RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3022
(258 letters)
>gnl|CDD|132720 cd02584, RNAP_II_Rpb1_C, Largest subunit (Rpb1) of Eukaryotic RNA
polymerase II (RNAP II), C-terminal domain. RNA
polymerase II (RNAP II) is a large multi-subunit complex
responsible for the synthesis of mRNA. RNAP II consists
of a 10-subunit core enzyme and a peripheral heterodimer
of two subunits. The largest core subunit (Rpb1) of
yeast RNAP II is the best characterized member of this
family. Structure studies suggest that RNAP complexes
from different organisms share a crab-claw-shape
structure. In yeast, Rpb1 and Rpb2, the largest and the
second largest subunits, each makes up one clamp, one
jaw, and part of the cleft. Rpb1 interacts with Rpb2 to
form the DNA entry and RNA exit channels in addition to
the catalytic center of RNA synthesis. The C-terminal
domain of Rpb1 makes up part of the foot and jaw
structures.
Length = 410
Score = 203 bits (520), Expect = 1e-63
Identities = 65/91 (71%), Positives = 75/91 (82%)
Query: 132 AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPS 191
+ PGEMVG +AAQS+GEPATQMTLNTFHFAGVS+KNVTLGVPRLKEIIN++K K PS
Sbjct: 22 SLVHPGEMVGTIAAQSIGEPATQMTLNTFHFAGVSAKNVTLGVPRLKEIINVAKNIKTPS 81
Query: 192 LTVFLTGQAARDAEKAKNVLCRLEHTTLRKV 222
LTV+L A+D EKAK + RLEHTTL+ V
Sbjct: 82 LTVYLEPGFAKDEEKAKKIQSRLEHTTLKDV 112
>gnl|CDD|236292 PRK08566, PRK08566, DNA-directed RNA polymerase subunit A';
Validated.
Length = 882
Score = 181 bits (463), Expect = 2e-52
Identities = 67/123 (54%), Positives = 91/123 (73%)
Query: 4 LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
L++T E ++ ++L ARD+ G A+K L N M G++GS +N++Q+ ACVGQQ+
Sbjct: 693 LEETLEMKIMQVLGKARDEAGEIAEKYLGLDNPAVIMARTGARGSMLNLTQMAACVGQQS 752
Query: 64 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
V G+RI G+R RTLPHF D G E+RGFV +SY +GLTP+EFFFHAMGGREGL+DTAV
Sbjct: 753 VRGERIRRGYRDRTLPHFKPGDLGAEARGFVRSSYKSGLTPTEFFFHAMGGREGLVDTAV 812
Query: 124 KTA 126
+T+
Sbjct: 813 RTS 815
>gnl|CDD|233843 TIGR02390, RNA_pol_rpoA1, DNA-directed RNA polymerase subunit A'.
This family consists of the archaeal A' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein.
Length = 867
Score = 167 bits (425), Expect = 3e-47
Identities = 62/125 (49%), Positives = 89/125 (71%)
Query: 4 LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
+++T E ++ +L ARD+ G A+K L N+ M G++GS +NI+Q+ A VGQQ+
Sbjct: 687 VEETLEMKIMEVLGKARDEAGEVAEKYLDPENHAVIMARTGARGSLLNITQMAAMVGQQS 746
Query: 64 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
V G RI G+R RTLPHF K D G ++RGFV +S+ GL P+E+FFHA GGREGL+DTAV
Sbjct: 747 VRGGRIRRGYRNRTLPHFKKGDIGAKARGFVRSSFKKGLDPTEYFFHAAGGREGLVDTAV 806
Query: 124 KTAET 128
+T+++
Sbjct: 807 RTSQS 811
>gnl|CDD|218372 pfam05000, RNA_pol_Rpb1_4, RNA polymerase Rpb1, domain 4. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 4, represents the funnel domain. The
funnel contain the binding site for some elongation
factors.
Length = 108
Score = 145 bits (368), Expect = 1e-44
Identities = 59/93 (63%), Positives = 68/93 (73%)
Query: 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQ 61
+ L++TFE +N ILN ARD G A KSL N++ M +G+KGS INISQ+ C GQ
Sbjct: 16 MTLEETFEALINNILNKARDPAGNIASKSLDPNNSIYMMADSGAKGSIINISQIAGCRGQ 75
Query: 62 QNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFV 94
QNVEGKRIPFGF RTLPHF KDD GPESRGFV
Sbjct: 76 QNVEGKRIPFGFSGRTLPHFKKDDEGPESRGFV 108
>gnl|CDD|147266 pfam04998, RNA_pol_Rpb1_5, RNA polymerase Rpb1, domain 5. RNA
polymerases catalyze the DNA dependent polymerisation of
RNA. Prokaryotes contain a single RNA polymerase
compared to three in eukaryotes (not including
mitochondrial. and chloroplast polymerases). This
domain, domain 5, represents the discontinuous cleft
domain that is required to from the central cleft or
channel where the DNA is bound.
