RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13107
(170 letters)
>gnl|CDD|240298 PTZ00162, PTZ00162, DNA-directed RNA polymerase II subunit 7;
Provisional.
Length = 176
Score = 213 bits (544), Expect = 1e-71
Identities = 79/169 (46%), Positives = 108/169 (63%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
MF+ + L + L P GP+ + ++ L S+VEG CT KYG+VI V I G +Q
Sbjct: 1 MFFVVELWKNVSLKPSQLGPRYQQIIEDMLRSQVEGQCTRKYGYVICVIRIIHNEPGRVQ 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
G G +V VKY+AIVF+PFK EVLDA+VT VNK+G FA+ GPL F+S +IP D +
Sbjct: 61 DGTGMIVVNVKYQAIVFKPFKDEVLDAIVTDVNKLGFFAQAGPLKAFVSRSAIPPDFVYD 120
Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDASGIFAIGTLMDDYLG 169
+S CY S G++ I+ + E+RL++ G R DAS +FAI T+ DYLG
Sbjct: 121 SDSAYPCYISSDGQIQIKPNTEVRLRLQGVRYDASNLFAIATINSDYLG 169
>gnl|CDD|239909 cd04462, S1_RNAPII_Rpb7, S1_RNAPII_Rpb7: Eukaryotic RNA polymerase
II (RNAPII) Rpb7 subunit C-terminal S1 domain. RNAPII is
composed of 12 subunits (Rpb1-12). Rpb4 and Rpb7 form a
heterodimer that associate with the RNAPII core. Rpb7 is
a homolog of the Rpc25 of RNA polymerase III, RpoE of
the archaeal RNA polymerase, and Rpa43 of eukaryotic RNA
polymerase I. Rpb7 has two domains, an N-terminal
ribonucleoprotein (RNP) domain and a C-terminal S1
domain, both of which bind single-stranded RNA. It is
possible that the S1 domain interacts with the nascent
RNA transcript, assisted by the RNP domain. In yeast,
Rpb4/Rpb7 is necessary for promoter-directed
transcription initiation. They also play a role in
regulating transcription-coupled repair in the
Rad26-dependent pathway, in efficient mRNA export, and
in transcription termination.
Length = 88
Score = 149 bits (378), Expect = 1e-47
Identities = 58/89 (65%), Positives = 75/89 (84%), Gaps = 1/89 (1%)
Query: 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQED 140
KGEV+DA+VT VNK G FAE+GPLS FIS H IP+DM+F PN++P C+ S + ++VI++D
Sbjct: 1 KGEVVDAIVTSVNKTGFFAEVGPLSIFISRHLIPSDMEFDPNASPPCFTS-NEDIVIKKD 59
Query: 141 DEIRLKIVGTRVDASGIFAIGTLMDDYLG 169
E+RLKI+GTRVDA+ IFAIGT+ DDYLG
Sbjct: 60 TEVRLKIIGTRVDATDIFAIGTIKDDYLG 88
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 150 bits (380), Expect = 1e-46
Identities = 55/172 (31%), Positives = 85/172 (49%), Gaps = 4/172 (2%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
M+ + LE + + P YFG L E VK++L + EG G G V+ V + IG G+I
Sbjct: 1 MYKLVELEDTVRIPPSYFGEDLEEAVKEELKEKYEGKLDGDVGLVVLVLDVKEIGEGIIV 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTDMQFC 120
PG G + VK+RA+VF+PF+GEV++ V +V + G F IGPL + I D
Sbjct: 61 PGDGSTYHEVKFRALVFKPFRGEVVEGEVVEVVEFGAFVRIGPLDGLVHVSQIMDD-YID 119
Query: 121 PNSNPVCYKSVHGEVVIQEDDEIRLKIVGTRVDAS---GIFAIGTLMDDYLG 169
+ + V++ D++R +IVG + + T+ LG
Sbjct: 120 YDEKNKVLIGEETKRVLKVGDKVRARIVGVSLKSRRPRESKIGLTMRQPGLG 171
>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 = 136 bits (344), Expect = 2e-42
Identities = 54/80 (67%), Positives = 62/80 (77%)
Query: 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQP 61
F+ I LEH ILLHP YFGP L E ++QKL EVEGTCTG YG++IAVT ID IG G I P
Sbjct: 1 FFKIELEHNILLHPSYFGPNLKEYLEQKLLEEVEGTCTGDYGYIIAVTDIDDIGEGKILP 60
Query: 62 GQGFVVYPVKYRAIVFRPFK 81
G G V +PVKY+AIVF+PFK
Sbjct: 61 GTGSVEFPVKYKAIVFKPFK 80
>gnl|CDD|236289 PRK08563, PRK08563, DNA-directed RNA polymerase subunit E';
Provisional.
