RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy230
(222 letters)
>gnl|CDD|240216 cd05790, S1_Rrp40, S1_Rrp40: Rrp40 S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. Rrp4 protein is a subunit of
the exosome complex. The exosome plays a central role in
3' to 5' RNA processing and degradation in eukarytes and
archaea. Its functions include the removal of
incorrectly processed RNA and the maintenance of proper
levels of mRNA, rRNA and a number of small RNA species.
In Saccharomyces cerevisiae, the exosome includes nine
core components, six of which are homologous to
bacterial RNase PH. These form a hexameric ring
structure. The other three subunits (RrP4, Rrp40, and
Csl4) contain an S1 RNA binding domain and are part of
the "S1 pore structure".
Length = 86
Score = 132 bits (335), Expect = 2e-40
Identities = 48/86 (55%), Positives = 63/86 (73%)
Query: 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKL 110
RYVP +GD VIG+V ++ GD ++VDIG +PA LSYLAFEGATK+N P + GD+V ++
Sbjct: 1 RYVPAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARV 60
Query: 111 LTANKDMESEMVCVDSRGKEFIMGIL 136
+ AN+DME E+ CVDS GK G L
Sbjct: 61 VKANRDMEPELSCVDSSGKADGFGPL 86
>gnl|CDD|224022 COG1097, RRP4, RNA-binding protein Rrp4 and related proteins
(contain S1 domain and KH domain) [Translation,
ribosomal structure and biogenesis].
Length = 239
Score = 109 bits (274), Expect = 2e-29
Identities = 59/211 (27%), Positives = 95/211 (45%), Gaps = 15/211 (7%)
Query: 3 GDTLSLNAEPRLILGPGLRRESSAILVSQSGILRHAKPFTYYVDYIQRRYVPTRGDLVIG 62
GD + AE LG G E I S G+L + + RY+P GD+VIG
Sbjct: 14 GDLVL--AEGSYKLGHGTYFEGGKIYSSVVGLLDVKGKLVRVIPL-EGRYIPEVGDVVIG 70
Query: 63 VVTSRVGDNYRVDIGSHDPAVLSYLAF-----EGATKKNPPKVETGDVVAGKLLTANKDM 117
+ ++VDIGS PA+LS F E A K P + GD+V K++ ++D
Sbjct: 71 KIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRDG 130
Query: 118 ESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAKRSRQKMELSIGM 177
E E+ K+ +G L +G ++ S +++ K +L L +++ E+ +G
Sbjct: 131 EVELTL-----KDEGLGKLKNGQIVKIPPSKVPRVIGKKGSMLNMLKEKTG--CEIIVGQ 183
Query: 178 NGKIWIRCESFSDTVRVGNLIMSCELLSYEE 208
NG+IW+ E+ S I E ++
Sbjct: 184 NGRIWVDGENESLEELAIEAIRKIEREAHTS 214
>gnl|CDD|239901 cd04454, S1_Rrp4_like, S1_Rrp4_like: Rrp4-like, S1-like RNA-binding
domain. S1-like RNA-binding domains are found in a wide
variety of RNA-associated proteins. Rrp4 protein, and
Rrp40 and Csl4 proteins, also represented in this group,
are subunits of the exosome complex. The exosome plays a
central role in 3' to 5' RNA processing and degradation
in eukarytes and archaea. Its functions include the
removal of incorrectly processed RNA and the maintenance
of proper levels of mRNA, rRNA and a number of small RNA
species. In Saccharomyces cerevisiae, the exosome
includes nine core components, six of which are
homologous to bacterial RNase PH. These form a hexameric
ring structure. The other three subunits (RrP4, Rrp40,
and Csl4) contain an S1 RNA binding domain and are part
of the "S1 pore structure".
Length = 82
Score = 73.4 bits (180), Expect = 3e-17
Identities = 23/76 (30%), Positives = 38/76 (50%), Gaps = 1/76 (1%)
Query: 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEGA-TKKNPPKVETGDVVAGK 109
RY+P GD+VIG+VT ++VDI S A L + K+ ++ GD++ K
Sbjct: 1 RYLPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAK 60
Query: 110 LLTANKDMESEMVCVD 125
+++ DM + D
Sbjct: 61 VISLGDDMNVLLTTAD 76
>gnl|CDD|235233 PRK04163, PRK04163, exosome complex RNA-binding protein Rrp4;
Provisional.