Length = 447
Score = 145 bits (369), Expect = 5e-41
Identities = 54/96 (56%), Positives = 63/96 (65%)
Query: 131 NAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 190
+ PGE VG +AAQS+GEP TQMTLNTFHFAGV+SKNVTLGVPRLKEIIN++K K P
Sbjct: 149 RSLVEPGEAVGIIAAQSIGEPGTQMTLNTFHFAGVASKNVTLGVPRLKEIINVAKNNKKP 208
Query: 191 SLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVLYII 226
+TV L D + K L+KV II
Sbjct: 209 VITVLLIKNIVSDKARVKKQREEKTLLLLKKVTIII 244
Score = 74.3 bits (183), Expect = 3e-15
Identities = 26/28 (92%), Positives = 26/28 (92%)
Query: 101 GLTPSEFFFHAMGGREGLIDTAVKTAET 128
GLTP EFFFH MGGREGLIDTAVKTAET
Sbjct: 1 GLTPQEFFFHTMGGREGLIDTAVKTAET 28
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 141 bits (358), Expect = 3e-38
Identities = 38/125 (30%), Positives = 61/125 (48%), Gaps = 6/125 (4%)
Query: 4 LKQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQN 63
+ + E L +A + + + G G+ +NISQ++ +GQQ
Sbjct: 631 IVEIIEVLGIEALRNAIIEEIKITLEEQGLDFV--DIRHMGLSGARMNISQIVQLIGQQG 688
Query: 64 VEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAV 123
V G++I F E+ G E+S+L GLT +E+F H +GGR GL+DTA+
Sbjct: 689 VMGEKISVL----ARAAFEVTVKHLEAEGPGESSFLEGLTENEYFGHPIGGRTGLVDTAL 744
Query: 124 KTAET 128
KTA++
Sbjct: 745 KTADS 749
Score = 59.9 bits (146), Expect = 3e-10
Identities = 29/94 (30%), Positives = 48/94 (51%), Gaps = 3/94 (3%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAG--VSSKNVTLGVPRLKEIINISKKPKAPSLT 193
G AA++ G TQM + T H+ G V+ T+G P L I++ +K P P
Sbjct: 413 HVPASGEAAAEARGLMGTQMNILTPHYGGPIVAPIQDTVGGPYLLTIVD-AKLPSTPVGE 471
Query: 194 VFLTGQAARDAEKAKNVLCRLEHTTLRKVLYIIL 227
++L + A D EKA+ + ++E TT + ++ I
Sbjct: 472 IYLKDEYADDREKAEAIAKKIELTTGKVIVSTIS 505
>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
polymerase III (RNAP III), C-terminal domain.
Eukaryotic RNA polymerase III (RNAP III) is a large
multi-subunit complex responsible for the synthesis of
tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is
also known as C160 in yeast. Structure studies suggest
that different RNA polymerase complexes share a similar
crab-claw-shape structure. The C-terminal domain of
Rpb1, the largest subunit of RNAP II, makes up part of
the foot and jaw structures of RNAP II. The similarity
between this domain and the C-terminal domain of Rpb1,
its counterpart in RNAP II, suggests a similar
functional and structural role.
Length = 300
Score = 125 bits (317), Expect = 1e-34
Identities = 53/92 (57%), Positives = 63/92 (68%), Gaps = 2/92 (2%)
Query: 131 NAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 190
AK PG VGA+AAQS+GEP TQMTL TFHFAGV+S N+TLGVPR+KEIIN SK P
Sbjct: 4 RAKVEPGTAVGAIAAQSIGEPGTQMTLKTFHFAGVASMNITLGVPRIKEIINASKNISTP 63
Query: 191 SLTVFLTGQAARDAEKAKNVLCRLEHTTLRKV 222
+T L RD + A+ V R+E T L +V
Sbjct: 64 IITAKLEND--RDEKSARIVKGRIEKTYLGEV 93
>gnl|CDD|132725 cd06528, RNAP_A'', A'' subunit of Archaeal RNA Polymerase (RNAP).
