RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1580
(267 letters)
>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
RNA-binding domain (KH). Splicing factor 1 (SF1)
specifically recognizes the intron branch point sequence
(BPS) UACUAAC in the pre-mRNA transcripts during
spliceosome assembly. We show that the KH-QUA2 region of
SF1 defines an enlarged KH (hnRNP K) fold which is
necessary and sufficient for BPS binding. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional modifiers
of mRNA.
Length = 120
Score = 141 bits (357), Expect = 1e-42
Identities = 53/125 (42%), Positives = 82/125 (65%), Gaps = 10/125 (8%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
T +V +PV+ +PK+NFVG +LGP+GN+LK+L+++T +++I G+GS++D KEEELR
Sbjct: 1 TEKVYIPVKQYPKYNFVGLILGPRGNTLKQLEKETGAKISIRGKGSMKDGKKEEELRGPK 60
Query: 83 DPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQEQMW 142
HL E LHV ITA PP EA A+ A+ E+ + + NDE+++EQ+
Sbjct: 61 YA---HLNEPLHVLITAETPPEEALAKAVEAIEELLKPAIE-------GGNDELKREQLR 110
Query: 143 EMQIL 147
E+ +L
Sbjct: 111 ELALL 115
>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
processing and modification].
Length = 269
Score = 58.4 bits (141), Expect = 4e-10
Identities = 27/82 (32%), Positives = 48/82 (58%), Gaps = 4/82 (4%)
Query: 18 KPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEE 77
+P K ++ +PV+++P+ NFVG L+GP+G++LK+L+ + ++AI G GS+ KE +
Sbjct: 144 RPSKYQNKIYIPVQEYPESNFVGLLIGPRGSTLKQLERISRAKIAIRGSGSV----KEGK 199
Query: 78 LRISGDPKFLHLLEELHVEITA 99
+ + LH I A
Sbjct: 200 ISSDTPESLKNAEAVLHCLIEA 221
>gnl|CDD|197652 smart00322, KH, K homology RNA-binding domain.
Length = 68
Score = 42.3 bits (100), Expect = 8e-06
Identities = 20/65 (30%), Positives = 38/65 (58%), Gaps = 11/65 (16%)
Query: 21 KVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRI 80
VTI V++P + VG ++G G+++K+++E+T ++ I G GS +E + I
Sbjct: 2 PVTIEVLIPA------DKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-----EERVVEI 50
Query: 81 SGDPK 85
+G P+
Sbjct: 51 TGPPE 55
>gnl|CDD|238053 cd00105, KH-I, K homology RNA-binding domain, type I. KH binds
single-stranded RNA or DNA. It is found in a wide
variety of proteins including ribosomal proteins,
transcription factors and post-transcriptional
modifiers of mRNA. There are two different KH domains
that belong to different protein folds, but they share
a single KH motif. The KH motif is folded into a beta
alpha alpha beta unit. In addition to the core, type II
KH domains (e.g. ribosomal protein S3) include
N-terminal extension and type I KH domains (e.g. hnRNP
K) contain C-terminal extension.
Length = 64
Score = 41.8 bits (99), Expect = 1e-05
Identities = 18/63 (28%), Positives = 35/63 (55%), Gaps = 9/63 (14%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
T RV+VP + VG+++G G+++K ++E+T ++ I G +E + I+G
Sbjct: 1 TERVLVPS------SLVGRIIGKGGSTIKEIREETGAKIKIPDSG---SGSEERIVTITG 51
Query: 83 DPK 85
P+
Sbjct: 52 TPE 54
>gnl|CDD|215657 pfam00013, KH_1, KH domain. KH motifs bind RNA in vitro.
Autoantibodies to Nova, a KH domain protein, cause
paraneoplastic opsoclonus ataxia.