Length = 235
Score = 49.5 bits (119), Expect = 2e-07
Identities = 34/153 (22%), Positives = 63/153 (41%), Gaps = 12/153 (7%)
Query: 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLSYLAFEG----ATKKNPPKV-ETGDV 105
+Y+P GDLVIG VT + VDI S A L G + K + GD
Sbjct: 58 KYIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDY 117
Query: 106 VAGKLLTANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNPKCPLLKQLAK 165
+ K+ ++ + + + +G +G + G ++ +++ K ++ L +
Sbjct: 118 IIAKVKDVDRTRDVVLT-LKGKG----LGKIEGGTIVEIKPVKVPRVIGKKGSMINMLKE 172
Query: 166 RSRQKMELSIGMNGKIWIRCESFSDTVRVGNLI 198
+ ++ +G NG+IWI+ D I
Sbjct: 173 ETG--CDIIVGQNGRIWIKGPDEEDEEIAIEAI 203
>gnl|CDD|240215 cd05789, S1_Rrp4, S1_Rrp4: Rrp4 S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. Rrp4 protein is a subunit
of the exosome complex. The exosome plays a central
role in 3' to 5' RNA processing and degradation in
eukarytes and archaea. Its functions include the
removal of incorrectly processed RNA and the
maintenance of proper levels of mRNA, rRNA and a number
of small RNA species. In Saccharomyces cerevisiae, the
exosome includes nine core components, six of which are
homologous to bacterial RNase PH. These form a
hexameric ring structure. The other three subunits
(RrP4, Rrp40, and Csl4) contain an S1 RNA binding
domain and are part of the "S1 pore structure".
Length = 86
Score = 42.5 bits (101), Expect = 7e-06
Identities = 17/35 (48%), Positives = 21/35 (60%)
Query: 51 RYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLS 85
RY+P GD+VIG VT ++VDI S AVL
Sbjct: 1 RYIPEVGDVVIGRVTEVGFKRWKVDINSPYDAVLP 35
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 31.0 bits (71), Expect = 0.066
Identities = 17/62 (27%), Positives = 31/62 (50%), Gaps = 3/62 (4%)
Query: 57 GDLVIGVVTSRVGDNYRVDIGSHDPAVL--SYLAFEGATKKNPPKVETGDVVAGKLLTAN 114
GD+V G VT VD+G+ ++ S L+ + K ++ GD V K+L+ +
Sbjct: 3 GDVVEGTVTEITPGGAFVDLGNGVEGLIPISELS-DKRVKDPEEVLKVGDEVKVKVLSVD 61
Query: 115 KD 116
++
Sbjct: 62 EE 63
>gnl|CDD|234032 TIGR02855, spore_yabG, sporulation peptidase YabG. Members of this
family are the protein YabG, demonstrated for Bacillus
subtilis to be an endopeptidase able to release
N-terminal peptides from a number of sporulation
proteins, including CotT, CotF, and SpoIVA. It appears
to be expressed under control of sigma-K [Cellular
processes, Sporulation and germination].
Length = 283
Score = 29.6 bits (67), Expect = 1.1
Identities = 23/70 (32%), Positives = 37/70 (52%), Gaps = 19/70 (27%)
Query: 36 RHAKPFTYYVDYIQ--RRYVPTRGDLVI--GVVTS------RVGDNY-----RVDIGSHD 80
RH+K Y+V+ ++ R+YVP+ LVI G S R G N+ RV+I + D
Sbjct: 179 RHSK---YFVETVREARKYVPSLDQLVIFAGACQSHFESLIRAGANFASSPSRVNIHALD 235
Query: 81 PA-VLSYLAF 89
P ++ ++F
Sbjct: 236 PVYIVEKISF 245
>gnl|CDD|237061 PRK12327, nusA, transcription elongation factor NusA; Provisional.
Length = 362
Score = 29.8 bits (68), Expect = 1.1
Identities = 14/42 (33%), Positives = 21/42 (50%), Gaps = 6/42 (14%)
Query: 44 YVDYIQRRYVPTRGDLVIGVVTSRVGDNYRVDIGSHDPAVLS 85
Y ++ +R GD+V GVV R V++G + AVL
Sbjct: 127 YNEFSERE-----GDIVTGVVQRRDNRFVYVNLGKIE-AVLP 162
>gnl|CDD|234013 TIGR02785, addA_Gpos, helicase-exonuclease AddAB, AddA subunit,
Firmicutes type. AddAB, also called RexAB, substitutes
for RecBCD in several bacterial lineages. These DNA
recombination proteins act before synapse and are
particularly important for DNA repair of double-stranded
breaks by homologous recombination. The term AddAB is
used broadly, with AddA homologous between the
Firmicutes (as modeled here) and the
alphaproteobacteria, while the partner AddB proteins
show no strong homology across the two groups of species
[DNA metabolism, DNA replication, recombination, and
repair].
