RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16768
(154 letters)
>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 = 126 bits (320), Expect = 2e-36
Identities = 44/81 (54%), Positives = 61/81 (75%)
Query: 2 ETNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFA 61
K+L+ T+G+N+ + ++ +LD+N++Y NDIH M +TYGIEAA R I++E+ NVF
Sbjct: 164 GGKTKYLVITEGVNLAALWKFSDILDVNRIYTNDIHAMLNTYGIEAARRAIVKEISNVFK 223
Query: 62 VYGIEVDPRHLSLVADYMTHS 82
VYGI VDPRHLSL+ADYMT
Sbjct: 224 VYGIAVDPRHLSLIADYMTFE 244
>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 = 88.1 bits (219), Expect = 3e-21
Identities = 34/77 (44%), Positives = 49/77 (63%)
Query: 4 NGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVY 63
+ LLKT+G N+ + + + ++D +K Y NDI M GIEAA I+ E++NVF
Sbjct: 348 GKEWLLKTEGNNLQAVMRLQGVIDNDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKFD 407
Query: 64 GIEVDPRHLSLVADYMT 80
GI V+ RHL+L+AD MT
Sbjct: 408 GIYVNRRHLALLADLMT 424
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 67.6 bits (166), Expect = 5e-14
Identities = 30/78 (38%), Positives = 41/78 (52%), Gaps = 12/78 (15%)
Query: 3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAV 62
+N K +LK +G+ D + N+IH + GIEAA II E+KN
Sbjct: 244 SNLKEVLKVEGV------------DATRTTTNNIHEIEEVLGIEAARNAIIEEIKNTLEE 291
Query: 63 YGIEVDPRHLSLVADYMT 80
G++VD RH+ LVAD MT
Sbjct: 292 QGLDVDIRHIMLVADMMT 309
>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 = 67.3 bits (165), Expect = 6e-14
Identities = 24/56 (42%), Positives = 32/56 (57%)
Query: 27 DLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82
D + N+IH + GIEAA II E+K G++VD RH+ LVAD MT+
Sbjct: 239 DPTRTTTNNIHEIEEVLGIEAARNAIINEIKRTLEEQGLDVDIRHIMLVADIMTYD 294
>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 = 66.5 bits (163), Expect = 8e-14
Identities = 20/54 (37%), Positives = 29/54 (53%)
Query: 27 DLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 80
+ N I + GIEAA II E++ +G+ +DPRH+ L+AD MT
Sbjct: 182 IGTRTTSNHIMEVEKVLGIEAARSTIINEIQYTMKSHGMSIDPRHIMLLADLMT 235
>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 = 61.7 bits (150), Expect = 1e-12
Identities = 25/48 (52%), Positives = 31/48 (64%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMTHS 82
IH M GIEAA IIRE++ V A G+ VD RH+ L+AD MT+S
Sbjct: 49 SIHEMLEALGIEAARETIIREIQKVLASQGVSVDRRHIELIADVMTYS 96
>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 = 63.4 bits (155), Expect = 1e-12
Identities = 26/75 (34%), Positives = 45/75 (60%), Gaps = 1/75 (1%)
Query: 7 HLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIE 66
+L+TDG+N+ + + + D + NDI + GIEAA + +++E++NV + G
Sbjct: 268 WVLETDGVNLREVLSHPGV-DPTRTTSNDIVEIFEVLGIEAARKALLKELRNVISFDGSY 326
Query: 67 VDPRHLSLVADYMTH 81
V+ RHL+L+ D MT
Sbjct: 327 VNYRHLALLCDVMTQ 341
>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 = 62.8 bits (153), Expect = 2e-12
Identities = 30/74 (40%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 9 LKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVD 68
+ T+G N+ + + + D + NDIH +A GIEAA II E+K G++VD
Sbjct: 227 IYTEGSNLKEVLKLEGV-DKTRTTTNDIHEIAEVLGIEAARNAIIEEIKRTLEEQGLDVD 285
Query: 69 PRHLSLVADYMTHS 82
RHL LVAD MT
Sbjct: 286 IRHLMLVADLMTWD 299
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 58.3 bits (141), Expect = 1e-10
Identities = 30/80 (37%), Positives = 39/80 (48%), Gaps = 12/80 (15%)
Query: 3 TNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAV 62
+N K +L+ D + D + Y NDI +A+ GIEAA II E K
Sbjct: 368 SNLKDVLEIDEV------------DPTRTYTNDIIEIATVLGIEAARNAIIHEAKRTLQE 415