Length = 59
Score = 35.6 bits (83), Expect = 0.002
Identities = 15/63 (23%), Positives = 35/63 (55%), Gaps = 13/63 (20%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
T R+++P + VG+++G G+++K ++E+T ++ I +++ + ISG
Sbjct: 1 TERILIPP------DKVGRIIGKGGSNIKEIREETGVKIRI-------PDDRDDTVTISG 47
Query: 83 DPK 85
P+
Sbjct: 48 TPE 50
>gnl|CDD|221895 pfam13014, KH_3, KH domain. KH motifs bind RNA in vitro. This
RNA-binding domain is required for the efficient
anchoring of ASH1-mRNA to the distal tip of the
daughter cell. ASH1 is a specific repressor of
transcription that localizes asymmetrically to the
daughter cell nucleus. RNA localisation is a widespread
mechanism for achieving localised protein synthesis.
Length = 42
Score = 34.5 bits (80), Expect = 0.003
Identities = 11/45 (24%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 38 FVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
VG ++G G ++K ++E+T ++ I E + I+G
Sbjct: 1 LVGAIIGKGGETIKEIREETGAKIQIP---KPEPGSGERIVTITG 42
>gnl|CDD|239089 cd02396, PCBP_like_KH, K homology RNA-binding domain, PCBP_like.
Members of this group possess KH domains in a tandem
arrangement. Most members, similar to the poly(C)
binding proteins (PCBPs) and Nova, containing three KH
domains, with the first and second domains, which are
represented here, in tandem arrangement, followed by a
large spacer region, with the third domain near the
C-terminal end of the protein. The poly(C) binding
proteins (PCBPs) can be divided into two groups, hnRNPs
K/J and the alphaCPs, which share a triple KH domain
configuration and poly(C) binding specificity. They
play roles in mRNA stabilization, translational
activation, and translational silencing. Nova-1 and
Nova-2 are nuclear RNA-binding proteins that regulate
splicing. This group also contains plant proteins that
seem to have two tandem repeat arrrangements, like
Hen4, a protein that plays a role in AGAMOUS (AG)
pre-mRNA processing and important step in plant
development. In general, KH binds single-stranded RNA
or DNA. It is found in a wide variety of proteins
including ribosomal proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 65
Score = 29.8 bits (68), Expect = 0.24
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 8/62 (12%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSIRDRHKEEELRISG 82
T+R++VP G ++G G+++K ++E+T ++ + S+ E + ISG
Sbjct: 1 TLRLLVPSSQ------AGSIIGKGGSTIKEIREETGAKIRVS--KSVLPGSTERVVTISG 52
Query: 83 DP 84
P
Sbjct: 53 KP 54
>gnl|CDD|239049 cd02134, NusA_KH, NusA_K homology RNA-binding domain (KH). NusA
is an essential multifunctional transcription
elongation factor that is universally conserved among
prokaryotes and archaea. NusA anti-termination function
plays an important role in the expression of ribosomal
rrn operons. During transcription of many other genes,
NusA-induced RNAP pausing provides a mechanism for
synchronizing transcription and translation . The
N-terminal RNAP-binding domain (NTD) is connected
through a flexible hinge helix to three globular
domains, S1, KH1 and KH2. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices.
Length = 61
Score = 27.5 bits (62), Expect = 1.1
Identities = 9/46 (19%), Positives = 19/46 (41%), Gaps = 6/46 (13%)
Query: 10 KMVDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQE 55
K+ +T + RV+VP +G +G G +++ +
Sbjct: 13 KVTSVTVLDDEEKRARVVVPDDQ------LGLAIGKGGQNVRLASK 52
>gnl|CDD|131743 TIGR02696, pppGpp_PNP, guanosine pentaphosphate synthetase
I/polynucleotide phosphorylase. Sohlberg, et al present
characterization of two proteins from Streptomyces
coelicolor. The protein in this family was shown to have
poly(A) polymerase activity and may be responsible for
polyadenylating RNA in this species. Reference 2 showed
that a nearly identical plasmid-encoded protein from
Streptomyces antibioticus is a bifunctional enzyme that
acts also as a guanosine pentaphosphate synthetase.