Archaeal RNA polymerase (RNAP), like bacterial RNAP, is
a large multi-subunit complex responsible for the
synthesis of all RNAs in the cell. The relative
positioning of the RNAP core is highly conserved between
archaeal RNAP and the three classes of eukaryotic RNAPs.
In archaea, the largest subunit is split into two
polypeptides, A' and A'', which are encoded by separate
genes in an operon. Sequence alignments reveal that the
archaeal A'' subunit corresponds to the C-terminal
one-third of the RNAPII largest subunit (Rpb1). In
subunit A'', several loops in the jaw domain are
shorter. The RNAPII Rpb1 interacts with the
second-largest subunit (Rpb2) to form the DNA entry and
RNA exit channels in addition to the catalytic center of
RNA synthesis.
Length = 363
Score = 124 bits (314), Expect = 1e-33
Identities = 47/93 (50%), Positives = 65/93 (69%)
Query: 131 NAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 190
+ PGE VG +AAQS+GEP TQMTL TFH+AGV+ NVTLG+PRL EI++ K+P P
Sbjct: 34 RSLIEPGEAVGIVAAQSIGEPGTQMTLRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTP 93
Query: 191 SLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
++T++L + D EKA+ V ++E TTL +
Sbjct: 94 TMTIYLEEEYKYDREKAEEVARKIEETTLENLA 126
>gnl|CDD|132722 cd02735, RNAP_I_Rpa1_C, Largest subunit (Rpa1) of Eukaryotic RNA
polymerase I (RNAP I), C-terminal domain. RNA
polymerase I (RNAP I) is a multi-subunit protein complex
responsible for the synthesis of rRNA precursor. It
consists of at least 14 different subunits, and the
largest one is homologous to subunit Rpb1 of yeast RNAP
II and subunit beta' of bacterial RNAP. Rpa1 is also
known as Rpa190 in yeast. Structure studies suggest that
different RNAP complexes share a similar crab-claw-shape
structure. The C-terminal domain of Rpb1, the largest
subunit of RNAP II, makes up part of the foot and jaw
structures of RNAP II. The similarity between this
domain and the C-terminal domain of Rpb1, its
counterpart in RNAP II, suggests a similar functional
and structural role.
Length = 309
Score = 121 bits (305), Expect = 9e-33
Identities = 51/96 (53%), Positives = 63/96 (65%), Gaps = 5/96 (5%)
Query: 130 CNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEII-NISKKPK 188
+ PGE VG LAAQS+GEP+TQMTLNTFHFAG NVTLG+PRL+EI+ SK K
Sbjct: 3 MRSLVEPGEAVGLLAAQSIGEPSTQMTLNTFHFAGRGEMNVTLGIPRLREILMTASKNIK 62
Query: 189 APSLTV-FLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
PS+T+ G++A AE K L R+ TL V+
Sbjct: 63 TPSMTLPLKNGKSAERAETLKKRLSRV---TLSDVV 95
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 121 bits (305), Expect = 3e-32
Identities = 47/84 (55%), Positives = 63/84 (75%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 195
PGE VG +AAQS+GEP TQMT+ TFH+AGV+ NVTLG+PRL EI++ K+P P +T++
Sbjct: 58 PGEAVGVVAAQSIGEPGTQMTMRTFHYAGVAEINVTLGLPRLIEIVDARKEPSTPMMTIY 117
Query: 196 LTGQAARDAEKAKNVLCRLEHTTL 219
L + A D EKA+ V ++E TTL
Sbjct: 118 LKDEYAYDREKAEEVARKIEATTL 141
>gnl|CDD|233842 TIGR02389, RNA_pol_rpoA2, DNA-directed RNA polymerase, subunit A''.
This family consists of the archaeal A'' subunit of the
DNA-directed RNA polymerase. The example from
Methanocaldococcus jannaschii contains an intein
[Transcription, DNA-dependent RNA polymerase].
