RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= 020983
(319 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 = 371 bits (956), Expect = e-130
Identities = 140/295 (47%), Positives = 176/295 (59%), Gaps = 33/295 (11%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+V+I EL DD KF L +TD S+AN+LRRVMIAEVPT+AIDLVEIE N+SVL+DEFIAH
Sbjct: 1 PRVEITELTDDKVKFILENTDLSVANSLRRVMIAEVPTLAIDLVEIEENTSVLHDEFIAH 60
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPLTS+ + CD D C+ CSVE L KC DQT +VTS+DL SS
Sbjct: 61 RLGLIPLTSDDVDEFLYYSRD--CDCDEFCDKCSVELTLDVKCTGDQTREVTSRDLVSS- 117
Query: 130 HSVVPVDFVDPAGYDSTD--QQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVT 187
V P DS D ++ GI+IVKLR+GQEL+LR IA+KGIGK+HAKWSP A VT
Sbjct: 118 GPKVNDVVPVPIRNDSEDNGEEDGILIVKLRKGQELKLRCIAKKGIGKEHAKWSPTAAVT 177
Query: 188 FMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKK 247
F Y+P+ + L E+K+ W +S A +
Sbjct: 178 FEYDPDNALRHTDYWYLEDEDKE-WPKS-------------------ENACIEEPPE--- 214
Query: 248 AEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDT 302
K L +I AK D F F VESTGA+ Q+VL+ +E+LK+KL ++L
Sbjct: 215 -----KDALFDIDAKPDKFYFNVESTGALPPEQIVLSGLEILKKKLADLQLQLSE 264
>gnl|CDD|214766 smart00662, RPOLD, RNA polymerases D. DNA-directed RNA polymerase
subunit D and bacterial alpha chain.
Length = 224
Score = 235 bits (602), Expect = 2e-77
Identities = 93/277 (33%), Positives = 127/277 (45%), Gaps = 54/277 (19%)
Query: 22 AKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERA 81
AKF L ++ANALRRV+++ VP +A+ V IE N+S + DE +AHRLGL PL S+
Sbjct: 1 AKFVLEPYGLTLANALRRVLLSSVPGMAVTSVYIEGNTSGVQDEVLAHRLGLKPLASDPD 60
Query: 82 MSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYS-SDHSVVPVDFVDP 140
C+ + CE CSV L K +VT+ DL S SD V V+
Sbjct: 61 GDEYQ----RDCECEEGCEKCSVTLTLDVKGPG----EVTAGDLKSDSDPDVEIVN---- 108
Query: 141 AGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINEDL 200
I I KLR GQEL L A A KG G HAKWSP +TV + Y P I ++
Sbjct: 109 ---------PDIPIAKLREGQELELEARAEKGRGYVHAKWSPVSTVEYRYIPRIPVD--- 156
Query: 201 MESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIY 260
S S ++ ++ P V D +
Sbjct: 157 -ASFSPVDRVAYQVECPRVVQRTDC----------------------------CRECDEG 187
Query: 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVR 297
+ D IF VE+ G++K + VL A ++LK+KL+A
Sbjct: 188 EEYDKLIFDVETNGSLKPEEAVLEAAKILKEKLEAFV 224
>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 = 219 bits (560), Expect = 4e-70
Identities = 106/305 (34%), Positives = 157/305 (51%), Gaps = 35/305 (11%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
K++I L D+ +F+L DAS+ANA RR+++AEVPT+AI+ V I N+SV+ DE +AHR
Sbjct: 2 KIEIISLSDEELEFDLIGVDASIANAFRRILLAEVPTMAIEKVYIYNNTSVIQDEVLAHR 61
Query: 71 LGLIPLTSE-RAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCH--SDQTLDVTSKDLYS 127
LGLIP+ ++ R R D + + + ++ F L+ KC + D T D
Sbjct: 62 LGLIPIKADPRLFEYREDSDDEPTEEN------TLVFELKVKCTRNPNAPKDSTDPDELY 115
Query: 128 SDHSVVPVDFV-DPAGYDSTDQQRG------------IIIVKLRRGQELRLRAIARKGIG 174
+H V D P G Q++ I+I KLR GQE+ L KGIG
Sbjct: 116 INHKVYSGDLKWVPIG----SQEKRFADNPIRPVHPDILIAKLRPGQEIDLELHCVKGIG 171
Query: 175 KDHAKWSPAATVTFMYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTG--QVYV 232
KDHAK+SP AT ++ PEI + + + E+ + + P V DI+ G + V
Sbjct: 172 KDHAKFSPVATASYRLLPEITLLKPITG----EDAEKLQKCFPPGVIDIEEVKGKKKAVV 227
Query: 233 VDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQK 292
+ T EV++ E K L + D FIF++ESTGA+ L L AI++LK+K
