RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5332
(287 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 = 353 bits (907), Expect = e-123
Identities = 128/226 (56%), Positives = 167/226 (73%), Gaps = 5/226 (2%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
+AID V++E N++VL DEFIA R+GLIPLTSD+V + + YSRDC C +FC +CSVE TLD
Sbjct: 39 LAIDLVEIEENTSVLHDEFIAHRLGLIPLTSDDVDEFLYYSRDCDCDEFCDKCSVELTLD 98
Query: 61 VKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAY 120
VKC DQTR VT+ DL S+ +V V D + GE D ILIVKLRKGQEL+LR
Sbjct: 99 VKCTGDQTREVTSRDLVSSGPKVNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCI 158
Query: 121 AKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPD----EWPKSEYSELDE-TQHEAP 175
AKKG GKEHAKW+PTA V FEYDPDN++RHT + + EWPKSE + ++E + +A
Sbjct: 159 AKKGIGKEHAKWSPTAAVTFEYDPDNALRHTDYWYLEDEDKEWPKSENACIEEPPEKDAL 218
Query: 176 YNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQLAH 221
++ +AKP+K++FNVES GAL PE IV+ G+ +LK+KL++LQ QL+
Sbjct: 219 FDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 199 bits (509), Expect = 9e-64
Identities = 80/225 (35%), Positives = 106/225 (47%), Gaps = 36/225 (16%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
MA+ V +E N++ + DE +A R+GL PL SD D Y RDC C + C +CSV TLD
Sbjct: 27 MAVTSVYIEGNTSGVQDEVLAHRLGLKPLASDPDGDE--YQRDCECEEGCEKCSVTLTLD 84
Query: 61 VKCVDDQTRHVTTADLKS-TDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRA 119
VK + VT DLKS +D V V DI I KLR+GQEL L A
Sbjct: 85 VKGPGE----VTAGDLKSDSDPDVEIVN--------------PDIPIAKLREGQELELEA 126
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDP----DNSMRHTLFPKPD----EWPKSEYSELDETQ 171
A+KG G HAKW+P + V + Y P D S + T
Sbjct: 127 RAEKGRGYVHAKWSPVSTVEYRYIPRIPVDASFSPVDRVAYQVECPRVVQR-------TD 179
Query: 172 HEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQ 216
+ + +K F+VE+ G+LKPE V+ +LK+KL
Sbjct: 180 CCRECDEGEEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAFV 224
>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 = 152 bits (385), Expect = 9e-45
Identities = 79/241 (32%), Positives = 113/241 (46%), Gaps = 42/241 (17%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTL 59
+AID V + N++VL DE +A R+GLIPL +D D Y +C+C C C+V TL
Sbjct: 39 LAIDDVNIYENTSVLFDEMLAHRLGLIPLRTDL--DLYKYRSECSCGGAGCPLCTVTLTL 96
Query: 60 DVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRA 119
V+ V + DLKS+D V PV D+I IVKL KGQ+L L A
Sbjct: 97 SVEG----PGTVYSGDLKSSDPDVKPVY--------------DNIPIVKLGKGQKLVLEA 138
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKP---DEWPKS-----EYSELDETQ 171
YA+ G GKEHAKW PT ++Y P + +E P+ E + E
Sbjct: 139 YARLGRGKEHAKWQPTTACGYKYYPVIEIDEDCDGCGKCVEECPRGVLELEEGKVVVEDL 198
Query: 172 HEAPYNWEAK-------------PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQ 218
+ + +++ F VES G+L P+ I++ + +LK+K L
Sbjct: 199 EDCSLCKLCERACDAGAIRVGWDEDRFIFEVESDGSLPPKEILLEALRILKEKADELIEA 258
Query: 219 L 219
L
Sbjct: 259 L 259
Score = 41.9 bits (99), Expect = 1e-04
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 239 PNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 276
+++ F VES G+L P+ I++ + +LK+K L L
Sbjct: 222 EDRFIFEVESDGSLPPKEILLEALRILKEKADELIEAL 259
>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 141 bits (359), Expect = 7e-41
Identities = 81/246 (32%), Positives = 117/246 (47%), Gaps = 50/246 (20%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTL 59
MAID V+ N++VL DE +A R+GLIPLT+D +D+ +CTC + C +C+V +L