Length = 367
Score = 120 bits (304), Expect = 3e-32
Identities = 48/100 (48%), Positives = 66/100 (66%)
Query: 124 KTAETACNAKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINI 183
+ E + PGE VG +AAQS+GEP TQMT+ TFH+AGV+ NVTLG+PRL EI++
Sbjct: 31 RVEEEYLRSLIDPGEAVGIVAAQSIGEPGTQMTMRTFHYAGVAELNVTLGLPRLIEIVDA 90
Query: 184 SKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
K P PS+T++L + +D EKA+ V ++E T L V
Sbjct: 91 RKTPSTPSMTIYLEDEYEKDREKAEEVAKKIEATKLEDVA 130
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 118 bits (298), Expect = 3e-30
Identities = 53/132 (40%), Positives = 77/132 (58%), Gaps = 8/132 (6%)
Query: 5 KQTFENQVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVGQQNV 64
++ E + L+ ARDK G SA + N K M G++GS N++Q+ +GQQ
Sbjct: 722 EEALEADIVNELDKARDKAGSSANDCIDADNAGKIMAKTGARGSMANLAQIAGALGQQKR 781
Query: 65 E--------GKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGRE 116
+ G R+ G++ R L HF + D P++ GFV+N+Y GL +EFFFHAMGGRE
Sbjct: 782 KTRIGFVLTGGRLHEGYKDRALSHFQEGDDNPDAHGFVKNNYREGLNAAEFFFHAMGGRE 841
Query: 117 GLIDTAVKTAET 128
GLID A +T ++
Sbjct: 842 GLIDKARRTEDS 853
Score = 94.7 bits (235), Expect = 5e-22
Identities = 35/92 (38%), Positives = 57/92 (61%)
Query: 132 AKCAPGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPS 191
AK PG+ +G ++AQS+ EP TQMTL TFH AG+ + +VT G+ R E+++ KP P+
Sbjct: 973 AKVEPGQAIGIISAQSIAEPGTQMTLRTFHAAGIKAMDVTHGLERFIELVDARAKPSTPT 1032
Query: 192 LTVFLTGQAARDAEKAKNVLCRLEHTTLRKVL 223
+ ++L + D EKA + L+ +R ++
Sbjct: 1033 MDIYLDDECKEDIEKAIEIARNLKELKVRALI 1064
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 111 bits (280), Expect = 3e-28
Identities = 48/91 (52%), Positives = 64/91 (70%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVF 195
P E VG +AAQS+GEP TQMT+ TFH+AGV+ NVTLG+PRL EI++ KKP P++T++
Sbjct: 181 PYEAVGIVAAQSIGEPGTQMTMRTFHYAGVAEMNVTLGLPRLIEIVDARKKPSTPTMTIY 240
Query: 196 LTGQAARDAEKAKNVLCRLEHTTLRKVLYII 226
L D EK + V ++E+TTL V II
Sbjct: 241 LKKDYREDEEKVREVAKKIENTTLIDVADII 271
>gnl|CDD|132719 cd00630, RNAP_largest_subunit_C, Largest subunit of RNA polymerase
(RNAP), C-terminal domain. RNA polymerase (RNAP) is a
large multi-subunit complex responsible for the
synthesis of RNA. It is the principal enzyme of the
transcription process, and is the 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. Structure studies revealed that prokaryotic
and eukaryotic RNAPs share a conserved crab-claw-shape
structure. The largest and the second largest subunits
each make up one clamp, one jaw, and part of the cleft.
The largest RNAP subunit (Rpb1) interacts with the
second-largest RNAP subunit (Rpb2) to form the DNA entry
and RNA exit channels in addition to the catalytic
center of RNA synthesis. The region covered by this
domain makes up part of the foot and jaw structures. In
archaea, some photosynthetic organisms, and some
organelles, this domain exists as a separate subunit,
while it forms the C-terminal region of the RNAP largest
subunit in eukaryotes and bacteria.
Length = 158
Score = 92.9 bits (231), Expect = 2e-23
Identities = 37/48 (77%), Positives = 42/48 (87%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINIS 184
GE VG LAAQS+GEP TQMTL TFHFAGV+S NVTLG+PRLKEI+N +
Sbjct: 1 GEAVGVLAAQSIGEPGTQMTLRTFHFAGVASMNVTLGLPRLKEILNAA 48
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 76.9 bits (189), Expect = 5e-16
Identities = 34/70 (48%), Positives = 47/70 (67%)
