RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11392
(169 letters)
>gnl|CDD|239822 cd04330, RNAP_III_Rpc25_N, RNAP_III_Rpc25_N: Rpc25, N-terminal
ribonucleoprotein (RNP) domain. Rpc25 is a subunit of
eukaryotic RNA polymerase (RNAP) III and is homologous
to Rpa43 of eukaryotic RNAP I, Rpb7 of eukaryotic RNAP
II, and RpoE of archaeal RNAP. Rpc25 has two domains,
an N-terminal RNP domain and a C-terminal
oligonucleotide-binding (OB) domain, both of which are
thought to bind single-stranded RNA. Rpc25
heterodimerizes with Rpc17 and plays an important role
in transcription initiation. RNAP III transcribes
diverse structural and catalytic RNAs including 5S
ribosomal RNAs, tRNAs, and a small number of snRNAs
involved in RNA and protein synthesis.
Length = 80
Score = 81.1 bits (201), Expect = 7e-21
Identities = 32/45 (71%), Positives = 36/45 (80%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFV 67
KV NVGLC+ LYDI ++ED I+PGDGASH KV FR VVFRPFV
Sbjct: 36 KVIQNVGLCICLYDILEVEDGYILPGDGASHYKVTFRMVVFRPFV 80
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 68.9 bits (169), Expect = 4e-15
Identities = 21/61 (34%), Positives = 43/61 (70%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEG 82
K+ +VGL +++ D+ +I + +I+PGDG+++ +V+FR +VF+PF E++ G++ + G
Sbjct: 37 KLDGDVGLVVLVLDVKEIGEGIIVPGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFG 96
Query: 83 V 83
Sbjct: 97 A 97
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and
eukaryotic form. This family seems to be confined to
the archea and eukaryotic taxa and are quite dissimilar
to E.coli rpoE [Transcription, DNA-dependent RNA
polymerase].
Length = 179
Score = 63.6 bits (155), Expect = 3e-13
Identities = 33/97 (34%), Positives = 54/97 (55%), Gaps = 15/97 (15%)
Query: 2 LYDITKIEDSVIIPGD--------GASHT-------KVFPNVGLCMMLYDITKIEDSVII 46
+Y ++KI D+V IP D +H ++ NVGLC+ +YDI I + +I
Sbjct: 1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVI 60
Query: 47 PGDGASHTKVEFRYVVFRPFVSEIIIGKIRSCSKEGV 83
PGDG+++ V FR +VF+P + EI+ G++ + G
Sbjct: 61 PGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGA 97
>gnl|CDD|202794 pfam03876, SHS2_Rpb7-N, SHS2 domain found in N terminus of
Rpb7p/Rpc25p/MJ0397. Rpb7 bind to Rpb4 to form a
heterodimer. This complex is thought to interact with
the nascent RNA strand during RNA polymerase II
elongation. This family includes the homologs from RNA
polymerase I and III. In RNA polymerase I, Rpa43 is at
least one of the subunits contacted by the
transcription factor TIF-IA. The N terminus of
Rpb7p/Rpc25p/MJ0397 has a SHS2 domain that is involved
in protein-protein interaction.
Length = 70
Score = 55.2 bits (134), Expect = 5e-11
Identities = 18/41 (43%), Positives = 28/41 (68%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVF 63
K P++G+ + + DI I + I+PGDGA++ KV FR +VF
Sbjct: 30 KYDPDLGVVIAVTDIKLIGEGKILPGDGAAYFKVTFRALVF 70
Score = 30.2 bits (69), Expect = 0.11
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 1 MLYDITKIEDSVIIPGDGASHTKV 24
+ DI I + I+PGDGA++ KV
Sbjct: 40 AVTDIKLIGEGKILPGDGAAYFKV 63
>gnl|CDD|238354 cd00655, RNAP_Rpb7_N_like, RNAP_Rpb7_N_like: This conserved
domain represents the N-terminal ribonucleoprotein
(RNP) domain of the Rpb7 subunit of eukaryotic RNA
polymerase (RNAP) II and its homologs, Rpa43 of
eukaryotic RNAP I, Rpc25 of eukaryotic RNAP III, and
RpoE (subunit E) of archaeal RNAP. These proteins have,
in addition to their N-terminal RNP domain, a
C-terminal oligonucleotide-binding (OB) domain. Each of
these subunits heterodimerizes with another RNAP
subunit (Rpb7 to Rpb4, Rpc25 to Rpc17, RpoE to RpoF,
and Rpa43 to Rpa14). The heterodimer is thought to
tether the RNAP to a given promoter via its
interactions with a promoter-bound transcription
factor.The heterodimer is also thought to bind and
position nascent RNA as it exits the polymerase
complex.