Length = 187
Score = 86.8 bits (216), Expect = 5e-22
Identities = 46/152 (30%), Positives = 76/152 (50%), Gaps = 7/152 (4%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
M+ + LE + + P FG L E + L + EG + G ++AV + IG G I
Sbjct: 1 MYKLVKLEDVVRIPPEMFGEDLEEAALEVLREKYEGRIDKELGIIVAVLDVKVIGEGKIV 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD--MQ 118
PG G + V++ A+VF+P EV++ V +V + G F IGP+ + H S D +
Sbjct: 61 PGDGATYHEVEFDALVFKPELQEVVEGEVVEVVEFGAFVRIGPVDGLL-HISQIMDDYIS 119
Query: 119 FCP-NSNPVCYKSVHGEVVIQEDDEIRLKIVG 149
+ P N + +S + V++ D +R +IV
Sbjct: 120 YDPKNGRLIGKES---KRVLKVGDVVRARIVA 148
>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 = 78.3 bits (194), Expect = 6e-20
Identities = 30/70 (42%), Positives = 39/70 (55%)
Query: 8 EHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVV 67
E + + P YFG L E +K++L + EG G VIAVT I IG G I PG G
Sbjct: 1 EDTVRIPPSYFGEDLKEAIKEELLEKYEGKYDPDLGVVIAVTDIKLIGEGKILPGDGAAY 60
Query: 68 YPVKYRAIVF 77
+ V +RA+VF
Sbjct: 61 FKVTFRALVF 70
>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 = 74.8 bits (184), Expect = 2e-17
Identities = 43/150 (28%), Positives = 72/150 (48%), Gaps = 5/150 (3%)
Query: 1 MFYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQ 60
M+ + + + P FG L E + +L + EG G I + I+ IG G +
Sbjct: 1 MYILSKIADTVRIPPDQFGEDLEEVITHQLNEKFEGRLDKNVGLCITIYDIEDIGEGKVI 60
Query: 61 PGQGFVVYPVKYRAIVFRPFKGEVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD--MQ 118
PG G + V +RA+VF+P GE+++ V ++ + G F +GP H S TD
Sbjct: 61 PGDGSAYHNVTFRALVFKPELGEIVEGEVIEIVEFGAFVSLGPFDGLF-HVSQVTDDYCY 119
Query: 119 FCPNSNPVCYKSVHGEVVIQEDDEIRLKIV 148
+ P + + K + V+ E D++R +IV
Sbjct: 120 YDPKESALIGKET--KKVLDEGDKVRARIV 147
>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 = 67.5 bits (165), Expect = 1e-15
Identities = 24/71 (33%), Positives = 35/71 (49%)
Query: 11 ILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQPGQGFVVYPV 70
+ + P+YFG K L + EG T G ++A+ I G I+PG G V
Sbjct: 10 VSVPPKYFGDDCKGVKKCLLQEKGEGDRTPVVGIILAIKDTKDIPEGAIRPGDGSAYVNV 69
Query: 71 KYRAIVFRPFK 81
+RA+VF+PF
Sbjct: 70 SFRAVVFKPFS 80
>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 = 57.2 bits (139), Expect = 1e-11
Identities = 24/78 (30%), Positives = 40/78 (51%)
Query: 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKYGFVIAVTTIDSIGAGLIQP 61
+ + LE + + P FG L E V + L + EG G +++V + +G G I
Sbjct: 1 YKLVELEDVVRVPPELFGEDLEEAVLEILKEKYEGRLDKDLGKIVSVLDVKDVGEGKIVH 60
Query: 62 GQGFVVYPVKYRAIVFRP 79
G G V + V++ A+VF+P
Sbjct: 61 GDGAVYHEVRFDALVFKP 78
>gnl|CDD|216000 pfam00575, S1, S1 RNA binding domain. The S1 domain occurs in a
wide range of RNA associated proteins. It is
structurally similar to cold shock protein which binds
nucleic acids. The S1 domain has an OB-fold structure.