Query: 153 TQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLC 212
T T+ TFH+AGV+ NVTLG+PR+ EI++ K+P P +TV L G+ A D EKA+ V
Sbjct: 541 THNTMRTFHYAGVAEINVTLGLPRMIEIVDARKEPSTPIMTVHLKGEYATDREKAEEVAK 600
Query: 213 RLEHTTLRKV 222
++E TL V
Sbjct: 601 KIESLTLGDV 610
Score = 41.0 bits (96), Expect = 5e-04
Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 5/54 (9%)
Query: 109 FHAMGGREGL----IDTAVKTAETA-CNAKCAPGEMVGALAAQSLGEPATQMTL 157
F + R+G+ ++ + +A NA P E VG +AAQS+GEP TQM+L
Sbjct: 24 FEKLSKRDGVTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIGEPGTQMSL 77
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 65.1 bits (159), Expect = 6e-12
Identities = 27/55 (49%), Positives = 39/55 (70%), Gaps = 3/55 (5%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSS--KNVTLGVPRLKEIINISKKPKA 189
GE VG +AAQS+GEP TQ+T+ TFH GV+ ++T G+PR+KE+ ++ PK
Sbjct: 871 GEAVGVIAAQSIGEPGTQLTMRTFHTGGVAGASGDITQGLPRVKELFE-ARTPKD 924
Score = 44.3 bits (105), Expect = 4e-05
Identities = 36/123 (29%), Positives = 57/123 (46%), Gaps = 24/123 (19%)
Query: 10 NQVNRILNDARDKTGGSAKKSL----TEYNNLKAMVVAGSKGSNINISQVIACVGQQNVE 65
+V I ++ +DK + K L ++N + M +G++G NISQ G + +
Sbjct: 649 RKVVSIWSETKDKVTDAMMKLLKKDTYKFNPIFMMADSGARG---NISQFRQLAGMRGLM 705
Query: 66 GKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKT 125
K P G + IK +S+ GLT E+F G R+GL DTA+KT
Sbjct: 706 AK--PSG---DIIELPIK------------SSFREGLTVLEYFISTHGARKGLADTALKT 748
Query: 126 AET 128
A++
Sbjct: 749 ADS 751
>gnl|CDD|132721 cd02655, RNAP_beta'_C, Largest subunit (beta') of Bacterial
DNA-dependent RNA polymerase (RNAP), C-terminal domain.
Bacterial RNA polymerase (RNAP) is a large multi-subunit
complex responsible for the synthesis of all RNAs in the
cell. This family also includes the eukaryotic
plastid-encoded RNAP beta" subunit. Structure studies
suggest that RNAP complexes from different organisms
share a crab-claw-shape structure with two pincers
defining a central cleft. Beta' and beta, the largest
and the second largest subunits of bacterial RNAP, each
makes up one pincer and part of the base of the cleft.
The C-terminal domain includes a G loop that forms part
of the floor of the downstream DNA-binding cavity. The
position of the G loop may determine the switch of the
bridge helix between flipped-out and normal
alpha-helical conformations.
Length = 204
Score = 60.6 bits (148), Expect = 4e-11
Identities = 24/44 (54%), Positives = 36/44 (81%), Gaps = 1/44 (2%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEI 180
GE VG +AAQS+GEP TQ+T+ TFH GV++ ++T G+PR++E+
Sbjct: 6 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVAT-DITQGLPRVEEL 48
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 59.7 bits (146), Expect = 3e-10
Identities = 28/54 (51%), Positives = 39/54 (72%), Gaps = 4/54 (7%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAP 190
GE VG +AAQS+GEP TQ+T+ TFH GV ++T G+PR+ E+ ++KPK P
Sbjct: 879 GEAVGVIAAQSIGEPGTQLTMRTFHTGGV---DITGGLPRVAELFE-ARKPKGP 928
Score = 35.8 bits (84), Expect = 0.020
Identities = 15/26 (57%), Positives = 18/26 (69%)
Query: 101 GLTPSEFFFHAMGGREGLIDTAVKTA 126
GLT E+F G R+GL DTA+KTA
Sbjct: 733 GLTVLEYFISTHGARKGLADTALKTA 758
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 59.1 bits (143), Expect = 6e-10
Identities = 26/52 (50%), Positives = 37/52 (71%), Gaps = 1/52 (1%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPK 188
