RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5031
(281 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 = 179 bits (455), Expect = 3e-55
Identities = 51/161 (31%), Positives = 71/161 (44%), Gaps = 38/161 (23%)
Query: 134 VSAFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWS 193
V +R GKS+L++FL L GFS E +T GI MW
Sbjct: 27 VGLYRTGKSYLMNFLAG---------------------KLTGFSLGSTVESETKGIWMWC 65
Query: 194 HVYIATLPTGEKAAVILLDTQGTFD-SESTVRDCATVFALSTMLSSIQIYNLSQNIQEDD 252
+ P K ++LLDT+G D +S ++ A +FAL+T+LSS +YN SQ I +
Sbjct: 66 VPH----PNKPKHTLVLLDTEGLGDVEKSDPKNDAWIFALATLLSSTFVYNSSQTINQQA 121
Query: 253 LQHLQLFTE------------YGRLALADTGTKPFQRLQFL 281
LQ L L TE YGR+A + F +
Sbjct: 122 LQQLHLVTELTELIRAKSSPRYGRVADSAEFVSFFPDFVWT 162
Score = 96.7 bits (241), Expect = 1e-23
Identities = 30/103 (29%), Positives = 42/103 (40%), Gaps = 29/103 (28%)
Query: 32 KHKFILDYEALERILLQDHVKDKHVVVVSVAGAFRKGKSFLLDFLLRYMNFTYIEEAPSG 91
H+ L+ EALE + + VVVV++ G +R GKS+L++FL
Sbjct: 1 DHQLELNEEALEIL----SAITQPVVVVAIVGLYRTGKSYLMNFLAG------------- 43
Query: 92 DWMGPDDVPLEGFSWRGGSERDTTGILMWSHVYIATLPTGEKV 134
L GFS E +T GI MW + P K
Sbjct: 44 --------KLTGFSLGSTVESETKGIWMWCVPH----PNKPKH 74
>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 = 129 bits (327), Expect = 1e-36
Identities = 51/151 (33%), Positives = 69/151 (45%), Gaps = 28/151 (18%)
Query: 136 AFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGGSERDTTGILMWSHV 195
+ GKSFLL+ L +GF S++ T GI MWS
Sbjct: 15 SQSSGKSFLLNHLFGTS---------------------DGFDVMDTSQQTTKGIWMWSDP 53
Query: 196 YIATLPTGEKAAVILLDTQGTFDSESTVR-DCATVFALSTMLSSIQIYNLSQNIQEDDLQ 254
+ T G+K AV+LLDT+GT E + A +FAL+T+LSS+ IYN+ Q I DDL
Sbjct: 54 FKDT--DGKKHAVLLLDTEGTDGRERGEFENDARLFALATLLSSVLIYNMWQTILGDDLD 111
Query: 255 HLQLFTE----YGRLALADTGTKPFQRLQFL 281
L + LA +KP L F+
Sbjct: 112 KLMGLLKTALETLGLAGLHNFSKPKPLLLFV 142
Score = 68.9 bits (169), Expect = 7e-14
Identities = 28/98 (28%), Positives = 34/98 (34%), Gaps = 29/98 (29%)
Query: 50 HVKDKHVVVVSVAGAFRKGKSFLLDFLLRYMNFTYIEEAPSGDWMGPDDVPLEGFSWRGG 109
VVVVSV G+ GKSFLL+ L +GF
Sbjct: 1 LDVGFPVVVVSVFGSQSSGKSFLLNHLFGTS---------------------DGFDVMDT 39
Query: 110 SERDTTGILMWSHVYIATLPTGEKVSAFRKGKSFLLDF 147
S++ T GI MWS + T V LLD
Sbjct: 40 SQQTTKGIWMWSDPFKDTDGKKHAV--------LLLDT 69
>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 = 0.79
Identities = 11/28 (39%), Positives = 20/28 (71%), Gaps = 2/28 (7%)
Query: 238 SIQIYNLSQNIQEDDLQHLQLFTEYGRL 265
+I++ NLS++ EDDL+ +LF +G +
Sbjct: 1 TIRVTNLSEDADEDDLR--ELFRPFGPI 26
>gnl|CDD|237510 PRK13795, PRK13795, hypothetical protein; Provisional.
Length = 636
Score = 30.0 bits (68), Expect = 1.4
Identities = 18/58 (31%), Positives = 24/58 (41%), Gaps = 13/58 (22%)
Query: 21 YGAIQIVKSEEKHKFILDYEALERI-----LLQDHV--------KDKHVVVVSVAGAF 65
GA +++K K I+D ALE I +L V K VVVV+ G
Sbjct: 115 EGAKRLLKKRLKKWVIVDKGALEPIKNGKNVLAPGVVEADLDIKKGDEVVVVTEDGEV 172
>gnl|CDD|232980 TIGR00450, mnmE_trmE_thdF, tRNA modification GTPase TrmE. TrmE,
also called MnmE and previously designated ThdF
(thiophene and furan oxidation protein), is a GTPase
involved in tRNA modification to create
5-methylaminomethyl-2-thiouridine in the wobble position
of some tRNAs. This protein and GidA form an
alpha2/beta2 heterotetramer [Protein synthesis, tRNA and
rRNA base modification].
