RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5032
(193 letters)
>gnl|CDD|111185 pfam02263, GBP, Guanylate-binding protein, N-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 264
Score = 178 bits (454), Expect = 2e-56
Identities = 50/159 (31%), Positives = 70/159 (44%), Gaps = 38/159 (23%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
+R GKS+L++FL L GFS E +T GI MW
Sbjct: 29 LYRTGKSYLMNFLAG---------------------KLTGFSLGSTVESETKGIWMWCVP 67
Query: 84 YIATLPTGEKAAVILLDTQGTFD-SESTVRDCATVFALSTMLSSIQIYNLSQNIQEDDLQ 142
+ P K ++LLDT+G D +S ++ A +FAL+T+LSS +YN SQ I + LQ
Sbjct: 68 H----PNKPKHTLVLLDTEGLGDVEKSDPKNDAWIFALATLLSSTFVYNSSQTINQQALQ 123
Query: 143 HLQLFTE------------YGRLALADTGTKPFQRLQFL 169
L L TE YGR+A + F +
Sbjct: 124 QLHLVTELTELIRAKSSPRYGRVADSAEFVSFFPDFVWT 162
>gnl|CDD|206650 cd01851, GBP, Guanylate-binding protein (GBP) family (N-terminal
domain). Guanylate-binding protein (GBP), N-terminal
domain. Guanylate-binding proteins (GBPs) define a group
of proteins that are synthesized after activation of the
cell by interferons. The biochemical properties of GBPs
are clearly different from those of Ras-like and
heterotrimeric GTP-binding proteins. They bind guanine
nucleotides with low affinity (micromolar range), are
stable in their absence and have a high turnover GTPase.
In addition to binding GDP/GTP, they have the unique
ability to bind GMP with equal affinity and hydrolyze
GTP not only to GDP, but also to GMP. Furthermore, two
unique regions around the base and the phosphate-binding
areas, the guanine and the phosphate caps, respectively,
give the nucleotide-binding site a unique appearance not
found in the canonical GTP-binding proteins. The
phosphate cap, which constitutes the region analogous to
switch I, completely shields the phosphate-binding site
from solvent such that a potential GTPase-activating
protein (GAP) cannot approach.
Length = 224
Score = 130 bits (330), Expect = 3e-38
Identities = 51/151 (33%), Positives = 69/151 (45%), Gaps = 28/151 (18%)
Query: 24 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 83
+ GKSFLL+ L +GF S++ T GI MWS
Sbjct: 15 SQSSGKSFLLNHLFGTS---------------------DGFDVMDTSQQTTKGIWMWSDP 53
Query: 84 YIATLPTGEKAAVILLDTQGTFDSESTVR-DCATVFALSTMLSSIQIYNLSQNIQEDDLQ 142
+ T G+K AV+LLDT+GT E + A +FAL+T+LSS+ IYN+ Q I DDL
Sbjct: 54 FKDT--DGKKHAVLLLDTEGTDGRERGEFENDARLFALATLLSSVLIYNMWQTILGDDLD 111
Query: 143 HLQLFTE----YGRLALADTGTKPFQRLQFL 169
L + LA +KP L F+
Sbjct: 112 KLMGLLKTALETLGLAGLHNFSKPKPLLLFV 142
>gnl|CDD|240854 cd12408, RRM_eIF3G_like, RNA recognition motif in eukaryotic
translation initiation factor 3 subunit G (eIF-3G) and
similar proteins. This subfamily corresponds to the RRM
of eIF-3G and similar proteins. eIF-3G, also termed
eIF-3 subunit 4, or eIF-3-delta, or eIF3-p42, or
eIF3-p44, is the RNA-binding subunit of eIF3, a large
multisubunit complex that plays a central role in the
initiation of translation by binding to the 40 S
ribosomal subunit and promoting the binding of
methionyl-tRNAi and mRNA. eIF-3G binds 18 S rRNA and
beta-globin mRNA, and therefore appears to be a
nonspecific RNA-binding protein. eIF-3G is one of the
cytosolic targets and interacts with mature
apoptosis-inducing factor (AIF). eIF-3G contains one RNA
recognition motif (RRM), also termed RBD (RNA binding
domain) or RNP (ribonucleoprotein domain). This family
also includes yeast eIF3-p33, a homolog of vertebrate
eIF-3G, plays an important role in the initiation phase
of protein synthesis in yeast. It binds both, mRNA and
rRNA, fragments due to an RRM near its C-terminus. .