Sbjct: 228 ANPRKDTLSREVLRHEEFKDKVELGRV---RDHFIFSIESTGALPPDVLFLEAIKILKEK 284
Query: 293 LDAVR 297
+
Sbjct: 285 CRKLL 289
>gnl|CDD|234837 PRK00783, PRK00783, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 263
Score = 216 bits (553), Expect = 2e-69
Identities = 103/285 (36%), Positives = 149/285 (52%), Gaps = 32/285 (11%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
+++I EL D A+F + + ANA+RR MIA+VPT+AID V N+SVL DE +AH
Sbjct: 1 MEIEILELDDRSARFVVEGVTPAFANAIRRAMIADVPTMAIDDVRFYENTSVLFDEILAH 60
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPLT++ + +C C+G+G C C+V L + V S DL SSD
Sbjct: 61 RLGLIPLTTD-LDKYKPPEECT-CEGEG-CPDCTVTLSLEVE----GPKTVYSGDLKSSD 113
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
V PVD I IVKL+ GQ+L L A AR G GK+HAKW P + +
Sbjct: 114 PDVKPVD-------------PNIPIVKLKEGQKLVLEAYARLGRGKEHAKWQPGSACGYK 160
Query: 190 YEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
Y P I ++ED +E + VE+ P V ++ + V D + +
Sbjct: 161 YYPRIEVSED------CDECEKCVEACPRGVLELKEGK--LVVTDLLNCSLCKLCERACP 212
Query: 250 AMGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
+ + E+ FIFTVES G++ +++L A+++LK+K D
Sbjct: 213 G----KAIRVSDDENKFIFTVESDGSLPVEEILLEALKILKRKAD 253
>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 = 207 bits (528), Expect = 9e-66
Identities = 106/284 (37%), Positives = 145/284 (51%), Gaps = 32/284 (11%)
Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHR 70
++++ EL DD A+F L + ANA+RR +I+EVPT+AID V I N+SVL DE +AHR
Sbjct: 2 EIEVLELDDDRARFVLEGVPPAFANAIRRAIISEVPTLAIDDVNIYENTSVLFDEMLAHR 61
Query: 71 LGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDH 130
LGLIPL ++ + + R +C G G C C+V L + V S DL SSD
Sbjct: 62 LGLIPLRTD--LDLYKYRSECSCGGAG-CPLCTVTLTLSVEGPG----TVYSGDLKSSDP 114
Query: 131 SVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMY 190
V PV YD+ I IVKL +GQ+L L A AR G GK+HAKW P + Y
Sbjct: 115 DVKPV-------YDN------IPIVKLGKGQKLVLEAYARLGRGKEHAKWQPTTACGYKY 161
Query: 191 EPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEA 250
P I I+ED VE P V +++ D + K E
Sbjct: 162 YPVIEIDEDCDGCGKC------VEECPRGVLELEEG------KVVVEDLEDCSLCKLCER 209
Query: 251 MGKPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
G + + ED FIF VES G++ +++L A+ +LK+K D
Sbjct: 210 ACDAGAIRVGWDEDRFIFEVESDGSLPPKEILLEALRILKEKAD 253
>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 = 159 bits (403), Expect = 1e-47
Identities = 87/183 (47%), Positives = 114/183 (62%), Gaps = 9/183 (4%)
Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAH 69
P+VKIRE D F L D +MANALRRVMIAEVPT+A+D VE+E N+SVL DE +AH
Sbjct: 1 PQVKIREADKDNVDFILSGVDLAMANALRRVMIAEVPTMAVDSVEVETNTSVLADEILAH 60
Query: 70 RLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSD 129
RLGLIPL S + + S + D C+ + C+ CSV L+A S+ T +V SKDL
Sbjct: 61 RLGLIPLQSMDILQLYRSPEED-CECEDHCDKCSVVLTLQAFAESESTTNVYSKDLVI-- 117
Query: 130 HSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFM 189
V G+ I+I KLR+GQE++L +A+KGIGK+HAK+ P A + F
Sbjct: 118 ---VSNLMGRNIGHPIIQ---DILICKLRKGQEIKLTCVAKKGIGKEHAKFGPVAAIEFR 171
Query: 190 YEP 192
Y+P
Sbjct: 172 YDP 174
Score = 38.7 bits (90), Expect = 0.001
Identities = 12/37 (32%), Positives = 22/37 (59%)
Query: 257 VEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKL 293
D++I VES G++ Q+V+ AI+ L++K+
Sbjct: 170 FRYDPVADTYIMNVESVGSLPPDQVVVEAIKTLQKKV 206
>gnl|CDD|223280 COG0202, RpoA, DNA-directed RNA polymerase, alpha subunit/40 kD
subunit [Transcription].