Length = 719
Score = 30.2 bits (68), Expect = 1.3
Identities = 13/46 (28%), Positives = 28/46 (60%), Gaps = 6/46 (13%)
Query: 24 IRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRMAILGRGSI 69
I V +PV + +G+++GPKG + ++Q++T ++I G++
Sbjct: 580 ITVKIPV------DKIGEVIGPKGKMINQIQDETGAEISIEDDGTV 619
>gnl|CDD|235057 PRK02628, nadE, NAD synthetase; Reviewed.
Length = 679
Score = 29.1 bits (66), Expect = 2.6
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 102 PPAEAHARIAYALAEVRRFLVPFTRSLFQ 130
P R AY LA ++++L F R F
Sbjct: 604 PGFPEDKRPAYDLATIKKWLEVFLRRFFS 632
>gnl|CDD|239087 cd02394, vigilin_like_KH, K homology RNA-binding
domain_vigilin_like. The vigilin family is a large and
extended family of multiple KH-domain proteins,
including vigilin, also called high density lipoprotein
binding protien (HBP), fungal Scp160 and bicaudal-C.
Yeast Scp160p has been shown to bind RNA and to
associate with both soluble and membrane-bound
polyribosomes as a mRNP component. Bicaudal-C is a
RNA-binding molecule believed to function in embryonic
development at the post-transcriptional level. In
general, KH binds single-stranded RNA or DNA. It is
found in a wide variety of proteins including ribosomal
proteins, transcription factors and
post-transcriptional modifiers of mRNA.
Length = 62
Score = 26.3 bits (59), Expect = 3.4
Identities = 9/35 (25%), Positives = 20/35 (57%), Gaps = 6/35 (17%)
Query: 23 TIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDT 57
T V +P + H ++G KG++++++ E+T
Sbjct: 1 TEEVEIPKKLHRF------IIGKKGSNIRKIMEET 29
>gnl|CDD|176512 cd08570, GDPD_YPL206cp_fungi, Glycerophosphodiester
phosphodiesterase domain of Saccharomyces cerevisiae
YPL206cp and similar proteins. This subfamily
corresponds to the glycerophosphodiester
phosphodiesterase domain (GDPD) present in Saccharomyces
cerevisiae YPL206cp and uncharacterized hypothetical
homologs existing in fungi. The product of S. cerevisiae
ORF YPL206c (PGC1), YPL206cp (Pgc1p), displays homology
to bacterial and mammalian glycerophosphodiester
phosphodiesterases (GP-GDE, EC 3.1.4.46), which
catalyzes the degradation of glycerophosphodiesters to
produce sn-glycerol-3-phosphate (G3P) and the
corresponding alcohols. S. cerevisiae YPL206cp is an
integral membrane protein with a single GDPD domain
following by a short hydrophobic C-terminal tail that
may function as a membrane anchor. This protein plays an
essential role in the regulation of the cardiolipin (CL)
biosynthetic pathway in yeast by removing the excess
phosphatidylglycerol (PG) content of membranes via a
phospholipase C-type degradation mechanism. YPL206cp has
been characterized as a PG-specific phospholipase C that
selectively catalyzes the cleavage of PG, not
glycerophosphoinositol (GPI) or glycerophosphocholine
(GPC), to diacylglycerol (DAG) and glycerophosphate.
Members in this family are distantly related to S.
cerevisiae YPL110cp, which selectively hydrolyzes
glycerophosphocholine (GPC), not glycerophosphoinositol
(GPI), to generate choline and glycerolphosphate, and
has been characterized as a cytoplasmic GPC-specific
phosphodiesterase.
Length = 234
Score = 28.0 bits (63), Expect = 4.3
Identities = 8/27 (29%), Positives = 17/27 (62%)
Query: 1 MKHQEPHGRKMVDITRDKPIKVTIRVI 27
++H+ P + M+DI RD ++ ++I
Sbjct: 93 VEHELPDVKLMLDIKRDNDPEILFKLI 119
>gnl|CDD|170047 PRK09687, PRK09687, putative lyase; Provisional.