Length = 77
Score = 28.7 bits (65), Expect = 0.47
Identities = 11/28 (39%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 126 SIQIYNLSQNIQEDDLQHLQLFTEYGRL 153
+I++ NLS++ EDDL+ +LF +G +
Sbjct: 1 TIRVTNLSEDADEDDLR--ELFRPFGPI 26
>gnl|CDD|241042 cd12598, RRM1_SRSF9, RNA recognition motif 1 in vertebrate
serine/arginine-rich splicing factor 9 (SRSF9). This
subgroup corresponds to the RRM1 of SRSF9, also termed
pre-mRNA-splicing factor SRp30C. SRSF9 is an essential
splicing regulatory serine/arginine (SR) protein that
has been implicated in the activity of many elements
that control splice site selection, the alternative
splicing of the glucocorticoid receptor beta in
neutrophils and in the gonadotropin-releasing hormone
pre-mRNA. SRSF9 can also interact with other proteins
implicated in alternative splicing, including YB-1,
rSLM-1, rSLM-2, E4-ORF4, Nop30, and p32. SRSF9 contains
two N-terminal RNA recognition motifs (RRMs), also
termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains), followed by an unusually
short C-terminal RS domains rich in serine-arginine
dipeptides. .
Length = 72
Score = 26.3 bits (58), Expect = 2.8
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 127 IQIYNLSQNIQEDDLQHLQLFTEYGRLALADT----GTKPFQRLQF 168
I + NL +++E DL+ LF +YGR+ + G PF ++F
Sbjct: 2 IYVGNLPSDVREKDLE--DLFYKYGRIRDIELKNRRGLVPFAFVRF 45
>gnl|CDD|213927 TIGR04314, methano7heme, methanogenesis multiheme c-type
cytochrome. Members of this protein family are
multiheme cytochrome c proteins of Methanosarcina
acetivorans C2A and several other archaeal methanogens.
All members have N-terminal signal peptides and are
presumed to act in electron transfer reactions
associated with methanogenesis. Putative heme-binding
motifs include five (or six) CXXCH motifs, a CXXXCH
motif, and a CXXXXCH motif. These proteins show multiple
regions of local homology, in the same order, with
multiheme cytochrome c proteins such as octaheme
tetrathionate reductase from Shewanella.
Length = 494
Score = 27.9 bits (62), Expect = 4.2
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 44 YIEEAPSGDWMGPDDVPLEGFSWRGGSERDT 74
+I P GD P PL+ FSW G D+
Sbjct: 280 HIPALPGGDL--PGGEPLKSFSWSNGEREDS 308
>gnl|CDD|220634 pfam10220, DUF2146, Uncharacterized conserved protein (DUF2146).
This is a family of proteins conserved from plants to
humans. In Dictyostelium it is annotated as Mss11p but
this could not be confirmed. Mss11p is required for the
activation of pseudo-hyphal and invasive growth by
Ste12p in yeast.
Length = 890
Score = 27.9 bits (62), Expect = 4.7
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 42 FTYIEEAPSGDWMGPDDV-PLEGFSWRGGSERDTT 75
++ SG M P + PL + GG
Sbjct: 855 LPFVYAGDSGPCMPPKENNPLNSYKLMGGILLAGM 889
>gnl|CDD|240809 cd12363, RRM_TRA2, RNA recognition motif in transformer-2 protein
homolog TRA2-alpha, TRA2-beta and similar proteins.
This subfamily corresponds to the RRM of two mammalian
homologs of Drosophila transformer-2 (Tra2), TRA2-alpha,
TRA2-beta (also termed SFRS10), and similar proteins
found in eukaryotes. TRA2-alpha is a 40-kDa
serine/arginine-rich (SR) protein that specifically
binds to gonadotropin-releasing hormone (GnRH) exonic
splicing enhancer on exon 4 (ESE4) and is necessary for
enhanced GnRH pre-mRNA splicing. It strongly stimulates
GnRH intron A excision in a dose-dependent manner. In
addition, TRA2-alpha can interact with either 9G8 or
SRp30c, which may also be crucial for ESE-dependent GnRH
pre-mRNA splicing. TRA2-beta is a serine/arginine-rich
(SR) protein that controls the pre-mRNA alternative
splicing of the calcitonin/calcitonin gene-related
peptide (CGRP), the survival motor neuron 1 (SMN1)
protein and the tau protein. Both, TRA2-alpha and
TRA2-beta, contains a well conserved RNA recognition
motif (RRM), also termed RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), flanked by the N- and
C-terminal arginine/serine (RS)-rich regions. .
Length = 78
Score = 26.0 bits (58), Expect = 4.8
Identities = 8/25 (32%), Positives = 14/25 (56%), Gaps = 2/25 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYGRL 153
++ LS E DL+ +F+ YG +
Sbjct: 4 VFGLSLYTTERDLRE--VFSRYGPI 26
>gnl|CDD|240811 cd12365, RRM_RNPS1, RNA recognition motif in RNA-binding protein
with serine-rich domain 1 (RNPS1) and similar proteins.