Length = 317
Score = 134 bits (340), Expect = 3e-37
Identities = 66/298 (22%), Positives = 105/298 (35%), Gaps = 49/298 (16%)
Query: 11 KVKIRELKDDYAKFEL----RDTDASMANALRRVMIAEVPTIAIDLVEIEV------NSS 60
KVKI EL D YAKF + R ++ NALRRV+++ +P A+ VEI+ +
Sbjct: 6 KVKIEELSDTYAKFVIEPLERGFGVTLGNALRRVLLSSIPGAAVTAVEIDGVLHEFDSIE 65
Query: 61 VLNDEFIAHRLGLIPLTS------ERAMSMRFSRDCDACDGDGQCEFCSVE--------F 106
+ ++ +AHRL L PL E + + + D +E
Sbjct: 66 GVQEDVLAHRLNLKPLAVKLDGDEEVTLELDKEGPGEVTASDITVPL-DLEVVNPDHVIA 124
Query: 107 HLRAKCHSDQTLDVTSKDLYSS----DHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQE 162
L + L V S D Y PV + +R+ Q
Sbjct: 125 TLTEDAKLEMELRVYSGDGYVPAEGNREDDPPVGPIAV----------DAPFSPVRKVQY 174
Query: 163 LRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHI-----NEDLMESLSLEEKQSWVESSP 217
+ A +G KDH KW P + E + I E L + L K VE
Sbjct: 175 IVEEARVGQGTDKDHLKWEPETNGSIRPEEALAIAAKILIEHLEVFVELCPKA--VEIEE 232
Query: 218 TKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKPGLVEIYAKEDSFIFTVESTGA 275
K + + + + +K+ G + E+ + + + VE+ G
Sbjct: 233 EKPEFPILLVLEAPIDELDLSVRSYNCLKRE---GIETIGELVQRTEEELLKVENLGK 287
>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 = 82.7 bits (205), Expect = 9e-20
Identities = 42/114 (36%), Positives = 54/114 (47%), Gaps = 21/114 (18%)
Query: 67 IAHRLGLIPLTSERAMS-MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDL 125
+AH GLIP SE + + ++ C +G CE CSV L K +VT+ DL
Sbjct: 6 VAHEFGLIPGVSEDVLEIILNLKEL-VCKIEG-CEECSVTLTLDVKG----PGEVTAGDL 59
Query: 126 YSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAK 179
S D V V+ I+I LR+GQEL L A A+KG G HAK
Sbjct: 60 ES-DPDVEIVN-------------PDILIATLRKGQELELEAYAKKGRGYVHAK 99
>gnl|CDD|237878 PRK14979, PRK14979, DNA-directed RNA polymerase subunit D;
Provisional.