Length = 1230
Score = 29.7 bits (67), Expect = 1.5
Identities = 25/79 (31%), Positives = 39/79 (49%), Gaps = 8/79 (10%)
Query: 101 ETGDVVAGKLLT--ANKDMESEMVCVDSRGKEFIMGILNDGYLLHTSISLCRKLLNP--- 155
E + V +L+T +K +E +V V GK+F LN YLL + L K ++P
Sbjct: 777 EAENAV--RLMTIHKSKGLEFPVVFVLGMGKQFNKQDLNSSYLLDRQLGLGIKYIDPQER 834
Query: 156 -KCPLLKQLAKRSRQKMEL 173
P L ++A + + K EL
Sbjct: 835 LSYPSLPKVAIKQKMKREL 853
>gnl|CDD|234762 PRK00439, leuD, 3-isopropylmalate dehydratase small subunit;
Reviewed.
Length = 163
Score = 28.6 bits (65), Expect = 1.7
Identities = 12/31 (38%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 80 DPAVLSYLAFEGATKKNPPKVETGD-VVAGK 109
DP L+ E + KV+ GD +VAGK
Sbjct: 26 DPQELAKHCMEDLDPEFAKKVKPGDIIVAGK 56
>gnl|CDD|223331 COG0253, DapF, Diaminopimelate epimerase [Amino acid transport and
metabolism].
Length = 272
Score = 28.4 bits (64), Expect = 3.1
Identities = 17/56 (30%), Positives = 18/56 (32%), Gaps = 9/56 (16%)
Query: 82 AVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVD----SRGKEFIM 133
+LA G KK VET AG L D V VD S I
Sbjct: 79 CFARFLAERGLVKKKEISVETL---AGILKVKVHDD--NTVSVDMGLPSFKPAEIP 129
>gnl|CDD|176047 cd08402, C2B_Synaptotagmin-1, C2 domain second repeat present in
Synaptotagmin 1. Synaptotagmin is a
membrane-trafficking protein characterized by a
N-terminal transmembrane region, a linker, and 2
C-terminal C2 domains. Synaptotagmin 1, a member of
the class 1 synaptotagmins, is located in the brain and
endocranium and localized to the synaptic vesicles and
secretory granules. It functions as a Ca2+ sensor for
fast exocytosis. It, like synaptotagmin-2, has an
N-glycosylated N-terminus. Synaptotagmin 4, a member of
class 4 synaptotagmins, is located in the brain. It
functions are unknown. It, like synaptotagmin-11, has
an Asp to Ser substitution in its C2A domain.
Previously all synaptotagmins were thought to be
calcium sensors in the regulation of neurotransmitter
release and hormone secretion, but it has been shown
that not all of them bind calcium. Of the 17
identified synaptotagmins only 8 bind calcium (1-3,
5-7, 9, 10). The function of the two C2 domains that
bind calcium are: regulating the fusion step of
synaptic vesicle exocytosis (C2A) and binding to
phosphatidyl-inositol-3,4,5-triphosphate (PIP3) in the
absence of calcium ions and to phosphatidylinositol
bisphosphate (PIP2) in their presence (C2B). C2B also
regulates also the recycling step of synaptic vesicles.
C2 domains fold into an 8-standed beta-sandwich that
can adopt 2 structural arrangements: Type I and Type
II, distinguished by a circular permutation involving
their N- and C-terminal beta strands. Many C2 domains
are Ca2+-dependent membrane-targeting modules that bind
a wide variety of substances including bind
phospholipids, inositol polyphosphates, and
intracellular proteins. Most C2 domain proteins are
either signal transduction enzymes that contain a
single C2 domain, such as protein kinase C, or membrane
trafficking proteins which contain at least two C2
domains, such as synaptotagmin 1. However, there are a
few exceptions to this including RIM isoforms and some
splice variants of piccolo/aczonin and intersectin
which only have a single C2 domain. C2 domains with a
calcium binding region have negatively charged
residues, primarily aspartates, that serve as ligands
for calcium ions. This cd contains the second C2
repeat, C2B, and has a type-I topology.