Length = 80
Score = 49.4 bits (118), Expect = 1e-08
Identities = 18/41 (43%), Positives = 26/41 (63%)
Query: 26 PNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPF 66
P VG+ + + D I + I PGDG+++ V FR VVF+PF
Sbjct: 39 PVVGIILAIKDTKDIPEGAIRPGDGSAYVNVSFRAVVFKPF 79
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E';
Provisional.
Length = 187
Score = 47.9 bits (115), Expect = 2e-07
Identities = 17/53 (32%), Positives = 36/53 (67%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPFVSEIIIGKI 75
++ +G+ + + D+ I + I+PGDGA++ +VEF +VF+P + E++ G++
Sbjct: 37 RIDKELGIIVAVLDVKVIGEGKIVPGDGATYHEVEFDALVFKPELQEVVEGEV 89
>gnl|CDD|239823 cd04331, RNAP_E_N, RNAP_E_N: RpoE, N-terminal ribonucleoprotein
(RNP) domain. RpoE (subunit E) is a subunit of the
archaeal RNA polymerase (RNAP) that is homologous to
Rpb7 of eukaryotic RNAP II, Rpc25 of eukaryotic RNAP
III, and Rpa43 of eukaryotic RNAP I. RpoE
heterodimerizes with RpoF, another RNA polymerase
subunit. RpoE has an elongated two-domain structure
that includes an N-terminal RNP domain and a C-terminal
oligonucleotide-binding (OB) domain. Both domains of
RpoE bind single-stranded RNA.
Length = 80
Score = 41.0 bits (97), Expect = 2e-05
Identities = 12/43 (27%), Positives = 26/43 (60%)
Query: 23 KVFPNVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRP 65
++ ++G + + D+ + + I+ GDGA + +V F +VF+P
Sbjct: 36 RLDKDLGKIVSVLDVKDVGEGKIVHGDGAVYHEVRFDALVFKP 78
>gnl|CDD|219782 pfam08292, RNA_pol_Rbc25, RNA polymerase III subunit Rpc25.
Rpc25 is a strongly conserved subunit of RNA polymerase
III and has homology to Rpa43 in RNA polymerase I, Rpb7
in RNA polymerase II and the archaeal RpoE subunit.
Rpc25 is required for transcription initiation and is
not essential for the elongating properties of RNA
polymerase III.
Length = 121
Score = 40.0 bits (94), Expect = 7e-05
Identities = 12/20 (60%), Positives = 15/20 (75%)
Query: 65 PFVSEIIIGKIRSCSKEGVH 84
PFV EI+ GKI+S S EG+
Sbjct: 1 PFVGEILTGKIKSSSAEGIK 20
>gnl|CDD|202479 pfam02944, BESS, BESS motif. The BESS motif is named after the
proteins in which it is found (BEAF, Suvar(3)7 and
Stonewall). The motif is 40 amino acid residues long and
is composed of two predicted alpha helices. Based on the
protein in which it is found and the presence of
conserved positively charged residues it is predicted to
be a DNA binding domain. This domain appears to be
specific to drosophila.
Length = 37
Score = 33.2 bits (77), Expect = 0.004
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 115 DPVRDFLMGAIAPALRSLPRHLFLKAKKEIFEAVHKY 151
D FL+ + P L+ L LK K +I + + +
Sbjct: 2 DSDDLFLLS-LLPTLKRLSPRQKLKFKIKIQQLLLEL 37
>gnl|CDD|239821 cd04329, RNAP_II_Rpb7_N, RNAP_II_Rpb7_N: Rpb7, N-terminal
ribonucleoprotein (RNP) domain. Rpb7 is a subunit of
eukaryotic RNA polymerase (RNAP) II that is homologous
to Rpc25 of RNAP III, RpoE of archaeal RNAP, and Rpa43
of eukaryotic RNAP I. Rpb7 heterodimerizes with Rpb4
and this heterodimer binds the 10-subunit core of RNAP
II, forming part of the floor of the DNA-binding cleft.
Rpb7 has two domains, an N-terminal RNP domain and a
C-terminal oligonucleotide-binding (OB) domain, both of
which bind single-stranded RNA. Rpb7 is thought to
interact with the nascent RNA strand as it exits the
RNAP II complex during transcription elongation. The
Rpb7/Rpb4 heterodimer is also thought to serve as an
upstream interface between the C-terminal domain of
Rpb1 and the transcription factor IIB (TFIIB),
recruiting pol II to the pol II promoter.