Length = 195
Score = 83.7 bits (207), Expect = 3e-19
Identities = 68/224 (30%), Positives = 94/224 (41%), Gaps = 49/224 (21%)
Query: 23 KFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAM 82
KF L+ S ++ALRR+MI+EVPT AI+ V NSS + DE +AHRLGLIP+ +
Sbjct: 17 KFSLK-APISFSSALRRIMISEVPTYAIENVYFYENSSSMYDEILAHRLGLIPIKGKPVS 75
Query: 83 S---MRFSRDCDACDGDGQCEFCSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVD 139
+ F+ +G C V S DL S + V
Sbjct: 76 GDEVITFT-----LSKEGPCT-------------------VYSSDLKSENGEV------- 104
Query: 140 PAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDHAKWSPAATVTFMYEPEIHINED 199
+ + I IVKL GQ+L + A G GK HAKW P V Y+ I+ D
Sbjct: 105 --AFKN------IPIVKLAEGQKLEIECEALVGTGKIHAKWQPCNAV---YK---QISND 150
Query: 200 LMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDE 243
+E Q E +I N + ++ + E DE
Sbjct: 151 EVEFKVESFGQMDAEDILRSALEILKNKAEKFLQELEGIELSDE 194
Score = 32.5 bits (74), Expect = 0.16
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 12/73 (16%)
Query: 247 KAEAMGKPGLVEIYAK------------EDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
+ E G +I+AK D F VES G + A ++ +A+E+LK K +
Sbjct: 121 EIECEALVGTGKIHAKWQPCNAVYKQISNDEVEFKVESFGQMDAEDILRSALEILKNKAE 180
Query: 295 AVRLSEDTVEADD 307
+ +E D
Sbjct: 181 KFLQELEGIELSD 193
>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 = 53.4 bits (129), Expect = 2e-09
Identities = 15/35 (42%), Positives = 24/35 (68%)
Query: 22 AKFELRDTDASMANALRRVMIAEVPTIAIDLVEIE 56
+F L D ++ NALRRV++++VP +AI V+I
Sbjct: 1 IEFLLEGEDHTLGNALRRVLLSDVPGVAIAGVKIP 35
Score = 43.4 bits (103), Expect = 8e-06
Identities = 11/39 (28%), Positives = 22/39 (56%)
Query: 256 LVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLD 294
+V + D I +E+ G+I + + A+++L +KLD
Sbjct: 50 VVGVGTDYDKLILRIETDGSITPEEALKEALKILIEKLD 88
>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 = 32.8 bits (75), Expect = 0.035
Identities = 12/32 (37%), Positives = 21/32 (65%)
Query: 12 VKIRELKDDYAKFELRDTDASMANALRRVMIA 43
VKI E + +Y F L + D ++ N+LRR+++
Sbjct: 1 VKILEKEKNYVDFVLENEDHTLGNSLRRILLK 32
Score = 32.8 bits (75), Expect = 0.037
Identities = 12/44 (27%), Positives = 25/44 (56%)
Query: 253 KPGLVEIYAKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAV 296
+ + ED FI +E+ G+I + + A+E+L++KL+ +
Sbjct: 43 EHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEILRKKLEHL 86
>gnl|CDD|132904 cd06928, RNAP_alpha_NTD, N-terminal domain of the Alpha subunit
of Bacterial RNA polymerase. The bacterial alpha
subunit of RNA polymerase (RNAP) consists of two
independently folded domains: an amino-terminal domain
(alphaNTD) and a carboxy-terminal domain (alphaCTD).
AlphaCTD is not required for RNAP assembly but
interacts with transcription activators. AlphaNTD is
essential in vivo and in vitro for RNAP assembly and
basal transcription. It is similar to the eukaryotic
RPB3/AC40/archaeal D subunit, and 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 alphaNTDs of plant plastid RNAP (PEP)
are also included in this subfamily. PEP is largely
responsible for the transcription of photosynthetic
genes and is closely related to the multi-subunit
bacterial RNAP, which is a large multi-subunit complex
responsible for the synthesis of all bacterial RNAs.
The bacterial RNAP core enzyme consists of four
subunits (beta', beta, alpha and omega). All residues
in the alpha subunit that is involved in dimerization
or in the interaction with other subunits are located
within alphaNTD.