Sbjct: 39 MAIDDVRFYENTSVLFDEILAHRLGLIPLTTD--LDKYKPPEECTCEGEGCPDCTVTLSL 96
Query: 60 DVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRA 119
+V+ + V + DLKS+D V PV +I IVKL++GQ+L L A
Sbjct: 97 EVE----GPKTVYSGDLKSSDPDVKPVD--------------PNIPIVKLKEGQKLVLEA 138
Query: 120 YAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEW-------PKS---------- 162
YA+ G GKEHAKW P + ++Y P R + DE P+
Sbjct: 139 YARLGRGKEHAKWQPGSACGYKYYP----RIEVSEDCDECEKCVEACPRGVLELKEGKLV 194
Query: 163 -------EYSELDETQHEAPYNW-EAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSN 214
+L E NK+ F VES G+L E I++ + +LK+K
Sbjct: 195 VTDLLNCSLCKLCERACPGKAIRVSDDENKFIFTVESDGSLPVEEILLEALKILKRKADE 254
Query: 215 LQTQLA 220
L L
Sbjct: 255 LIEALE 260
>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 = 133 bits (337), Expect = 2e-38
Identities = 74/223 (33%), Positives = 106/223 (47%), Gaps = 60/223 (26%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILY---SRDCTCVDFCSECSVEF 57
MA+D V++E N++VL+DE +A R+GLIPL S +++ LY DC C D C +CSV
Sbjct: 39 MAVDSVEVETNTSVLADEILAHRLGLIPLQSMDILQ--LYRSPEEDCECEDHCDKCSVVL 96
Query: 58 TLDVKCVDDQTRHVTTADLKSTDAR-----VVPVTSRNRDADMNEYGETDDILIVKLRKG 112
TL + T +V + DL P+ DILI KLRKG
Sbjct: 97 TLQAFAESESTTNVYSKDLVIVSNLMGRNIGHPII--------------QDILICKLRKG 142
Query: 113 QELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQH 172
QE++L AKKG GKEHAK+ P A + F YDP
Sbjct: 143 QEIKLTCVAKKGIGKEHAKFGPVAAIEFRYDP---------------------------- 174
Query: 173 EAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 215
+ Y NVES G+L P+ +V+ + L++K++++
Sbjct: 175 --------VADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASI 209
Score = 34.5 bits (79), Expect = 0.035
Identities = 11/42 (26%), Positives = 26/42 (61%)
Query: 231 APYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 272
+ ++ + Y NVES G+L P+ +V+ + L++K++++
Sbjct: 168 IEFRYDPVADTYIMNVESVGSLPPDQVVVEAIKTLQKKVASI 209
>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 = 109 bits (274), Expect = 3e-28
Identities = 71/267 (26%), Positives = 106/267 (39%), Gaps = 69/267 (25%)
Query: 1 MAIDWVQLEANSTVLSDEFIASRIGLIPLTSDEVVDRILYSRDCTCVDFCSECSVEFTLD 60
MAI+ V + N++V+ DE +A R+GLIP+ +D Y R+ + + E ++ F L
Sbjct: 39 MAIEKVYIYNNTSVIQDEVLAHRLGLIPIKAD--PRLFEY-REDSDDEPTEENTLVFELK 95
Query: 61 VKC----------VDDQTR----HVTTADLK----------STDARVVPVTSRNRDADMN 96
VKC D V + DLK D + PV
Sbjct: 96 VKCTRNPNAPKDSTDPDELYINHKVYSGDLKWVPIGSQEKRFADNPIRPVH--------- 146
Query: 97 EYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPD--------NSM 148
DILI KLR GQE+ L + KG GK+HAK++P A + P+
Sbjct: 147 -----PDILIAKLRPGQEIDLELHCVKGIGKDHAKFSPVATASYRLLPEITLLKPITGED 201
Query: 149 RHTL---FPK------PDEWPKSEY---SELDETQHEAPYNWEAK--------PNKYFFN 188
L FP + K D E + E K + + F+
Sbjct: 202 AEKLQKCFPPGVIDIEEVKGKKKAVVANPRKDTLSREVLRHEEFKDKVELGRVRDHFIFS 261
Query: 189 VESAGALKPENIVIMGVTVLKQKLSNL 215
+ES GAL P+ + + + +LK+K L
Sbjct: 262 IESTGALPPDVLFLEAIKILKEKCRKL 288
Score = 39.9 bits (94), Expect = 8e-04
Identities = 11/33 (33%), Positives = 21/33 (63%)
Query: 240 NKYFFNVESAGALKPENIVIMGVTVLKQKLSNL 272
+ + F++ES GAL P+ + + + +LK+K L
Sbjct: 256 DHFIFSIESTGALPPDVLFLEAIKILKEKCRKL 288
>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 = 103 bits (258), Expect = 9e-28
Identities = 51/115 (44%), Positives = 61/115 (53%), Gaps = 20/115 (17%)
Query: 20 IASRIGLIPLTSDEVVDRILYSRDCTC-VDFCSECSVEFTLDVKCVDDQTRHVTTADLKS 78
+A GLIP S++V++ IL ++ C ++ C ECSV TLDVK VT DL+S
Sbjct: 6 VAHEFGLIPGVSEDVLEIILNLKELVCKIEGCEECSVTLTLDVKG----PGEVTAGDLES 61