Query: 63 YGIEVDPRHLSLVADYMTHS 82
G+ VD RH+ LVAD MT
Sbjct: 416 QGLNVDIRHIMLVADMMTFD 435
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 56.4 bits (136), Expect = 4e-10
Identities = 30/80 (37%), Positives = 44/80 (55%), Gaps = 1/80 (1%)
Query: 1 METNGKHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVF 60
E + +++L T G N+ + + + D ++ N+I + GIEAA II E+ N
Sbjct: 701 HENDEEYVLYTQGSNLREVFKIEGV-DTSRTTTNNIIEIQEVLGIEAARNAIINEMMNTL 759
Query: 61 AVYGIEVDPRHLSLVADYMT 80
G+EVD RHL LVAD MT
Sbjct: 760 EQQGLEVDIRHLMLVADIMT 779
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 52.7 bits (126), Expect = 1e-08
Identities = 38/151 (25%), Positives = 63/151 (41%), Gaps = 11/151 (7%)
Query: 1 METNGK--HLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKN 58
+E +G+ +++T G N+ + + + +D+ ND +A T GIEAA I E+ +
Sbjct: 1160 VEKDGRDEWIIQTSGSNLAAVLEMK-CIDIANTITNDCFEIAGTLGIEAARNAIFNELAS 1218
Query: 59 VFAVYGIEVDPRHLSLVADYMTHS----EFDLIIMVSKSWMLDEVKSTTARSVTPACEPN 114
+ G+EVD R++ LVAD M L + E S A++
Sbjct: 1219 ILEDQGLEVDNRYIMLVADIMCSRGTIEAIGLQAAGVRHGFAGEKDSPLAKAAFEITTHT 1278
Query: 115 SHHDVKKIEFKKQNKILPLVLQNSLTGSSYP 145
H E KI +L + G + P
Sbjct: 1279 IAHAALGGEI---EKIKG-ILDALIMGQNIP 1305
>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 = 45.1 bits (107), Expect = 4e-06
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 21 QYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 80
L+D + I + S GI+AA ++ +++ ++ G V HL LVAD MT
Sbjct: 247 PVMDLIDWERSMPYSIQQIKSVLGIDAAFEQFVQRLESAVSMTGKSVLREHLLLVADSMT 306
Query: 81 HS 82
+S
Sbjct: 307 YS 308
>gnl|CDD|223164 COG0086, RpoC, DNA-directed RNA polymerase, beta' subunit/160 kD
subunit [Transcription].
Length = 808
Score = 39.5 bits (93), Expect = 3e-04
Identities = 23/76 (30%), Positives = 36/76 (47%), Gaps = 2/76 (2%)
Query: 6 KHLLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGI 65
+ +++ +G + I QY DL + N+I + GIEA II E+K G+
Sbjct: 602 EIVIEAEGSVLKLILQYEEG-DLTRTERNNIVEIIEVLGIEALRNAIIEEIKITLEEQGL 660
Query: 66 E-VDPRHLSLVADYMT 80
+ VD RH+ L M
Sbjct: 661 DFVDIRHMGLSGARMN 676
>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 = 34.1 bits (78), Expect = 0.023
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 38 YMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 80
Y A+ ++ R ++ EV+NV+ G+++ +H+ ++ MT
Sbjct: 1078 YEAAQESLQKVQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMT 1120
>gnl|CDD|173305 PRK14844, PRK14844, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Provisional.
Length = 2836
Score = 33.1 bits (75), Expect = 0.048
Identities = 13/45 (28%), Positives = 26/45 (57%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
D+H + G+EA +I E++ V+ + G+ +D +HL ++ M
Sbjct: 2637 DLHDILRVLGLEALAHYMISEIQQVYRLQGVRIDNKHLEVILKQM 2681
>gnl|CDD|235052 PRK02597, rpoC2, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1331
Score = 32.7 bits (75), Expect = 0.076
Identities = 11/43 (25%), Positives = 25/43 (58%)
Query: 38 YMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 80
Y A+ ++ R ++ EV+NV+ G+++ +H+ ++ MT
Sbjct: 1079 YEAALEALQKLQRFLVNEVQNVYQSQGVDISDKHIEVIVRQMT 1121
>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 = 28.9 bits (65), Expect = 1.2
Identities = 12/46 (26%), Positives = 27/46 (58%)
Query: 35 DIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 80
D H + GI+A +++EV+ V+ + G+E++ +H+ ++ M
Sbjct: 988 DPHDLLRIKGIQAVQEYLVKEVQKVYRLQGVEINDKHIEVIVRQML 1033
>gnl|CDD|214567 smart00220, S_TKc, Serine/Threonine protein kinases, catalytic
domain. Phosphotransferases. Serine or
threonine-specific kinase subfamily.
