RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12829
(181 letters)
>gnl|CDD|132909 cd07031, RNAP_II_RPB3, RPB3 subunit of Eukaryotic RNA polymerase
II. The eukaryotic RPB3 subunit of RNA polymerase
(RNAP) II is involved in the assembly of RNAP subunits.
RNAP is a large multi-subunit complex responsible for
the synthesis of RNA. It is the principal enzyme of the
transcription process, and is a final target in many
regulatory pathways that control gene expression in all
living cells. At least three distinct RNAP complexes are
found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP
III. RNAP II is responsible for the synthesis of mRNA
precursor. The RPB3 subunit is similar to the bacterial
RNAP alpha subunit in that it contains two subdomains:
one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The RPB3 subunit heterodimerizes with the
RPB11 subunit, and together with RPB10 and RPB12,
anchors the two largest subunits, RPB1 and RPB2, and
stabilizes their association.
Length = 265
Score = 296 bits (760), Expect = e-103
Identities = 111/175 (63%), Positives = 133/175 (76%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V IT+LTD+ VKF +E+T+LSVANSLRRV IAE PT+AID V++E N++VL DEFIA
Sbjct: 1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAH 60
Query: 67 RIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
R+GLIPLTSD+V + + YSRDC C +FC +CSVE TLDVKC DQTR VT+ DL S+ +
Sbjct: 61 RLGLIPLTSDDVDEFLYYSRDCDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSSGPK 120
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
V V D + GE D ILIVKLRKGQEL+LR AKKG GKEHAKW+PTA
Sbjct: 121 VNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAA 175
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 180 bits (458), Expect = 1e-57
Identities = 71/164 (43%), Positives = 92/164 (56%), Gaps = 21/164 (12%)
Query: 19 VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEV 78
KF +E L++AN+LRRV ++ P MA+ V +E N++ + DE +A R+GL PL SD
Sbjct: 1 AKFVLEPYGLTLANALRRVLLSSVPGMAVTSVYIEGNTSGVQDEVLAHRLGLKPLASDPD 60
Query: 79 VDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKS-TDARVVPVTSRNRDA 137
D Y RDC C + C +CSV TLDVK + VT DLKS +D V V
Sbjct: 61 GD--EYQRDCECEEGCEKCSVTLTLDVKGPGE----VTAGDLKSDSDPDVEIV------- 107
Query: 138 DMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAG 181
DI I KLR+GQEL L A A+KG G HAKW+P +
Sbjct: 108 -------NPDIPIAKLREGQELELEARAEKGRGYVHAKWSPVST 144
>gnl|CDD|132908 cd07030, RNAP_D, D subunit of Archaeal RNA polymerase. The D
subunit of archaeal RNA polymerase (RNAP) is involved in
the assembly of RNAP subunits. RNAP is a large
multi-subunit complex responsible for the synthesis of
RNA. It is the principal enzyme of the transcription
process, and is a final target in many regulatory
pathways that control gene expression in all living
cells. A single distinct RNAP complex is found in
archaea, which may be responsible for the synthesis of
all RNAs. The archaeal RNAP harbors homologues of all
eukaryotic RNAP II subunits with two exceptions (RPB8
and RPB9). The 12 archaeal subunits are designated by
letters and can be divided into three functional groups
that are engaged in: (I) catalysis (A'/A", B'/B" or B);
(II) assembly (L, N, D and P); and (III) auxiliary
functions (F, E, H and K). The D subunit is equivalent
to the RPB3 subunit of eukaryotic RNAP II. It contains
two subdomains: one subdomain is similar the eukaryotic
Rpb11/AC19/archaeal L subunit which is involved in
dimerization, and the other is an inserted beta sheet
subdomain. The assembly of the two largest archaeal RNAP
subunits that provide most of the enzyme's catalytic
functions depends on the presence of the archaeal D/L
heterodimer.