Query: 79 TDARVVPVTSRNRDADMNEYGETDDILIVKLRKGQELRLRAYAKKGFGKEHAKWN 133
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 = 91.6 bits (228), Expect = 2e-21
Identities = 47/293 (16%), Positives = 92/293 (31%), Gaps = 56/293 (19%)
Query: 1 MAIDWVQLE------ANSTVLSDEFIASRIGLIPLTSD---EVVDRILYSRDCTCVDFCS 51
A+ V+++ + + ++ +A R+ L PL + + ++ S
Sbjct: 47 AAVTAVEIDGVLHEFDSIEGVQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTAS 106
Query: 52 ECSVEFTLDVKC-------VDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGETDDI 104
+ +V L+V + + + + S D V +R D + D
Sbjct: 107 DITVPLDLEVVNPDHVIATLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGP--IAVDA 164
Query: 105 LIVKLRKGQELRLRAYAKKGFGKEHAKWNPTAGVCFEYDPD-----NSMRHTLFPKPDEW 159
+RK Q + A +G K+H KW P + + L +
Sbjct: 165 PFSPVRKVQYIVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELC 224
Query: 160 PKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 219
PK+ E ++ + EA ++ +V S LK E I +G V
Sbjct: 225 PKAVEIEEEKPEFPILLVLEAPIDELDLSVRSYNCLKREGIETIGELVQ----------- 273
Query: 220 AHDRVFYVINEAPYNWEAKPNKYFFNVESAGALKPENIVI----MGVTVLKQK 268
+ + VE+ G E I +G+ + +
Sbjct: 274 ------------------RTEEELLKVENLGKKSLEEIKEKLAELGLELGMEL 308
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 195
Score = 60.2 bits (146), Expect = 5e-11
Identities = 57/225 (25%), Positives = 81/225 (36%), Gaps = 87/225 (38%)
Query: 2 AIDWVQLEANSTVLSDEFIASRIGLIPLT-----SDEVVDRILYSRDCTCVDFCSECSVE 56
AI+ V NS+ + DE +A R+GLIP+ DEV+ S++ C
Sbjct: 42 AIENVYFYENSSSMYDEILAHRLGLIPIKGKPVSGDEVI-TFTLSKEGPCT--------- 91
Query: 57 FTLDVKCVDDQTRHVTTADLKSTDARVVPVTSRNRDADMNEYGET--DDILIVKLRKGQE 114
V ++DLKS E GE +I IVKL +GQ+
Sbjct: 92 --------------VYSSDLKS------------------ENGEVAFKNIPIVKLAEGQK 119
Query: 115 LRLRAYAKKGFGKEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEA 174
L + A G GK HAKW P V Y ++ + E
Sbjct: 120 LEIECEALVGTGKIHAKWQPCNAV-------------------------YKQISNDEVE- 153
Query: 175 PYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLSNLQTQL 219
F VES G + E+I+ + +LK K +L
Sbjct: 154 ------------FKVESFGQMDAEDILRSALEILKNKAEKFLQEL 186
>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 = 38.7 bits (91), Expect = 2e-04
Identities = 12/87 (13%), Positives = 24/87 (27%), Gaps = 33/87 (37%)
Query: 127 KEHAKWNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQHEAPYNWEAKPNKYF 186
AK++P V + +K
Sbjct: 35 PHPAKFSPVKKVNYRVV---------------------------------GVGTDYDKLI 61
Query: 187 FNVESAGALKPENIVIMGVTVLKQKLS 213
+E+ G++ PE + + +L +KL
Sbjct: 62 LRIETDGSITPEEALKEALKILIEKLD 88
Score = 36.8 bits (86), Expect = 0.001
Identities = 11/53 (20%), Positives = 22/53 (41%), Gaps = 3/53 (5%)
Query: 221 HDRVFYVINEAPY---NWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLS 270
H F + + Y +K +E+ G++ PE + + +L +KL
Sbjct: 36 HPAKFSPVKKVNYRVVGVGTDYDKLILRIETDGSITPEEALKEALKILIEKLD 88
>gnl|CDD|233692 TIGR02031, BchD-ChlD, magnesium chelatase ATPase subunit D. This
model represents one of two ATPase subunits of the
trimeric magnesium chelatase responsible for insertion
of magnesium ion into protoporphyrin IX. This is an
essential step in the biosynthesis of both chlorophyll
and bacteriochlorophyll. This subunit is found in green
plants, photosynthetic algae, cyanobacteria and other
photosynthetic bacteria. Unlike subunit I (TIGR02030),
this subunit is not found in archaea [Biosynthesis of
cofactors, prosthetic groups, and carriers, Chlorophyll
and bacteriochlorphyll].