Length = 280
Score = 28.2 bits (63), Expect = 5.1
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 2/61 (3%)
Query: 78 LRISGDPKFLHLLEELHVEITAFAPPAEAHARIAYALAEVRRFL-VPFTRSLFQDYNDEI 136
R +P + + E +ITAF +A+AL+ + +P +L +D N ++
Sbjct: 117 HRCKKNPLYSPKIVE-QSQITAFDKSTNVRFAVAFALSVINDEAAIPLLINLLKDPNGDV 175
Query: 137 R 137
R
Sbjct: 176 R 176
>gnl|CDD|239092 cd02409, KH-II, KH-II (K homology RNA-binding domain, type II).
KH binds single-stranded RNA or DNA. It is found in a
wide variety of proteins including ribosomal proteins
(e.g. ribosomal protein S3), transcription factors
(e.g. NusA_K), and post-transcriptional modifiers of
mRNA (e.g. hnRNP K). There are two different KH domains
that belong to different protein folds, but they share
a single KH motif. The KH motif is a
beta-alpha-alpha-beta-beta unit that folds into an
alpha-beta structure with a three stranded beta-sheet
interupted by two contiguous helices. In addition to
their KH core domain, KH-II proteins have an N-terminal
alpha helical extension while KH-I proteins have a
C-terminal alpha helical extension.
Length = 68
Score = 26.1 bits (58), Expect = 5.2
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 7/50 (14%)
Query: 12 VDITRDKPIKVTIRVIVPVRDHPKFNFVGKLLGPKGNSLKRLQEDTMTRM 61
V+I R P ++ I ++V G ++G KG +++ LQ+ +
Sbjct: 16 VEIER-TPDRIEIIIVVARGQ------PGLVIGKKGQNIRALQKLLQKLL 58
>gnl|CDD|188022 TIGR00095, TIGR00095, RNA methyltransferase, RsmD family. This
model represents a family of uncharacterized bacterial
proteins. Members are present in nearly every complete
bacterial genome, always in a single copy. PSI-BLAST
analysis shows homology to several families of
SAM-dependent methyltransferases, including ribosomal
RNA adenine dimethylases [Protein synthesis, tRNA and
rRNA base modification].
Length = 190
Score = 27.8 bits (62), Expect = 5.2
Identities = 8/27 (29%), Positives = 14/27 (51%)
Query: 216 NRKRPLLTAGSSRPTMSPTKRTVLSIL 242
RK + S+RPT + ++ +IL
Sbjct: 19 GRKLKVPPGPSTRPTTDRVRESLFNIL 45
>gnl|CDD|224771 COG1858, MauG, Cytochrome c peroxidase [Inorganic ion transport and
metabolism].
Length = 364
Score = 28.2 bits (63), Expect = 5.3
Identities = 18/104 (17%), Positives = 31/104 (29%), Gaps = 15/104 (14%)
Query: 99 AFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDY----NDEIRQEQMWEMQILKEDGGAA 154
F + IA A+A R L+ S F + + + +++ + + K A
Sbjct: 176 MFDLGDVSFDNIADAIAAFERTLITPD-SRFDRFLRGDDAALTEQEKRGLALFKGKANCA 234
Query: 155 SCSESSESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPA 198
+C N+ Y V N PA
Sbjct: 235 ACHNGINLGGNSF----------HPFGDFTYYNVGVPRNPGLPA 268
>gnl|CDD|114205 pfam05467, Herpes_U47, Herpesvirus glycoprotein U47.