Length = 259
Score = 162 bits (413), Expect = 2e-50
Identities = 72/173 (41%), Positives = 98/173 (56%), Gaps = 21/173 (12%)
Query: 8 SVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASR 67
+ + +L D+ +F +E + AN++RR I+E PT+AID V + N++VL DE +A R
Sbjct: 2 EIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHR 61
Query: 68 IGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDAR 126
+GLIPL +D D Y +C+C C C+V TL V+ V + DLKS+D
Sbjct: 62 LGLIPLRTDL--DLYKYRSECSCGGAGCPLCTVTLTLSVEG----PGTVYSGDLKSSDPD 115
Query: 127 VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
V PV D+I IVKL KGQ+L L AYA+ G GKEHAKW PT
Sbjct: 116 VKPV--------------YDNIPIVKLGKGQKLVLEAYARLGRGKEHAKWQPT 154
>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 155 bits (394), Expect = 1e-47
Identities = 72/174 (41%), Positives = 103/174 (59%), Gaps = 21/174 (12%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
+ I +L D + +F VE + AN++RR IA+ PTMAID V+ N++VL DE +A
Sbjct: 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAH 60
Query: 67 RIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDA 125
R+GLIPLT+D +D+ +CTC + C +C+V +L+V+ + V + DLKS+D
Sbjct: 61 RLGLIPLTTD--LDKYKPPEECTCEGEGCPDCTVTLSLEVE----GPKTVYSGDLKSSDP 114
Query: 126 RVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPT 179
V PV +I IVKL++GQ+L L AYA+ G GKEHAKW P
Sbjct: 115 DVKPV--------------DPNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPG 154
>gnl|CDD|132906 cd07028, RNAP_RPB3_like, RPB3 subunit of RNA polymerase. The
eukaryotic RPB3 subunit of RNA polymerase (RNAP), as
well as its archaeal (D subunit) and bacterial (alpha
subunit) counterparts, is involved in the assembly of
RNAP subunits. RNAP is a large multi-subunit complex
responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III, for the synthesis of
ribosomal RNA precursor, mRNA precursor, and 5S and
tRNA, respectively. A single distinct RNAP complex is
found in prokaryotes and archaea, which may be
responsible for the synthesis of all RNAs. The RPB3
subunit is similar to the bacterial RNAP alpha subunit
in that it contains two subdomains: one subdomain is
similar to the eukaryotic Rpb11/AC19/archaeal L subunit
which is involved in dimerization; and the other is an
inserted beta sheet subdomain. The assembly of the two
largest eukaryotic RNAP subunits that provide most of
the enzyme's catalytic functions depends on the presence
of RPB3/RPB11 heterodimer subunits. This is also true
for the archaeal (D/L subunits) and bacterial (alpha
subunit) counterparts.
Length = 212
Score = 145 bits (366), Expect = 4e-44
Identities = 77/182 (42%), Positives = 103/182 (56%), Gaps = 24/182 (13%)
Query: 7 PSVHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIAS 66
P V I + +NV F + +L++AN+LRRV IAE PTMA+D V++E N++VL+DE +A
Sbjct: 1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAH 60
Query: 67 RIGLIPLTSDEVVDRILY---SRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKST 123
R+GLIPL S +++ LY DC C D C +CSV TL + T +V + DL
Sbjct: 61 RLGLIPLQSMDILQ--LYRSPEEDCECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVIV 118
Query: 124 DAR-----VVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
P+ DILI KLRKGQE++L AKKG GKEHAK+ P
Sbjct: 119 SNLMGRNIGHPI--------------IQDILICKLRKGQEIKLTCVAKKGIGKEHAKFGP 164
Query: 179 TA 180
A
Sbjct: 165 VA 166
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase
(RNAP) I and RNAP III. The eukaryotic AC40 subunit of
RNA polymerase (RNAP) I and RNAP III is involved in the
assembly of RNAP subunits. RNAP is a large multi-subunit
complex responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III. RNAP I is responsible for
the synthesis of ribosomal RNA precursor, while RNAP III
functions in the synthesis of 5S and tRNA. The AC40
subunit is the equivalent of the RPB3 subunit of RNAP
II. The RPB3 subunit is similar to the bacterial RNAP
alpha subunit in that it contains two subdomains: one
subdomain is similar the eukaryotic Rpb11/AC19/archaeal
L subunit which is involved in dimerization; and the
other is an inserted beta sheet subdomain. The RPB3
subunit heterodimerizes with the RPB11 subunit, and
together with RPB10 and RPB12, anchors the two largest
subunits, RPB1 and RPB2, and stabilizes their
association. The homology of AC40 to RPB3 suggests a
similar function. The AC40 subunit is likely to
associate with the RPB11 counterpart, AC19, to form a
heterodimer, which stabilizes the association of the two
largest subunits of RNAP I and RNAP III.