Length = 215
Score = 32.4 bits (75), Expect = 0.22
Identities = 16/49 (32%), Positives = 29/49 (59%), Gaps = 4/49 (8%)
Query: 12 VKIRELKDDYAKFEL----RDTDASMANALRRVMIAEVPTIAIDLVEIE 56
K+ +++Y +F + R ++ NALRRV+++ +P AI V+IE
Sbjct: 1 SKVENKRENYGRFVIEPLERGQGTTLGNALRRVLLSSLPGAAITAVKIE 49
>gnl|CDD|233037 TIGR00592, pol2, DNA polymerase (pol2). All proteins in this
superfamily for which functions are known are DNA
polymerases.This family is based on the phylogenomic
analysis of JA Eisen (1999, Ph.D. Thesis, Stanford
University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 1172
Score = 31.9 bits (72), Expect = 0.46
Identities = 18/75 (24%), Positives = 26/75 (34%), Gaps = 5/75 (6%)
Query: 189 MYEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKA 248
P I NE + +L + + + P +D+ P G + E K
Sbjct: 515 SLNPSIIRNEIVSIPDTLHREFALDKPPPEPPYDVHPCVGTRPKDCSFPLDLKGEFPGK- 573
Query: 249 EAMGKPGLVEIYAKE 263
KP LVE A E
Sbjct: 574 ----KPSLVEDLATE 584
>gnl|CDD|199908 cd10719, DnaJ_zf, Zinc finger domain of DnaJ and HSP40.
Central/middle or CxxCxGxG-motif containing domain of
DnaJ/Hsp40 (heat shock protein 40). DnaJ proteins are
highly conserved and play crucial roles in protein
translation, folding, unfolding, translocation, and
degradation. They act primarily by stimulating the
ATPase activity of Hsp70s, an important chaperonin
family. Hsp40 proteins are characterized by the presence
of an N-terminal J domain, which mediates the
interaction with Hsp70. This central domain contains
four repeats of a CxxCxGxG motif and binds to two Zinc
ions. It has been implicated in substrate binding.
Length = 65
Score = 28.4 bits (64), Expect = 0.76
Identities = 6/27 (22%), Positives = 8/27 (29%), Gaps = 5/27 (18%)
Query: 82 MSMRFSRDCDACDGDGQ-----CEFCS 103
+ C C G G+ C C
Sbjct: 36 GFFQTQTTCPTCGGTGKIIKDPCPKCK 62
>gnl|CDD|216058 pfam00684, DnaJ_CXXCXGXG, DnaJ central domain. The central
cysteine-rich (CR) domain of DnaJ proteins contains four
repeats of the motif CXXCXGXG where X is any amino acid.
The isolated cysteine rich domain folds in zinc
dependent fashion. Each set of two repeats binds one
unit of zinc. Although this domain has been implicated
in substrate binding, no evidence of specific
interaction between the isolated DNAJ cysteine rich
domain and various hydrophobic peptides has been found.
Length = 65
Score = 28.5 bits (64), Expect = 0.88
Identities = 6/26 (23%), Positives = 10/26 (38%), Gaps = 5/26 (19%)
Query: 82 MSMRFSRDCDACDGDGQ-----CEFC 102
+ + C C G G+ C+ C
Sbjct: 36 GVFQMQQTCPKCGGTGKIIKDPCKVC 61
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet known
if PHD fingers have a common molecular function. Several
reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is a
ubiquitin ligase have been refuted as these domains were
RING fingers misidentified as PHD fingers.
Length = 47
Score = 27.6 bits (61), Expect = 1.0
Identities = 9/40 (22%), Positives = 13/40 (32%), Gaps = 5/40 (12%)
Query: 90 CDACDGDG---QCEFCSVEFHLRAKCHSDQTLDVTSKDLY 126
C D G QC+ C +H C L+ +
Sbjct: 5 CGKPDDGGELLQCDGCDRWYH--QTCLGPPLLEEEPDGKW 42
>gnl|CDD|236285 PRK08554, PRK08554, peptidase; Reviewed.
Length = 438
Score = 29.7 bits (67), Expect = 2.3
Identities = 19/74 (25%), Positives = 34/74 (45%), Gaps = 2/74 (2%)
Query: 103 SVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDF--VDPAGYDSTDQQRGIIIVKLRRG 160
++ +RA +S + ++ T K++ + V+ + AGY T I+ V LR
Sbjct: 313 VLKLDIRAMSYSKEDIERTLKEVLEFNLPEAEVEIRTNEKAGYLFTPPDEEIVKVALRVL 372
Query: 161 QELRLRAIARKGIG 174
+EL A +G G
Sbjct: 373 KELGEDAEPVEGPG 386
>gnl|CDD|224172 COG1252, Ndh, NADH dehydrogenase, FAD-containing subunit [Energy
production and conversion].