Length = 74
Score = 48.8 bits (117), Expect = 2e-08
Identities = 19/81 (23%), Positives = 36/81 (44%), Gaps = 13/81 (16%)
Query: 78 RPFKGEVLDAVVTQVNKVGMFAEIG-PLSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVV 136
+P +G+V+ VT+V K G F ++G + FI I D + + V
Sbjct: 1 KPEEGDVVKGTVTRVTKGGAFVDLGNGVEGFIPISEISDD------------RVEDPDEV 48
Query: 137 IQEDDEIRLKIVGTRVDASGI 157
++ DE+ +K++ + I
Sbjct: 49 LKVGDEVEVKVLKVDKERGRI 69
>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 = 46.0 bits (110), Expect = 2e-07
Identities = 24/88 (27%), Positives = 35/88 (39%), Gaps = 16/88 (18%)
Query: 2 FYHISLEHEILLHPRYFGPQLYETVKQKLYSEVEGTCTGKY--------GFVIAVTTIDS 53
F +E + + P F L + ++ +L KY G I + I
Sbjct: 1 FILSEIEDTVRIPPSQFSRPLNDAIEDEL--------NKKYANKVIQNVGLCICLYDILE 52
Query: 54 IGAGLIQPGQGFVVYPVKYRAIVFRPFK 81
+ G I PG G Y V +R +VFRPF
Sbjct: 53 VEDGYILPGDGASHYKVTFRMVVFRPFV 80
>gnl|CDD|188207 TIGR02279, PaaC-3OHAcCoADH, 3-hydroxyacyl-CoA dehydrogenase PaaC.
This 3-hydroxyacyl-CoA dehydrogenase is involved in the
degradation of phenylacetic acid, presumably in steps
following the opening of the phenyl ring. The sequences
included in this model are all found in aparrent operons
with other related genes such as paaA, paaB, paaD, paaE,
paaF and paaN. Some genomes contain these other genes
without an apparent paaC in the same operon - possibly
in these cases a different dehydrogenase involved in
fatty acid degradation may fill in the needed activity.
This enzyme has domains which are members of the
pfam02737 and pfam00725 families.
Length = 503
Score = 31.4 bits (71), Expect = 0.23
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 6/42 (14%)
Query: 26 VKQKLYSEVEGTCTGKYGFVIAVTT----IDSIGAGLIQPGQ 63
VK+ L++++E C +IA T I +I AGL +P +
Sbjct: 98 VKKALFAQLEELCPADT--IIASNTSSLSITAIAAGLARPER 137
>gnl|CDD|197648 smart00316, S1, Ribosomal protein S1-like RNA-binding domain.
Length = 72
Score = 29.1 bits (66), Expect = 0.23
Identities = 14/79 (17%), Positives = 32/79 (40%), Gaps = 13/79 (16%)
Query: 81 KGEVLDAVVTQVNKVGMFAEIGP-LSCFISHHSIPTDMQFCPNSNPVCYKSVHGEVVIQE 139
G+V++ VT++ G F ++G + I + + E V++
Sbjct: 2 VGDVVEGTVTEITPGGAFVDLGNGVEGLIPISELSDK------------RVKDPEEVLKV 49
Query: 140 DDEIRLKIVGTRVDASGIF 158
DE+++K++ + I
Sbjct: 50 GDEVKVKVLSVDEEKGRII 68
>gnl|CDD|180917 PRK07279, dnaE, DNA polymerase III DnaE; Reviewed.
Length = 1034
Score = 29.2 bits (66), Expect = 1.2
Identities = 18/49 (36%), Positives = 27/49 (55%), Gaps = 8/49 (16%)
Query: 130 SVHGE-VVIQED---DEIRLK----IVGTRVDASGIFAIGTLMDDYLGL 170
S+H VV+ +D + I LK ++ T+ DA + A G L D+LGL
Sbjct: 446 SIHAAGVVMSDDDLTNHIPLKYGDDMMITQYDAHAVEANGLLKMDFLGL 494
>gnl|CDD|239907 cd04460, S1_RpoE, S1_RpoE: RpoE, S1-like RNA-binding domain.
S1-like RNA-binding domains are found in a wide variety
of RNA-associated proteins. RpoE is subunit E of
archaeal RNA polymerase. Archaeal cells contain a single
RNA polymerase made up of 12 subunits, which are
homologous to the 12 subunits (RPB1-12) of eukaryotic
RNA polymerase II. RpoE is homologous to Rpa43 of
eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA
polymerase II, and Rpc25 of eukaryotic RNA polymerase
III. RpoE is composed of two domains, the N-terminal RNP
(ribonucleoprotein) domain and the C-terminal S1 domain.