G VG +AAQS+GEP TQ+T+ TFH GV+ ++T G+PR+ E+ +KPK
Sbjct: 974 GTAVGIIAAQSIGEPGTQLTMRTFHSGGVAGDDITQGLPRVAELFEA-RKPK 1024
Score = 42.6 bits (100), Expect = 2e-04
Identities = 30/119 (25%), Positives = 56/119 (47%), Gaps = 22/119 (18%)
Query: 11 QVNRILNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNINISQVIACVG-QQNVEGKRI 69
QV I +A ++ G + E N + M +G++G+ I Q+ G +++G+ I
Sbjct: 762 QVVDIWTEATEEVGEAMLAGFDEDNPIYMMADSGARGNIKQIRQLAGMRGLMADMKGEII 821
Query: 70 PFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 128
LP ++ ++ GL+ E+F G R+GL+DTA++TA++
Sbjct: 822 -------DLP--------------IKANFREGLSVLEYFISTHGARKGLVDTALRTADS 859
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 54.5 bits (131), Expect = 2e-08
Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 136 PGEMVGALAAQSLGEPATQMTLNTFHFAGVSSKN 169
PGE VG +AAQS+GEP TQ+TL TFH G +S++
Sbjct: 2276 PGEAVGVVAAQSIGEPGTQLTLRTFHVGGTASRS 2309
Score = 31.4 bits (71), Expect = 0.60
Identities = 34/129 (26%), Positives = 50/129 (38%), Gaps = 24/129 (18%)
Query: 2 LALKQTFENQVNRILNDARDKTGGSAKKSLTE----YNNLKAMVVAGSKGSNINISQVIA 57
L Q N++ + DK ++ + +N++ M +G++GS I Q+ A
Sbjct: 2048 LLTDQERYNKIIDTWTEVNDKMSKEMMTAIAKDKEGFNSIYMMADSGARGSAAQIRQLSA 2107
Query: 58 CVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESRGFVENSYLAGLTPSEFFFHAMGGREG 117
G P G T P F E GL E+F G R+G
Sbjct: 2108 MRGLMTK-----PDGSIIET----------PIISNFKE-----GLNVLEYFNSTHGARKG 2147
Query: 118 LIDTAVKTA 126
L DTA+KTA
Sbjct: 2148 LADTALKTA 2156
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 54.2 bits (131), Expect = 2e-08
Identities = 20/34 (58%), Positives = 25/34 (73%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 170
GE VG +AAQS+GEP TQ+T+ TFH GV + V
Sbjct: 311 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 344
Score = 34.2 bits (79), Expect = 0.061
Identities = 32/97 (32%), Positives = 50/97 (51%), Gaps = 28/97 (28%)
Query: 35 NNLKAMVVAGSKGSNINISQVIACVGQQ----NVEGKRIPFGFRKRTLPHFIKDDYGPES 90
N++ M +G++G N+SQV VG + N +G+ I LP IK +
Sbjct: 120 NSVYMMAFSGARG---NMSQVRQLVGMRGLMANPQGEII-------DLP--IKTN----- 162
Query: 91 RGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAE 127
F E GLT +E+ + G R+GL+DTA++TA+
Sbjct: 163 --FRE-----GLTVTEYVISSYGARKGLVDTALRTAD 192
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 53.0 bits (128), Expect = 6e-08
Identities = 19/29 (65%), Positives = 22/29 (75%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGV 165
GE VG +A QS+GEP TQ+TL TFH GV
Sbjct: 315 GEAVGIIAGQSIGEPGTQLTLRTFHTGGV 343
Score = 32.2 bits (74), Expect = 0.30
Identities = 12/26 (46%), Positives = 19/26 (73%)
Query: 101 GLTPSEFFFHAMGGREGLIDTAVKTA 126
GL+ +E+ G R+G++DTAV+TA
Sbjct: 172 GLSLTEYIISCYGARKGVVDTAVRTA 197
>gnl|CDD|233841 TIGR02388, rpoC2_cyan, DNA-directed RNA polymerase, beta'' subunit.
The family consists of the product of the rpoC2 gene, a
subunit of DNA-directed RNA polymerase of cyanobacteria
and chloroplasts. RpoC2 corresponds largely to the
C-terminal region of the RpoC (the beta' subunit) of
other bacteria. Members of this family are designated
beta'' in chloroplasts/plastids, and beta' (confusingly)
in Cyanobacteria, where RpoC1 is called beta' in
chloroplasts/plastids and gamma in Cyanobacteria. We
prefer to name this family beta'', after its organellar
members, to emphasize that this RpoC1 and RpoC2 together
replace RpoC in other bacteria [Transcription,
DNA-dependent RNA polymerase].