Length = 405
Score = 29.5 bits (67), Expect = 2.7
Identities = 25/87 (28%), Positives = 39/87 (44%), Gaps = 17/87 (19%)
Query: 219 KVFDIDPNTGQVYVVDAEAYTYDDEVIKKAEAMG-------KPGLVEIYAKEDSFIFTVE 271
+V DID + +V + D +YD V+ A+G PG E YA + T+E
Sbjct: 79 EVTDIDRDAKKVTLADLGEISYDYLVV----ALGSETNYFGIPGAAE-YA---FGLKTLE 130
Query: 272 STGAIKASQLVLNAIEVLKQKLDAVRL 298
A++ + +L A E Q+ D L
Sbjct: 131 --DALRLRRHLLEAFEKASQEEDDRAL 155
>gnl|CDD|181918 PRK09508, leuO, leucine transcriptional activator; Reviewed.
Length = 314
Score = 28.4 bits (64), Expect = 5.5
Identities = 23/63 (36%), Positives = 30/63 (47%), Gaps = 11/63 (17%)
Query: 100 EFCSV-----EFHLRA-KCHSDQTLDVTSKDLYSSDHSVVPVD----FVDPAGYDSTDQQ 149
EF SV E L A K H +T + LY+ H+VV +D F P YD+ D+Q
Sbjct: 175 EFTSVPLFKDELVLVASKNHPRIKGPITEEQLYNEQHAVVSLDRFASFSQPW-YDTVDKQ 233
Query: 150 RGI 152
I
Sbjct: 234 ASI 236
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain. Cadherins
are glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium. They
play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing proteins
exist as monomers, homodimers, or heterodimers.
Length = 98
Score = 26.9 bits (60), Expect = 5.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 213 VESSPTKVFDIDPNTGQVYVV 233
V + +F IDP+TG++
Sbjct: 37 VSGNEDGLFSIDPSTGEITTA 57
>gnl|CDD|107202 cd00640, Trp-synth-beta_II, Tryptophan synthase beta superfamily
(fold type II); this family of pyridoxal phosphate
(PLP)-dependent enzymes catalyzes beta-replacement and
beta-elimination reactions. This CD corresponds to
aminocyclopropane-1-carboxylate deaminase (ACCD),
tryptophan synthase beta chain (Trp-synth_B),
cystathionine beta-synthase (CBS), O-acetylserine
sulfhydrylase (CS), serine dehydratase (Ser-dehyd),
threonine dehydratase (Thr-dehyd), diaminopropionate
ammonia lyase (DAL), and threonine synthase (Thr-synth).
ACCD catalyzes the conversion of
1-aminocyclopropane-1-carboxylate to alpha-ketobutyrate
and ammonia. Tryptophan synthase folds into a tetramer,
where the beta chain is the catalytic PLP-binding
subunit and catalyzes the formation of L-tryptophan from
indole and L-serine. CBS is a tetrameric hemeprotein
that catalyzes condensation of serine and homocysteine
to cystathionine. CS is a homodimer that catalyzes the
formation of L-cysteine from O-acetyl-L-serine.
Ser-dehyd catalyzes the conversion of L- or D-serine to
pyruvate and ammonia. Thr-dehyd is active as a homodimer
and catalyzes the conversion of L-threonine to
2-oxobutanoate and ammonia. DAL is also a homodimer and
catalyzes the alpha, beta-elimination reaction of both
L- and D-alpha, beta-diaminopropionate to form pyruvate
and ammonia. Thr-synth catalyzes the formation of
threonine and inorganic phosphate from
O-phosphohomoserine.