Length = 136
Score = 27.4 bits (61), Expect = 3.9
Identities = 14/42 (33%), Positives = 24/42 (57%), Gaps = 3/42 (7%)
Query: 51 RYVPTRGDLVIGVVTSRVGDNYRVDI-GSHDPAVLSYLAFEG 91
RYVPT G L + ++ ++ + ++D+ G DP V +L G
Sbjct: 9 RYVPTAGKLTVVILEAK--NLKKMDVGGLSDPYVKIHLMQNG 48
>gnl|CDD|147641 pfam05582, Peptidase_U57, YabG peptidase U57. YabG is a protease
involved in the proteolysis and maturation of SpoIVA and
YrbA proteins, conserved with the cortex and/or coat
assembly by Bacillus subtilis.
Length = 287
Score = 27.9 bits (63), Expect = 4.5
Identities = 19/61 (31%), Positives = 29/61 (47%), Gaps = 18/61 (29%)
Query: 36 RHAKPFTYYVDYIQ--RRYVPTRGDLVI--GVVTS------RVGDNY-----RVDIGSHD 80
R++K Y+V+ ++ R+Y P+ LVI G S G N+ RV I + D
Sbjct: 180 RNSK---YFVETVKEARKYEPSLDQLVIFAGACQSHYEAIIEAGANFASSPSRVLIHALD 236
Query: 81 P 81
P
Sbjct: 237 P 237
>gnl|CDD|233716 TIGR02087, LEUD_arch, 3-isopropylmalate dehydratase, small subunit.
This subfamily is most closely related to the
3-isopropylmalate dehydratase, small subunits which form
TIGR00171. This subfamily includes the members of
TIGR02084 which are gene clustered with other genes of
leucine biosynthesis. The rest of the subfamily includes
mainly archaeal species which exhibit two hits to this
model. In these cases it is possible that one or the
other of the hits does not have a 3-isopropylmalate
dehydratase activity but rather one of the other related
aconitase-like activities.
Length = 154
Score = 27.0 bits (60), Expect = 6.4
Identities = 15/31 (48%), Positives = 17/31 (54%), Gaps = 1/31 (3%)
Query: 80 DPAVLSYLAFEGATKKNPPKVETGDV-VAGK 109
DP L+ A EG + KV GDV VAGK
Sbjct: 25 DPDELASHAMEGIDPEFAKKVRPGDVIVAGK 55
>gnl|CDD|223402 COG0325, COG0325, Predicted enzyme with a TIM-barrel fold [General
function prediction only].
Length = 228
Score = 26.8 bits (60), Expect = 9.4
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 159 LLKQLAKRSRQKMELSIGMNG--KIWIRCESFSDTVRVGNLI 198
L +L + ELS+GM+ +I I + VR+G I
Sbjct: 183 LFDELKAKYPPIDELSMGMSNDYEIAIAEG--ATMVRIGTAI 222
>gnl|CDD|129223 TIGR00117, acnB, aconitate hydratase 2. Aconitate hydratase
(aconitase) is an enzyme of the TCA cycle. This model
describes aconitase 2, AcnB, which has weak similarity
to aconitase 1. It is found almost exclusively in the
Proteobacteria [Energy metabolism, TCA cycle].
Length = 844
Score = 27.2 bits (60), Expect = 9.5
Identities = 16/75 (21%), Positives = 29/75 (38%)
Query: 74 VDIGSHDPAVLSYLAFEGATKKNPPKVETGDVVAGKLLTANKDMESEMVCVDSRGKEFIM 133
V++ + PA + T + PP V+ V L A E++ + ++
Sbjct: 31 VELLKNPPAGEEEFLLDLLTNRVPPGVDEAAYVKAGFLAAIAKGEAKCPLISPEKAIELL 90
Query: 134 GILNDGYLLHTSISL 148
G + GY +H I
Sbjct: 91 GTMQGGYNVHPLIDA 105
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
0.321 0.138 0.404
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,185,639
Number of extensions: 1037292
Number of successful extensions: 772
Number of sequences better than 10.0: 1
Number of HSP's gapped: 768
Number of HSP's successfully gapped: 30
Length of query: 222
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 129
Effective length of database: 6,812,680
Effective search space: 878835720
Effective search space used: 878835720
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: 57 (25.6 bits)