Length = 80
Score = 32.5 bits (75), Expect = 0.019
Identities = 13/40 (32%), Positives = 24/40 (60%)
Query: 27 NVGLCMMLYDITKIEDSVIIPGDGASHTKVEFRYVVFRPF 66
+ G + + DI I + I+PG G+ V+++ +VF+PF
Sbjct: 40 DYGYIIAVTDIDDIGEGKILPGTGSVEFPVKYKAIVFKPF 79
>gnl|CDD|131977 TIGR02931, anfK_nitrog, Fe-only nitrogenase, beta subunit.
Nitrogenase is the enzyme of biological nitrogen
fixation. The most wide-spread and most efficient
nitrogenase contains a molybdenum cofactor. This protein
family, AnfK, represents the beta subunit of the
iron-only alternative nitrogenase. It is homologous to
NifK and VnfK, of the molybdenum-containing and the
vanadium (V)-containing types, respectively [Central
intermediary metabolism, Nitrogen fixation].
Length = 461
Score = 29.5 bits (66), Expect = 0.81
Identities = 14/40 (35%), Positives = 22/40 (55%)
Query: 98 DSTVKDILKYFAEKDKPDPVRDFLMGAIAPALRSLPRHLF 137
D V D +K+FA+KDKP+ + + G + P +HL
Sbjct: 152 DVAVHDFVKHFAKKDKPNDKINLITGWVNPGDVKELKHLL 191
>gnl|CDD|238133 cd00215, PTS_IIA_lac, PTS_IIA, PTS system, lactose/cellobiose
specific IIA subunit. The bacterial phosphoenolpyruvate:
sugar phosphotransferase system (PTS) is a multi-protein
system involved in the regulation of a variety of
metabolic and transcriptional processes. This family is
one of four structurally and functionally distinct group
IIA PTS system cytoplasmic enzymes, necessary for the
uptake of carbohydrates across the cytoplasmic membrane
and their phosphorylation. This family of proteins
normally function as a homotrimer, stabilized by a
centrally located metal ion. Separation into subunits is
thought to occur after phosphorylation.
Length = 97
Score = 27.6 bits (62), Expect = 1.6
Identities = 10/36 (27%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 134 RHLFLKAKKEIFEAVHKY--EMIAEEQSGDQYEYTL 167
L +A + EA H +++ +E SG++ E +L
Sbjct: 35 EELLEEANDSLNEA-HHAQTKLLQQEASGEKVEVSL 69
>gnl|CDD|198353 cd07775, FGGY_AI-2K, Autoinducer-2 kinases; a subfamily of the FGGY
family of carbohydrate kinases. This subfamily is
composed of bacterial autoinducer-2 (AI-2) kinases and
similar proteins. AI-2 is a small chemical
quorum-sensing signal involved in interspecies
communication in bacteria. Cytoplasmic autoinducer-2
kinase, encoded by the lsrK gene from Salmonella
enterica serovar Typhimurium lsr (luxS regulated)
operon, is the prototypical member of this subfamily.
AI-2 kinase catalyzes the phosphorylation of
intracellular AI-2 to phospho-AI-2, which leads to the
inactivation of lsrR, the repressor of the lsr operon.
Members of this family are homologs of glycerol
kinase-like proteins and belong to the FGGY family of
carbohydrate kinases, the monomers of which contain two
large domains, which are separated by a deep cleft that
forms the active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
Length = 452
Score = 28.6 bits (64), Expect = 1.8
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 1/31 (3%)
Query: 127 PALRSLPRHLFLKAKK-EIFEAVHKYEMIAE 156
AL +LPR L+LK + +I+E MI++
Sbjct: 130 FALGALPRLLWLKQHRPDIYEKTASVTMISD 160
>gnl|CDD|187887 cd09757, Cas8c_I-C, CRISPR/Cas system-associated protein Cas8c.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Zn-finger domain containing protein, distant homologs of
Cas8 proteins; signature gene for I-C subtype; also
known as Csd1 family.
Length = 569
Score = 28.4 bits (64), Expect = 1.8
Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 1/41 (2%)
Query: 129 LRSLPRHLFL-KAKKEIFEAVHKYEMIAEEQSGDQYEYTLG 168
LR R + L + EI + ++ + +Q E+ LG
Sbjct: 519 LRKEKRAVNLERLIGEILDGLNPDDFPRTLSLEEQGEFALG 559
>gnl|CDD|224364 COG1447, CelC, Phosphotransferase system cellobiose-specific
component IIA [Carbohydrate transport and metabolism].
Length = 105
Score = 27.2 bits (61), Expect = 1.9
Identities = 11/36 (30%), Positives = 19/36 (52%), Gaps = 3/36 (8%)
Query: 134 RHLFLKAKKEIFEAVHKY--EMIAEEQSGDQYEYTL 167
L +A + EA H ++I +E SG++ E +L
Sbjct: 39 EELIQEANDALNEA-HHVQTKLIQKEASGEKIEVSL 73
>gnl|CDD|221000 pfam11145, DUF2921, Protein of unknown function (DUF2921). This
eukaryotic family of proteins has no known function.