This subfamily corresponds to the RRM of RNPS1 and its
eukaryotic homologs. RNPS1, also termed RNA-binding
protein prevalent during the S phase, or SR-related
protein LDC2, was originally characterized as a general
pre-mRNA splicing activator, which activates both
constitutive and alternative splicing of pre-mRNA in
vitro.It has been identified as a protein component of
the splicing-dependent mRNP complex, or exon-exon
junction complex (EJC), and is directly involved in mRNA
surveillance. Furthermore, RNPS1 is a splicing regulator
whose activator function is controlled in part by CK2
(casein kinase II) protein kinase phosphorylation. It
can also function as a squamous-cell carcinoma antigen
recognized by T cells-3 (SART3)-binding protein, and is
involved in the regulation of mRNA splicing. RNPS1
contains an N-terminal serine-rich (S) domain, a central
RNA recognition motif (RRM), also termed RBD (RNA
binding domain) or RNP (ribonucleoprotein domain), and
the C-terminal arginine/serine/proline-rich (RS/P)
domain. .
Length = 73
Score = 25.6 bits (57), Expect = 5.0
Identities = 8/28 (28%), Positives = 18/28 (64%), Gaps = 4/28 (14%)
Query: 127 IQIYNLSQNIQEDDLQHLQ-LFTEYGRL 153
+ + L++N+ +D HL+ +F+ YG +
Sbjct: 1 LHVGKLTRNVNKD---HLKEIFSNYGTV 25
>gnl|CDD|214636 smart00360, RRM, RNA recognition motif.
Length = 73
Score = 25.6 bits (57), Expect = 5.1
Identities = 7/23 (30%), Positives = 16/23 (69%), Gaps = 2/23 (8%)
Query: 129 IYNLSQNIQEDDLQHLQLFTEYG 151
+ NL + E++L+ +LF+++G
Sbjct: 4 VGNLPPDTTEEELR--ELFSKFG 24
>gnl|CDD|176792 cd08814, DED_Caspase_10_repeat2, Death Effector Domain, repeat 2,
of Caspase-10. Death effector domain (DED) found in
Caspase-10, repeat 2. Caspases are aspartate-specific
cysteine proteases with functions in apoptosis and
immune signaling. Initiator caspases are the first to be
activated following death- or inflammation-inducing
signals. Caspase-10 is an initiator of death receptor
mediated apoptosis. Together with FADD, caspase-8 and
the pseudo-caspase c-FLIP, it forms the death-inducing
signaling complex (DISC), whose formation is triggered
by the activation of type 1 tumor necrosis factor (TNF)
receptors such as Fas, TNF receptor 1, and TRAIL
receptor. It contains two N-terminal DED domains and a
C-terminal caspase domain. DEDs comprise a subfamily of
the Death Domain (DD) superfamily. DDs are
protein-protein interaction domains found in a variety
of domain architectures. Their common feature is that
they form homodimers by self-association or heterodimers
by associating with other members of the DD superfamily
including PYRIN and CARD (Caspase activation and
recruitment domain). They serve as adaptors in signaling
pathways and can recruit other proteins into signaling
complexes.
Length = 79
Score = 25.9 bits (57), Expect = 5.5
Identities = 7/16 (43%), Positives = 12/16 (75%)
Query: 129 IYNLSQNIQEDDLQHL 144
+Y LS+NI +DL+ +
Sbjct: 8 LYELSENITSEDLKDI 23
>gnl|CDD|224520 COG1604, COG1604, CRISPR system related protein, RAMP superfamily
[Defense mechanisms].
Length = 257
Score = 27.0 bits (60), Expect = 6.9
Identities = 13/45 (28%), Positives = 18/45 (40%), Gaps = 4/45 (8%)
Query: 27 KGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPL----EGFSWR 67
K LD + + Y EE P GDW P + +G +R
Sbjct: 169 KDCFLSLDVINPHYQSYYQEEQPPGDWDSPKPIKFLTVSKGVRFR 213
>gnl|CDD|237402 PRK13504, PRK13504, sulfite reductase subunit beta; Provisional.
Length = 569
Score = 26.7 bits (60), Expect = 8.2
Identities = 10/28 (35%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 137 QEDDLQHLQLFTEYGRLALADTGTKPFQ 164
D HL LF E GR + D +P +
Sbjct: 349 GIDGKWHLTLFIENGR--IKDYPGRPLK 374
>gnl|CDD|234712 PRK00281, PRK00281, undecaprenyl pyrophosphate phosphatase;
Reviewed.
Length = 268
Score = 26.6 bits (60), Expect = 9.5
Identities = 7/26 (26%), Positives = 10/26 (38%)
Query: 66 WRGGSERDTTGILMWSHVYIATLPTG 91
G D + V +AT+P G
Sbjct: 73 SGKGGRGDREDRRLLLLVIVATIPAG 98
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
0.318 0.133 0.394
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,714,275
Number of extensions: 874854
Number of successful extensions: 691
Number of sequences better than 10.0: 1
Number of HSP's gapped: 683
Number of HSP's successfully gapped: 18
Length of query: 193
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 101
Effective length of database: 6,857,034
Effective search space: 692560434
Effective search space used: 692560434
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 (21.7 bits)
S2: 56 (25.2 bits)