Length = 589
Score = 31.7 bits (72), Expect = 0.46
Identities = 16/70 (22%), Positives = 30/70 (42%), Gaps = 2/70 (2%)
Query: 154 PKPDEWPKSEYSELDETQHEAPYNWEAKPNKYFFNVESAGALKPENIVIMGVTVLKQKLS 213
P P+ E E D+T + + P + F ++ A P+NI+ TV +++
Sbjct: 279 PPEPPEPEEEPDEPDQTDPDDGEETDQIPEELMF--DAVEADLPDNILATLQTVQRRRGR 336
Query: 214 NLQTQLAHDR 223
Q ++ R
Sbjct: 337 AGGEQKSNHR 346
>gnl|CDD|241001 cd12557, RRM3_RBM15, RNA recognition motif 3 in vertebrate RNA
binding motif protein 15 (RBM15). This subgroup
corresponds to the RRM3 of RBM15, also termed one-twenty
two protein 1 (OTT1), conserved in eukaryotes, a novel
mRNA export factor component of the NXF1 pathway. It
binds to NXF1 and serves as receptor for the RNA export
element RTE. It also possesses mRNA export activity and
can facilitate the access of DEAD-box protein DBP5 to
mRNA at the nuclear pore complex (NPC). RBM15 belongs to
the Spen (split end) protein family, which contains
three N-terminal RNA recognition motifs (RRMs), also
known as RBD (RNA binding domain) or RNP
(ribonucleoprotein domain), and a C-terminal SPOC (Spen
paralogue and ortholog C-terminal) domain. This family
also includes a RBM15-MKL1 (OTT-MAL) fusion protein that
RBM15 is N-terminally fused to megakaryoblastic leukemia
1 protein (MKL1) at the C-terminus in a translocation
involving chromosome 1 and 22, resulting in acute
megakaryoblastic leukemia. The fusion protein could
interact with the mRNA export machinery. Although it
maintains the specific transactivator function of MKL1,
the fusion protein cannot activate RTE-mediated mRNA
expression and has lost the post-transcriptional
activator function of RBM15. However, it has
transdominant suppressor function contributing to its
oncogenic properties. .
Length = 73
Score = 28.8 bits (64), Expect = 0.75
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 132 WNPTAGVCFEYDPDNSMRHTLFPKPDEWPKSEYSELDETQ 171
W P A + E+D ++R + K D W +Y LD Q
Sbjct: 10 WVPLAALAREFDRFGTIRTIDYRKGDSWAYIQYESLDAAQ 49
>gnl|CDD|177448 PHA02665, PHA02665, hypothetical protein; Provisional.
Length = 322
Score = 30.3 bits (68), Expect = 1.1
Identities = 12/39 (30%), Positives = 19/39 (48%), Gaps = 4/39 (10%)
Query: 28 PLTSDEVVDRILYSRDCTCVDFCSECSVEFTLDVKCVDD 66
L+ DEV L++RD VD+ +V F ++ D
Sbjct: 155 VLSGDEV----LFTRDLAHVDYDPNSAVVFKMEYDLATD 189
>gnl|CDD|132901 cd00460, RNAP_RPB11_RPB3, RPB11 and RPB3 subunits of RNA
polymerase. The eukaryotic RPB11 and RPB3 subunits of
RNA polymerase (RNAP), as well as their archaeal (L and
D subunits) and bacterial (alpha subunit) counterparts,
are involved in the assembly of RNAP, 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 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 = 86
Score = 27.0 bits (60), Expect = 3.3
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 184 KYFFNVESAGALKPENIVIMGVTVLKQKLSNL 215
K+ +E+ G++ PE + V +L++KL +L
Sbjct: 55 KFILRIETVGSIPPEEALRRAVEILRKKLEHL 86
Score = 27.0 bits (60), Expect = 3.3
Identities = 10/32 (31%), Positives = 20/32 (62%)
Query: 241 KYFFNVESAGALKPENIVIMGVTVLKQKLSNL 272
K+ +E+ G++ PE + V +L++KL +L
Sbjct: 55 KFILRIETVGSIPPEEALRRAVEILRKKLEHL 86
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
0.317 0.132 0.398
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: 14,434,856
Number of extensions: 1341647
Number of successful extensions: 1250
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1228
Number of HSP's successfully gapped: 33
Length of query: 287
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 191
Effective length of database: 6,679,618
Effective search space: 1275807038
Effective search space used: 1275807038
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: 58 (26.0 bits)