Length = 291
Score = 129 bits (326), Expect = 4e-37
Identities = 65/196 (33%), Positives = 96/196 (48%), Gaps = 41/196 (20%)
Query: 9 VHITDLTDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRI 68
+ I L+DE ++F + + S+AN+ RR+ +AE PTMAI+ V + N++V+ DE +A R+
Sbjct: 3 IEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHRL 62
Query: 69 GLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKC----------VDDQTR----H 114
GLIP+ +D Y R+ + + E ++ F L VKC D
Sbjct: 63 GLIPIKAD--PRLFEY-REDSDDEPTEENTLVFELKVKCTRNPNAPKDSTDPDELYINHK 119
Query: 115 VTTADLK----------STDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 164
V + DLK D + PV DILI KLR GQE+ L +
Sbjct: 120 VYSGDLKWVPIGSQEKRFADNPIRPV--------------HPDILIAKLRPGQEIDLELH 165
Query: 165 AKKGFGKEHAKWNPTA 180
KG GK+HAK++P A
Sbjct: 166 CVKGIGKDHAKFSPVA 181
>gnl|CDD|110031 pfam01000, RNA_pol_A_bac, RNA polymerase Rpb3/RpoA insert domain.
Members of this family include: alpha subunit from
eubacteria alpha subunits from chloroplasts Rpb3
subunits from eukaryotes RpoD subunits from archaeal.
Length = 117
Score = 101 bits (254), Expect = 3e-28
Identities = 51/115 (44%), Positives = 61/115 (53%), Gaps = 20/115 (17%)
Query: 64 IASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKS 122
+A GLIP S++V++ IL ++ C ++ C ECSV TLDVK VT DL+S
Sbjct: 6 VAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKG----PGEVTAGDLES 61
Query: 123 TDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 177
D V V DILI LRKGQEL L AYAKKG G HAK N
Sbjct: 62 -DPDVEIVN--------------PDILIATLRKGQELELEAYAKKGRGYVHAKEN 101
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD
subunit [Transcription].