This S1 domain binds ssRNA and ssDNA. This family is
classified based on the C-terminal S1 domain. The
function of RpoE is not fully understood. In eukaryotes,
RPB7 and RPB4 form a heterodimer that reversibly
associates with the RNA polymerase II core.
Length = 99
Score = 27.3 bits (61), Expect = 1.8
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 7/70 (10%)
Query: 83 EVLDAVVTQVNKVGMFAEIGPLSCFISHHSIPTD--MQFCP-NSNPVCYKSVHGEVVIQE 139
EV++ V +V G F IGP+ + H S D + + P N + ++ + V++
Sbjct: 1 EVVEGEVVEVVDFGAFVRIGPVDGLL-HISQIMDDYISYDPKNKRLIGEET---KRVLKV 56
Query: 140 DDEIRLKIVG 149
D +R +IV
Sbjct: 57 GDVVRARIVA 66
>gnl|CDD|163004 TIGR02761, TraE_TIGR, type IV conjugative transfer system protein
TraE. TraE is a component of type IV secretion systems
involved in conjugative transfer of plasmid DNA. The
function of the TraE protein is unknown.
Length = 181
Score = 27.7 bits (62), Expect = 2.3
Identities = 11/33 (33%), Positives = 14/33 (42%), Gaps = 2/33 (6%)
Query: 3 YHISLEHEILLHPRYFGPQLYETVKQKLYSEVE 35
+H LL Y PQ Y +K +L E E
Sbjct: 87 ESADAQHNALL--GYVEPQNYGQIKSRLAKEAE 117
>gnl|CDD|239917 cd04471, S1_RNase_R, S1_RNase_R: RNase R C-terminal S1 domain.
RNase R is a processive 3' to 5' exoribonuclease, which
is a homolog of RNase II. RNase R degrades RNA with
secondary structure having a 3' overhang of at least 7
nucleotides. RNase R and PNPase play an important role
in the degradation of RNA with extensive secondary
structure, such as rRNA, tRNA, and certain mRNA which
contains repetitive extragenic palindromic sequences.
The C-terminal S1 domain binds ssRNA.
Length = 83
Score = 25.8 bits (58), Expect = 4.8
Identities = 8/20 (40%), Positives = 12/20 (60%)
Query: 82 GEVLDAVVTQVNKVGMFAEI 101
GE D V++ V G+F E+
Sbjct: 2 GEEFDGVISGVTSFGLFVEL 21
>gnl|CDD|119411 cd00206, snake_toxin, Snake toxin domain, present in short and long
neurotoxins, cytotoxins and short toxins, and in other
miscellaneous venom peptides. The toxin acts by binding
to the nicotinic acetylcholine receptors in the
postsynaptic membrane of skeletal muscles and preventing
the binding of acetylcholine, thereby blocking the
excitation of muscles. This domain contains 60-75 amino
acids that are fixed by 4-5 disulfide bridges and is
nearly all beta sheet; it exists as either monomers or
dimers.
Length = 64
Score = 25.1 bits (55), Expect = 6.7
Identities = 8/29 (27%), Positives = 13/29 (44%)
Query: 104 LSCFISHHSIPTDMQFCPNSNPVCYKSVH 132
L+C+ P + CP+ +CYK
Sbjct: 1 LTCYNCPSPFPFTTETCPDGENICYKKSW 29
>gnl|CDD|223613 COG0539, RpsA, Ribosomal protein S1 [Translation, ribosomal
structure and biogenesis].
Length = 541
Score = 26.5 bits (59), Expect = 8.8
Identities = 7/28 (25%), Positives = 15/28 (53%)
Query: 81 KGEVLDAVVTQVNKVGMFAEIGPLSCFI 108
GE+++ +T K G+ +I + F+
Sbjct: 105 NGEIVEGKITGKVKGGLTVDIEGVRAFL 132
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
0.324 0.143 0.434
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: 8,898,545
Number of extensions: 811564
Number of successful extensions: 660
Number of sequences better than 10.0: 1
Number of HSP's gapped: 655
Number of HSP's successfully gapped: 33
Length of query: 170
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 80
Effective length of database: 6,945,742
Effective search space: 555659360
Effective search space used: 555659360
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.9 bits)