs). It is essential for the
initial processing at the A0-A2 cleavage sites in the 35
S pre-rRNA. MRD1 contains 5 conserved RNA recognition
motifs (RRMs), also termed RBDs (RNA binding domains) or
RNPs (ribonucleoprotein domains), which may play an
important structural role in organizing specific rRNA
processing events. .
Length = 79
Score = 27.0 bits (60), Expect = 3.6
Identities = 10/45 (22%), Positives = 20/45 (44%)
Query: 140 TSQEEERAELRKFESSGQCQISIDTRTQTLSGVAFPLLPDAESSV 184
+++ KF + ++ID ++ G A+ L D E +V
Sbjct: 14 CKEDDLEKLFSKFGELSEVHVAIDKKSGKSKGFAYVLFLDPEDAV 58
>gnl|CDD|241019 cd12575, RRM1_hnRNPD_like, RNA recognition motif 1 in heterogeneous
nuclear ribonucleoprotein hnRNP D0, hnRNP A/B, hnRNP DL
and similar proteins. This subfamily corresponds to the
RRM1 in hnRNP D0, hnRNP A/B, hnRNP DL and similar
proteins. hnRNP D0 is 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. hnRNP A/B 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
members 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 = 74
Score = 26.8 bits (59), Expect = 4.8
Identities = 18/60 (30%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 140 TSQEEERAELRKFESSGQCQISIDTRTQTLSGVAFPLLPDAESSVHKLIKAKYNYVQFRI 199
T++++ + KF C I ID T G F L DA SV K++ K + + R+
Sbjct: 10 TTKKDLKEYFSKFGEVVDCTIKIDPVTGRSRGFGFVLFKDAA-SVEKVLDQKEHKLDGRV 68
>gnl|CDD|218911 pfam06147, DUF968, Protein of unknown function (DUF968). Family of
uncharacterized prophage proteins that are also found in
bacteria and eukaryotes.
Length = 200
Score = 28.0 bits (63), Expect = 5.3
Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 9/53 (16%)
Query: 189 KAKYNYVQFRIDLQEETINLVQSGEVTLKQL---------PSMIPTDSARYHL 232
A+ N V + +D+ + + E+TLKQ +P + R
Sbjct: 8 LARLNLVNWILDVVRVELGVSDDREITLKQRCWWAVRNDIEDALPEEVLRRSF 60
>gnl|CDD|223588 COG0514, RecQ, Superfamily II DNA helicase [DNA replication,
recombination, and repair].
Length = 590
Score = 28.4 bits (64), Expect = 5.6
Identities = 12/38 (31%), Positives = 21/38 (55%), Gaps = 1/38 (2%)
Query: 183 SVHKLIKAKYNYVQFRIDLQEETINLVQSGEVTLKQLP 220
+++K + Y FR Q+E I+ + SG+ TL +P
Sbjct: 4 EAQQVLKQVFGYASFRPG-QQEIIDALLSGKDTLVVMP 40
>gnl|CDD|216109 pfam00770, Peptidase_C5, Adenovirus endoprotease. This family of
adenovirus thiol endoproteases specifically cleave
Gly-Ala peptides in viral precursor peptides.
Length = 183
Score = 28.1 bits (63), Expect = 5.7
Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 3/40 (7%)
Query: 44 FDKYVPDLIQEAQP-CYILYRFDSKNETGGHDWLLIFWSP 82
FDK P I + + C I+ + ETGG WL + W+P
Sbjct: 6 FDKRFPGFISKDKLQCAIVN--TAGRETGGVHWLALAWNP 43
>gnl|CDD|218110 pfam04489, DUF570, Protein of unknown function (DUF570). Protein
of unknown function, found in herpesvirus and
cytomegalovirus.
Length = 422
Score = 28.3 bits (63), Expect = 6.3
Identities = 12/48 (25%), Positives = 25/48 (52%), Gaps = 2/48 (4%)
Query: 19 FKVSIENEALVLAGYKKVVGTWTQDFDKYVPDLIQ-EAQPCYILYRFD 65
F +++EN ++ G +K++GT P + E P Y++ +F+
Sbjct: 256 FTINVENLYVI-HGGRKLLGTLATVSCYQTPPSLTTENMPSYLVLQFE 302
>gnl|CDD|223122 COG0044, PyrC, Dihydroorotase and related cyclic amidohydrolases
[Nucleotide transport and metabolism].
Length = 430
Score = 28.1 bits (63), Expect = 7.4
Identities = 19/66 (28%), Positives = 31/66 (46%), Gaps = 8/66 (12%)
Query: 208 LVQSGEVTLKQLPSMIPTDSARYHLFNFRHEF---EGKIIDSVVFIYSMPGYSLPIKERM 264
LV+ G ++L++L ++ T+ AR +F + EG D V+ P I+
Sbjct: 336 LVKKGRLSLERLVELLSTNPAR--IFGLPPKGAIEEGADADLVLV---DPDEEWTIRAEE 390
Query: 265 LYSSCK 270
LYS K
Sbjct: 391 LYSKAK 396
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
0.316 0.134 0.390
Gapped
Lambda K H
0.267 0.0743 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,528,689
Number of extensions: 1678039
Number of successful extensions: 1272
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1254
Number of HSP's successfully gapped: 36
Length of query: 339
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 241
Effective length of database: 6,590,910
Effective search space: 1588409310
Effective search space used: 1588409310
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: 59 (26.5 bits)