Length = 442
Score = 29.4 bits (66), Expect = 2.6
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 13/79 (16%)
Query: 1 MKKEVDLKMGGDFEEDSLPQYGAIQ-IVKSEEKHKFILDYEALERILLQDHVKDKHVVVV 59
+ EV++ D+EED Q Q ++ + K IL+ LE+ L D K +
Sbjct: 159 AQVEVNI----DYEEDDDEQDSLNQLLLSIIAELKDILNSYKLEK--LDDGFK------L 206
Query: 60 SVAGAFRKGKSFLLDFLLR 78
++ G+ GKS LL+ LL+
Sbjct: 207 AIVGSPNVGKSSLLNALLK 225
>gnl|CDD|130409 TIGR01342, acon_putative, aconitate hydratase, putative, Aquifex
type. This model represents a small family of proteins
homologous (and likely functionally equivalent to)
aconitase 1. Members are found, so far in the anaerobe
Clostridium acetobutylicum, in the microaerophilic,
early-branching bacterium Aquifex aeolicus, and in the
halophilic archaeon Halobacterium sp. NRC-1. No member
is experimentally characterized [Energy metabolism, TCA
cycle].
Length = 658
Score = 29.2 bits (65), Expect = 2.6
Identities = 22/92 (23%), Positives = 40/92 (43%), Gaps = 1/92 (1%)
Query: 95 GPDDVPLEGFSWRGGSERDTTGILMWSHVYI-ATLPTGEKVSAFRKGKSFLLDFLLRYMN 153
GP+ PL F G T ++M ++ +P G + FR + +F L ++
Sbjct: 455 GPNIKPLPEFDPLGADIEGETALIMEDNITTDHIIPAGADILKFRSNIEAISEFTLHRID 514
Query: 154 FTYIEEAPSGDWMGPDDVPLEGFSWRGGSERD 185
+ E A + D G + + G ++ GS R+
Sbjct: 515 DEFAERAKAADEKGKAGIIIAGENYGQGSSRE 546
>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 = 5.2
Identities = 15/46 (32%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 239 IQIYNLSQNIQEDDLQHLQLFTEYGRLALADT----GTKPFQRLQF 280
I + NL +++E DL+ LF +YGR+ + G PF ++F
Sbjct: 2 IYVGNLPSDVREKDLE--DLFYKYGRIRDIELKNRRGLVPFAFVRF 45
>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 = 7.0
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 82 FTYIEEAPSGDWMGPDDV-PLEGFSWRGGSERDTT 115
++ SG M P + PL + GG
Sbjct: 855 LPFVYAGDSGPCMPPKENNPLNSYKLMGGILLAGM 889
Score = 27.9 bits (62), Expect = 7.0
Identities = 8/35 (22%), Positives = 12/35 (34%), Gaps = 1/35 (2%)
Query: 154 FTYIEEAPSGDWMGPDDV-PLEGFSWRGGSERDTT 187
++ SG M P + PL + GG
Sbjct: 855 LPFVYAGDSGPCMPPKENNPLNSYKLMGGILLAGM 889
>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 = 7.6
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 84 YIEEAPSGDWMGPDDVPLEGFSWRGGSERDT 114
+I P GD P PL+ FSW G D+
Sbjct: 280 HIPALPGGDL--PGGEPLKSFSWSNGEREDS 308
Score = 27.9 bits (62), Expect = 7.6
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 156 YIEEAPSGDWMGPDDVPLEGFSWRGGSERDT 186
+I P GD P PL+ FSW G D+
Sbjct: 280 HIPALPGGDL--PGGEPLKSFSWSNGEREDS 308
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 27.7 bits (62), Expect = 9.3
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 4/44 (9%)
Query: 110 SERDTTGILMWSHVYIATLPTGEKVSAFRKGKSFLLDFLLRYMN 153
S D + +L W ++++L ++ A RK +L+FLLR +
Sbjct: 286 SSDDLSDLLSWIPPFLSSLSGSQRQQACRK----ILNFLLRRLQ 325
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
0.320 0.138 0.415
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: 14,896,727
Number of extensions: 1453710
Number of successful extensions: 1175
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1164
Number of HSP's successfully gapped: 30
Length of query: 281
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 185
Effective length of database: 6,679,618
Effective search space: 1235729330
Effective search space used: 1235729330
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 58 (26.1 bits)