Length = 871
Score = 28.2 bits (63), Expect = 2.4
Identities = 14/67 (20%), Positives = 25/67 (37%), Gaps = 1/67 (1%)
Query: 30 LCMMLYDITKIEDSVIIPGDGASHTKVEFRYV-VFRPFVSEIIIGKIRSCSKEGVHDSQS 88
LCM+ I S+ G ++ R+ F I++G+I S + + S
Sbjct: 331 LCMVACRIGNSSASLSNAVVGDCSLRLSLRFPTTFSIRDRSIVVGEIWSANTGPSNFPLS 390
Query: 89 SNQPEQP 95
+ P
Sbjct: 391 FRRIVPP 397
>gnl|CDD|129903 TIGR00823, EIIA-LAC, phosphotransferase system enzyme II,
lactose-specific, factor III. The PTS
Lactose-N,N?-Diacetylchitobiose-b-glucoside (Lac) Family
(TC 4.A.3)Bacterial PTS transporters transport and
concomitantly phosphorylate their sugar substrates, and
typically consist of multiple subunits or protein
domains.The Lac family includes several sequenced
lactose (b-galactoside) permeases of Gram-positive
bacteria as well as the E. coli N,N?-diacetylchitobiose
(Chb)permease which can transport aromatic b-glucosides
and cellobiose as well as the chitin disaccharide, Chb,
but only Chb induces expression of the chboperon. While
the Lac permeases consist of two polypeptide chains (IIA
and IICB), the Chb permease of E. coli consists of three
(IIA, IIB and IIC). In B. subtilis, a PTS permease
similar to the Chb permease of E. coli is believed to
transport lichenan (a b-1,3;1,4 glucan) degradation
products, oligosaccharides of 2-4 glucose units. This
model is specific for the IIA subunit of the Lac PTS
family [Transport and binding proteins, Carbohydrates,
organic alcohols, and acids].
Length = 99
Score = 25.9 bits (57), Expect = 6.4
Identities = 11/36 (30%), Positives = 18/36 (50%), Gaps = 3/36 (8%)
Query: 134 RHLFLKAKKEIFEAVHKY--EMIAEEQSGDQYEYTL 167
R L +A + EA H ++A+E G + E +L
Sbjct: 37 RALVEQAGMCLNEA-HLAQTSLLAQEAGGGKMEVSL 71
>gnl|CDD|202178 pfam02255, PTS_IIA, PTS system, Lactose/Cellobiose specific IIA
subunit. The bacterial phosphoenolpyruvate: sugar
phosphotransferase system (PTS) is a multi-protein
system involved in the regulation of a variety of
metabolic and transcriptional processes. The
lactose/cellobiose-specific family are one of four
structurally and functionally distinct group IIA PTS
system enzymes. This family of proteins normally
function as a homotrimer, stabilised by a centrally
located metal ion. Separation into subunits is thought
to occur after phosphorylation.
Length = 96
Score = 25.5 bits (57), Expect = 6.5
Identities = 9/31 (29%), Positives = 18/31 (58%), Gaps = 3/31 (9%)
Query: 139 KAKKEIFEAVHKY--EMIAEEQSGDQYEYTL 167
+A + + EA H ++I +E G++ E +L
Sbjct: 39 EANEALLEA-HNAQTKLIQKEAGGEKVEVSL 68
>gnl|CDD|182407 PRK10359, PRK10359, lipopolysaccharide core biosynthesis protein;
Provisional.
Length = 232
Score = 26.3 bits (58), Expect = 7.9
Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 13/68 (19%)
Query: 102 KDILKYFAEKDKPDP--VRDFLMG-----------AIAPALRSLPRHLFLKAKKEIFEAV 148
K ILK FA K K ++ F+ G + + +L A+++
Sbjct: 56 KYILKVFAPKVKRTERFLKSFVKGDYYENLIVQTDRVRSEGLASLNDFYLLAERKTLRYA 115
Query: 149 HKYEMIAE 156
H Y M+ E
Sbjct: 116 HTYIMLIE 123
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
0.319 0.137 0.395
Gapped
Lambda K H
0.267 0.0639 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,725,771
Number of extensions: 803781
Number of successful extensions: 787
Number of sequences better than 10.0: 1
Number of HSP's gapped: 784
Number of HSP's successfully gapped: 37
Length of query: 169
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 79
Effective length of database: 6,945,742
Effective search space: 548713618
Effective search space used: 548713618
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 (21.7 bits)
S2: 55 (25.2 bits)