Length = 317
Score = 104 bits (262), Expect = 2e-27
Identities = 41/192 (21%), Positives = 77/192 (40%), Gaps = 22/192 (11%)
Query: 9 VHITDLTDENVKFQVEDTE----LSVANSLRRVFIAETPTMAIDWVQLE------ANSTV 58
V I +L+D KF +E E +++ N+LRRV ++ P A+ V+++ +
Sbjct: 7 VKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIEG 66
Query: 59 LSDEFIASRIGLIPLTSD---EVVDRILYSRDCTCVDFCSECSVEFTLDVKC-------V 108
+ ++ +A R+ L PL + + ++ S+ +V L+V +
Sbjct: 67 VQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPLDLEVVNPDHVIATL 126
Query: 109 DDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKG 168
+ + + S D V +R D + D +RK Q + A +G
Sbjct: 127 TEDAKLEMELRVYSGDGYVPAEGNREDDPPVGP--IAVDAPFSPVRKVQYIVEEARVGQG 184
Query: 169 FGKEHAKWNPTA 180
K+H KW P
Sbjct: 185 TDKDHLKWEPET 196
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 195
Score = 80.7 bits (199), Expect = 3e-19
Identities = 54/171 (31%), Positives = 77/171 (45%), Gaps = 50/171 (29%)
Query: 15 TDENVKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLEANSTVLSDEFIASRIGLIPLT 74
E KF ++ +S +++LRR+ I+E PT AI+ V NS+ + DE +A R+GLIP+
Sbjct: 12 IGEEFKFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIK 70
Query: 75 -----SDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDDQTRHVTTADLKSTDARVVP 129
DEV+ S++ C V ++DLKS
Sbjct: 71 GKPVSGDEVI-TFTLSKEGPCT-----------------------VYSSDLKS------- 99
Query: 130 VTSRNRDADMNEYGET--DDILIVKLRKGQELRLRAYAKKGFGKEHAKWNP 178
E GE +I IVKL +GQ+L + A G GK HAKW P
Sbjct: 100 -----------ENGEVAFKNIPIVKLAEGQKLEIECEALVGTGKIHAKWQP 139
>gnl|CDD|216354 pfam01193, RNA_pol_L, RNA polymerase Rpb3/Rpb11 dimerisation
domain. The two eukaryotic subunits Rpb3 and Rpb11
dimerise to from a platform onto which the other
subunits of the RNA polymerase assemble (D/L in
archaea). The prokaryotic equivalent of the Rpb3/Rpb11
platform is the alpha-alpha dimer. The dimerisation
domain of the alpha subunit/Rpb3 is interrupted by an
insert domain (pfam01000). Some of the alpha subunits
also contain iron-sulphur binding domains (pfam00037).
Rpb11 is found as a continuous domain. Members of this
family include: alpha subunit from eubacteria, alpha
subunits from chloroplasts, Rpb3 subunits from
eukaryotes, Rpb11 subunits from eukaryotes, RpoD
subunits from archaeal spp, and RpoL subunits from
archaeal spp.
Length = 88
Score = 41.1 bits (97), Expect = 2e-05
Identities = 11/35 (31%), Positives = 24/35 (68%)
Query: 19 VKFQVEDTELSVANSLRRVFIAETPTMAIDWVQLE 53
++F +E + ++ N+LRRV +++ P +AI V++
Sbjct: 1 IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIP 35
>gnl|CDD|177448 PHA02665, PHA02665, hypothetical protein; Provisional.
Length = 322
Score = 29.1 bits (65), Expect = 1.1
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 72 PLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDD 110
L+ DEV L++RD VD+ +V F ++ D
Sbjct: 155 VLSGDEV----LFTRDLAHVDYDPNSAVVFKMEYDLATD 189
>gnl|CDD|218767 pfam05827, ATP-synt_S1, Vacuolar ATP synthase subunit S1
(ATP6S1). This family consists of eukaryotic vacuolar
ATP synthase subunit S1 proteins.
Length = 277
Score = 28.1 bits (63), Expect = 2.2
Identities = 6/21 (28%), Positives = 10/21 (47%)
Query: 3 YANQPSVHITDLTDENVKFQV 23
+ +QP + +D T E F
Sbjct: 50 FISQPGLSASDFTTEKDNFPN 70
>gnl|CDD|181738 PRK09265, PRK09265, aminotransferase AlaT; Validated.
Length = 404
Score = 26.7 bits (60), Expect = 9.0
Identities = 10/21 (47%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 64 IASRIGLIPLTSDEVVDRILY 84
IA + LI + +DE+ D+ILY
Sbjct: 196 IARQHNLI-IFADEIYDKILY 215
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 0.132 0.386
Gapped
Lambda K H
0.267 0.0772 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,938,011
Number of extensions: 794060
Number of successful extensions: 684
Number of sequences better than 10.0: 1
Number of HSP's gapped: 666
Number of HSP's successfully gapped: 19
Length of query: 181
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 90
Effective length of database: 6,901,388
Effective search space: 621124920
Effective search space used: 621124920
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 (25.3 bits)