Length = 627
Score = 28.3 bits (62), Expect = 5.3
Identities = 23/100 (23%), Positives = 41/100 (41%), Gaps = 6/100 (6%)
Query: 154 ASCSESSESSVNNPLLYAENTSPVENLTPPEYTLVDPAFNRIQPATEAINIPTKTMTTAA 213
+S S+ +S+ +P + P N+ PE V F + T + T T+T
Sbjct: 242 SSTPSSTSASITSPHI------PSTNIPTPEPPPVTKNFTELHTDTIKVTPNTPTITAQT 295
Query: 214 LVNRKRPLLTAGSSRPTMSPTKRTVLSILTRARVSQSKPT 253
+ K+ + + RP +PT L+I A + + T
Sbjct: 296 TESIKKIVKRSDFPRPMYTPTDIPTLTIRLNATIKTEQNT 335
>gnl|CDD|226640 COG4171, SapC, ABC-type antimicrobial peptide transport system,
permease component [Defense mechanisms].
Length = 296
Score = 27.8 bits (62), Expect = 5.6
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 4/47 (8%)
Query: 93 LHVEITAFAPPAEAHARIAYALAEVRRFLVPFTRSLFQDYNDEIRQE 139
L + + AFA P+ ++A A LA + RF+ RS++ +DE+ +E
Sbjct: 146 LAIIVVAFAGPSLSNAMFAVWLALLPRFI----RSIYSAVHDELEKE 188
>gnl|CDD|218439 pfam05109, Herpes_BLLF1, Herpes virus major outer envelope
glycoprotein (BLLF1). This family consists of the BLLF1
viral late glycoprotein, also termed gp350/220. It is
the most abundantly expressed glycoprotein in the viral
envelope of the Herpesviruses and is the major antigen
responsible for stimulating the production of
neutralising antibodies in vivo.
Length = 830
Score = 27.8 bits (61), Expect = 7.1
Identities = 16/82 (19%), Positives = 28/82 (34%), Gaps = 2/82 (2%)
Query: 172 ENTSPVENLTPPEYTLVDPAFNRIQPATEAINIPTKTMTTAALVNRKRPLLTAGSSRPTM 231
E+TSP T P A + T+ + P++ ++ T
Sbjct: 484 EDTSPTSRTTSATPNATSPT--PAVTTPNATSPTTQKTSDTPNATSPTPIVIGVTTTATS 541
Query: 232 SPTKRTVLSILTRARVSQSKPT 253
PT T + T +V++ P
Sbjct: 542 PPTGTTSVPNATSPQVTEESPV 563
>gnl|CDD|218954 pfam06246, Isy1, Isy1-like splicing family. Isy1 protein is
important in the optimisation of splicing.
Length = 253
Score = 27.3 bits (61), Expect = 8.5
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 5/27 (18%)
Query: 131 DYNDEI----RQEQMWEMQILKEDGGA 153
D NDEI R+++ WE +I +E GG
Sbjct: 76 DLNDEINKLFREKRHWEDRI-RELGGP 101
>gnl|CDD|217705 pfam03739, YjgP_YjgQ, Predicted permease YjgP/YjgQ family. Members
of this family are predicted integral membrane proteins
of unknown function. They are about 350 amino acids long
and contain about 6 transmembrane regions. They are
predicted to be permeases although there is no
verification of this.
Length = 354
Score = 27.2 bits (61), Expect = 9.6
Identities = 15/74 (20%), Positives = 29/74 (39%), Gaps = 3/74 (4%)
Query: 43 LGPKGNSLKRLQEDTMT-RMAILGRGSIRDRHKEEELRISGDPKFLHLLEELHVEITAFA 101
G L L D +++ + EEL +S ++ L+ +++ +
Sbjct: 210 FDKDGGELSILSFDRYEIDLSLTPQDLSSLTEDPEELSLSELYAYIKRLKASGLDVRKYR 269
Query: 102 PPAEAHARIAYALA 115
AE H R+A L+
Sbjct: 270 --AELHRRLALPLS 281
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
0.317 0.132 0.376
Gapped
Lambda K H
0.267 0.0737 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 13,720,034
Number of extensions: 1316201
Number of successful extensions: 1155
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1152
Number of HSP's successfully gapped: 34
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
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: 58 (26.1 bits)