Length = 244
Score = 27.9 bits (63), Expect = 6.2
Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 7/55 (12%)
Query: 245 IKKAEAMGKPGLVEIYAKEDSFIFTVESTGAIK---ASQLVLNAIEVLKQKLDAV 296
+ + + + K G IY K + TG+ K A L+L A E K +
Sbjct: 3 LVRLKRLSKLGGANIYLKLEFL----NPTGSFKDRGALNLILLAEEEGKLPKGVI 53
>gnl|CDD|216913 pfam02169, LPP20, LPP20 lipoprotein. This family contains the
LPP20 lipoprotein, which is a non-essential class of
lipoprotein.
Length = 91
Score = 26.5 bits (59), Expect = 6.8
Identities = 11/47 (23%), Positives = 19/47 (40%), Gaps = 1/47 (2%)
Query: 21 YAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSSVLNDEFI 67
YA A+ +A R + +V I V++SVL + +
Sbjct: 15 YAVGSAPSLRAAKLDAYRE-LAEQVYGQVISSQSTTVSNSVLTSDSV 60
>gnl|CDD|202093 pfam02023, SCAN, SCAN domain. The SCAN domain (named after
SRE-ZBP, CTfin51, AW-1 and Number 18 cDNA) is found in
several pfam00096 proteins. The domain has been shown to
be able to mediate homo- and hetero-oligomerisation.
Length = 93
Score = 26.4 bits (59), Expect = 6.8
Identities = 13/32 (40%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 192 PEIHINEDLMESLSLE--------EKQSWVES 215
PEIH E ++E L LE E Q+WV+
Sbjct: 38 PEIHTKEQILELLVLEQFLTILPEELQAWVQE 69
>gnl|CDD|111929 pfam03088, Str_synth, Strictosidine synthase. Strictosidine
synthase (E.C. 4.3.3.2) is a key enzyme in alkaloid
biosynthesis. It catalyzes the condensation of
tryptamine with secologanin to form strictosidine.
Length = 89
Score = 26.2 bits (58), Expect = 8.5
Identities = 11/33 (33%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 222 DIDPNTGQVYVVDAEAYTYDDEVIKKAEAMGKP 254
D+DP TG +Y D+ + YD + A G
Sbjct: 4 DVDPETGVLYFTDS-SSRYDRRQVIFAMLEGDK 35
>gnl|CDD|237150 PRK12608, PRK12608, transcription termination factor Rho;
Provisional.
Length = 380
Score = 27.7 bits (62), Expect = 9.3
Identities = 18/51 (35%), Positives = 26/51 (50%), Gaps = 5/51 (9%)
Query: 127 SSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRLRAIARKGIGKDH 177
S D S+ VD V P G QRG+I+ R G+ + L+ IA + +H
Sbjct: 116 SDDLSMRVVDLVAPIGKG----QRGLIVAPPRAGKTVLLQQIAA-AVAANH 161
>gnl|CDD|219030 pfam06441, EHN, Epoxide hydrolase N terminus. This family
represents the N-terminal region of the eukaryotic
epoxide hydrolase protein. Epoxide hydrolases
(EC:3.3.2.3) comprise a group of functionally related
enzymes that catalyze the addition of water to oxirane
compounds (epoxides), thereby usually generating vicinal
trans-diols. EHs have been found in all types of living
organisms, including mammals, invertebrates, plants,
fungi and bacteria. In animals, the major interest in EH
is directed towards their detoxification capacity for
epoxides since they are important safeguards against the
cytotoxic and genotoxic potential of oxirane derivatives
that are often reactive electrophiles because of the
high tension of the three-membered ring system and the
strong polarization of the C--O bonds. This is of
significant relevance because epoxides are frequent
intermediary metabolites which arise during the
biotransformation of foreign compounds. This family is
often found in conjunction with pfam00561.
Length = 108
Score = 26.3 bits (59), Expect = 9.3
Identities = 6/25 (24%), Positives = 13/25 (52%)
Query: 286 IEVLKQKLDAVRLSEDTVEADDQFG 310
++ LK++L R ++ D +G
Sbjct: 11 LDDLKRRLALTRWPDEETVPDWSYG 35
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 0.134 0.379
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: 16,489,810
Number of extensions: 1606152
Number of successful extensions: 1582
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1554
Number of HSP's successfully gapped: 45
Length of query: 319
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 222
Effective length of database: 6,635,264
Effective search space: 1473028608
Effective search space used: 1473028608
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: 59 (26.4 bits)