Length = 1227
Score = 50.6 bits (121), Expect = 3e-07
Identities = 20/34 (58%), Positives = 25/34 (73%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 170
GE VG +AAQS+GEP TQ+T+ TFH GV + V
Sbjct: 309 GEAVGIIAAQSIGEPGTQLTMRTFHTGGVFTGEV 342
Score = 37.5 bits (87), Expect = 0.007
Identities = 28/98 (28%), Positives = 50/98 (51%), Gaps = 28/98 (28%)
Query: 35 NNLKAMVVAGSKGSNINISQVIACVGQQ----NVEGKRIPFGFRKRTLPHFIKDDYGPES 90
N++ M +G++G N+SQV VG + N +G+ I LP
Sbjct: 119 NSVYMMAFSGARG---NMSQVRQLVGMRGLMANPQGEII-------DLP----------- 157
Query: 91 RGFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAET 128
++ ++ GLT +E+ + G R+GL+DTA++TA++
Sbjct: 158 ---IKTNFREGLTVTEYVISSYGARKGLVDTALRTADS 192
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 50.0 bits (119), Expect = 6e-07
Identities = 20/34 (58%), Positives = 26/34 (76%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNV 170
GE VG +AAQS+GEP TQ+T+ TFH GV ++ V
Sbjct: 2333 GEAVGVIAAQSVGEPGTQLTMRTFHIGGVMTRGV 2366
Score = 34.2 bits (78), Expect = 0.074
Identities = 31/98 (31%), Positives = 45/98 (45%), Gaps = 20/98 (20%)
Query: 32 TEYNNLKAMVVAGSKGSNINISQVIACVGQQNVEGKRIPFGFRKRTLPHFIKDDYGPESR 91
++YN++ MV +G++GS SQ+ G + + K P G T P
Sbjct: 2138 SKYNSVYMMVNSGARGST---SQMKQLAGMRGLMTK--PSGEIIET----------PIIS 2182
Query: 92 GFVENSYLAGLTPSEFFFHAMGGREGLIDTAVKTAETA 129
F E GL E+F G R+GL DTA+KTA +
Sbjct: 2183 NFRE-----GLNVFEYFNSTHGARKGLADTALKTANSG 2215
>gnl|CDD|132724 cd02737, RNAP_IV_NRPD1_C, Largest subunit (NRPD1) of Higher plant
RNA polymerase IV, C-terminal domain. Higher plants
have five multi-subunit nuclear RNA polymerases: RNAP I,
RNAP II and RNAP III, which are essential for viability;
plus the two isoforms of the non-essential polymerase
RNAP IV (IVa and IVb), which specialize in small
RNA-mediated gene silencing pathways. RNAP IVa and/or
RNAP IVb might be involved in RNA-directed DNA
methylation of endogenous repetitive elements, silencing
of transgenes, regulation of flowering-time genes,
inducible regulation of adjacent gene pairs, and
spreading of mobile silencing signals. NRPD1a is the
largest subunit of RNAP IVa, whereas NRPD1b is the
largest subunit of RNAP IVb. The full subunit
compositions of RNAP IVa and RNAP IVb are not known, nor
are their templates or enzymatic products. However, it
has been shown that RNAP IVa and, to a lesser extent,
RNAP IVb are crucial for several RNA-mediated gene
silencing phenomena.
Length = 381
Score = 29.7 bits (67), Expect = 1.5
Identities = 18/62 (29%), Positives = 27/62 (43%), Gaps = 8/62 (12%)
Query: 137 GEMVGALAAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEII--NISKKPKAPSLTV 194
GE VG+LAA ++ EPA + L+ + + LKE++ K K V
Sbjct: 1 GEPVGSLAATAISEPAYKALLDP------PQSLESSPLELLKEVLECRSKSKSKENDRRV 54
Query: 195 FL 196
L
Sbjct: 55 IL 56
>gnl|CDD|224138 COG1217, TypA, Predicted membrane GTPase involved in stress
response [Signal transduction mechanisms].
Length = 603
Score = 28.7 bits (65), Expect = 3.2
Identities = 17/40 (42%), Positives = 18/40 (45%), Gaps = 3/40 (7%)
Query: 134 CAPGEMVGALAAQSLGEPATQMTL--NTFHFAGVSSKNVT 171
C P AL A S+ EP MT N FAG K VT
Sbjct: 289 CDPDNPE-ALPALSVDEPTLSMTFSVNDSPFAGKEGKFVT 327
>gnl|CDD|173774 cd00223, TOPRIM_TopoIIB_SPO, TOPRIM_TopoIIB_SPO:
topoisomerase-primase (TOPRIM) nucleotidyl
transferase/hydrolase domain of the type found in the
type IIB family of DNA topoisomerases and Spo11. This
subgroup contains proteins similar to Sulfolobus
shibatae topoisomerase VI (TopoVI) and Saccharomyces
cerevisiae meiotic recombination factor: Spo11. Type
II DNA topoisomerases catalyze the ATP-dependent
transport of one DNA duplex through another, in the
process generating transient double strand breaks via
covalent attachments to both DNA strands at the 5'
positions. TopoVI enzymes are heterotetramers found in
archaea and plants. Spo11 plays a role in generating the
double strand breaks that initiate homologous
recombination during meiosis. S. shibatae TopoVI
relaxes both positive and negative supercoils, and in
addition has a strong decatenase activity. The TOPRIM
domain has two conserved motifs, one of which centers at
a conserved glutamate and the other one at two conserved
aspartates (DxD. For topoisomerases the conserved
glutamate is believed to act as a general base in strand
joining and, as a general acid in strand cleavage. The
DXD motif may co-ordinate Mg2+, a cofactor required for
full catalytic function.
Length = 160
Score = 27.2 bits (61), Expect = 5.3
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 15/67 (22%)
Query: 169 NVTLGVPRLK-------EIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLEHTTLRK 221
+ +L P L+ +II + P P L+ RD ++AK++L R L +
Sbjct: 82 SESLATPDLRWLGLRPSDIIRLPDLPLLP-----LS---ERDLKRAKSLLRRPRFKELPE 133
Query: 222 VLYIILR 228
+
Sbjct: 134 WKRELQL 140
>gnl|CDD|178472 PLN02884, PLN02884, 6-phosphofructokinase.
Length = 411
Score = 27.9 bits (62), Expect = 5.6
Identities = 20/60 (33%), Positives = 29/60 (48%), Gaps = 12/60 (20%)
Query: 47 GSNINISQVI---ACVGQQNVEGKRIPFGFRKRTLPHFIKDDYG--PESRGFVENSYLAG 101
G N I Q++ G +N+ G IPFG+R F + P SR V+N +L+G
Sbjct: 67 GLNDVIRQIVFTLEIYGVKNIVG--IPFGYRG-----FFEKGLSEMPLSRKVVQNIHLSG 119
>gnl|CDD|165425 PHA03154, PHA03154, hypothetical protein; Provisional.
Length = 304
Score = 27.3 bits (60), Expect = 7.3
Identities = 27/94 (28%), Positives = 39/94 (41%), Gaps = 15/94 (15%)
Query: 178 KEIINISKKPKAPSLTVFLTGQAARDAEKAKNVLCRLE------------HTTLRKVLYI 225
+EIIN +K L L + E AKN+LC +E + K+ I
Sbjct: 72 QEIINKAKSNIIYFLNEILNAEYGEVKELAKNILCDVEIDKPDCELSAYLAQEIPKL--I 129
Query: 226 ILRPATHYQV-ELISGARRVASLRLFGQEPPFLY 258
+L+ TH++V E I R L G EP +
Sbjct: 130 VLKYPTHFKVCEEIIPNGRWCLHNLLGIEPYYKD 163
>gnl|CDD|216171 pfam00883, Peptidase_M17, Cytosol aminopeptidase family, catalytic
domain. The two associated zinc ions and the active
site are entirely enclosed within the C-terminal
catalytic domain in leucine aminopeptidase.
Length = 311
Score = 27.2 bits (61), Expect = 8.1
Identities = 12/50 (24%), Positives = 23/50 (46%), Gaps = 8/50 (16%)
Query: 144 AAQSLGEPATQMTLNTFHFAGVSSKNVTLGVPRLKEIINISKKPKAPSLT 193
AA+ GE +M L+ + + SK + ++ NI + A ++T
Sbjct: 225 AAEESGEKVWRMPLHEDYKKQLKSK--------IADLANIGGRRGAGAIT 266
>gnl|CDD|234151 TIGR03261, phnS2, putative 2-aminoethylphosphonate ABC
transporter, periplasmic
2-aminoethylphosphonate-binding protein. This ABC
transporter extracellular solute-binding protein is
found in a number of genomes in operon-like contexts
strongly suggesting a substrate specificity for
2-aminoethylphosphonate (2-AEP). The characterized
PhnSTUV system is absent in the genomes in which this
system is found. These genomes encode systems for the
catabolism of 2-AEP, making the need for a
2-AEP-specific transporter likely [Transport and
binding proteins, Amino acids, peptides and amines].
Length = 334
Score = 27.1 bits (60), Expect = 9.6
Identities = 19/47 (40%), Positives = 23/47 (48%), Gaps = 1/47 (2%)
Query: 5 KQTFENQVNRI-LNDARDKTGGSAKKSLTEYNNLKAMVVAGSKGSNI 50
K FE I +N RD TG K L E NN +A VV G S++
Sbjct: 39 KDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGLAASSL 85
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 0.134 0.382
Gapped
Lambda K H
0.267 0.0700 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,871,144
Number of extensions: 1199818
Number of successful extensions: 980
Number of sequences better than 10.0: 1
Number of HSP's gapped: 974
Number of HSP's successfully gapped: 48
Length of query: 258
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 163
Effective length of database: 6,723,972
Effective search space: 1096007436
Effective search space used: 1096007436
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: 58 (26.2 bits)