Length = 254
Score = 28.3 bits (64), Expect = 1.7
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 9/45 (20%)
Query: 52 IIREVK--------NVFAVYGIEVDPRHLSLVADYMTHSE-FDLI 87
I+RE+K N+ +Y + D L LV +Y + FDL+
Sbjct: 44 ILREIKILKKLKHPNIVRLYDVFEDEDKLYLVMEYCEGGDLFDLL 88
>gnl|CDD|184899 PRK14906, PRK14906, DNA-directed RNA polymerase subunit beta'/alpha
domain fusion protein; Provisional.
Length = 1460
Score = 27.9 bits (62), Expect = 2.6
Identities = 8/35 (22%), Positives = 21/35 (60%)
Query: 45 IEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYM 79
R I+ +V++V+ G++++ +H+ ++A M
Sbjct: 1099 PNTTLRYIVSQVQDVYVSQGVDINDKHIEVIARQM 1133
>gnl|CDD|234549 TIGR04332, gamma_Glu_sys, poly-gamma-glutamate system protein.
Poly(gamma-glutamic acid), or PGA, is an extracellular
structural polymer found in Bacillus subtilis and a
number of other species. PGA is sometimes
capsule-forming, sometimes secretory, and may be
produced by Gram-positive (single plasma membrane) and
Gram-negative (inner and outer membranes), so export
and/or attachment machinery may differ from system to
system. Members of this family occur in a subset of PGA
operons, in lineages that include Francisella,
Leptospira, Treponema, Thermotoga, Fusobacterium, and
Clostridium, among others. Because gene symbols pgsWXYZ
are not yet in use, we suggest pgsW, as one of a series
of poly-gamma-glutamate synthesis auxiliary proteins.
Length = 307
Score = 27.2 bits (61), Expect = 3.2
Identities = 9/21 (42%), Positives = 15/21 (71%)
Query: 131 LPLVLQNSLTGSSYPANHPDF 151
L +++ +SL S+Y AN P+F
Sbjct: 137 LKVIIISSLGASTYGANDPEF 157
>gnl|CDD|213311 cd05958, ABCL, 2-aminobenzoate-CoA ligase (ABCL). ABCL catalyzes
the initial step in the 2-aminobenzoate aerobic
degradation pathway by activating 2-aminobenzoate to
2-aminobenzoyl-CoA. The reaction is carried out via a
two-step process; the first step is ATP-dependent and
forms a 2-aminobenzoyl-AMP intermediate, and the second
step forms the 2-aminobenzoyl-CoA ester and releases
the AMP. 2-Aminobenzoyl-CoA is further converted to
2-amino-5-oxo-cyclohex-1-ene-1-carbonyl-CoA catalyzed
by 2-aminobenzoyl-CoA monooxygenase/reductase. ABCL has
been purified from cells aerobically grown with
2-aminobenzoate as sole carbon, energy, and nitrogen
source, and has been characterized as a monomer.
Length = 487
Score = 27.5 bits (61), Expect = 3.3
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 5/38 (13%)
Query: 22 YRHLLDLNKLYVNDI-HYMASTYGIEAANRVIIREVKN 58
Y+ LLD N I H + G+ NRV++R
Sbjct: 63 YQDLLD----RANRIAHVLVEDLGVVPGNRVLLRSANT 96
>gnl|CDD|212542 cd11600, HDAC_Clr3, Class II Histone deacetylase Clr3 and similar
proteins. Clr3 is a class II Histone deacetylase
Zn-dependent enzyme that catalyzes hydrolysis of an
N(6)-acetyl-lysine residue of a histone to yield a
deacetylated histone (EC 3.5.1.98). Clr3 is the homolog
of the class-II HDAC HdaI in S. cerevisiae, and is
essential for silencing in heterochromatin regions, such
as centromeric regions, ribosomal DNA, the mating-type
region and telomeric loci. Clr3 has also been implicated
in the regulation of stress-related genes; the histone
acetyltransferase, Gcn5, in S. cerevisiae,
preferentially acetylates global histone H3K14 while
Clr3 preferentially deacetylates H3K14ac, and therefore,
interplay between Gcn5 and Clr3 is crucial for the
regulation of many stress-response genes.
Length = 313
Score = 27.3 bits (61), Expect = 3.6
Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 31 LYVNDIHYMASTYG----IEAANRVIIREVKNVFAV 62
LYVN+ + IEA V VKN FAV
Sbjct: 74 LYVNNDTAFCARLSCGGAIEACRAVAEGRVKNAFAV 109
>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 = 26.7 bits (60), Expect = 4.8
Identities = 10/51 (19%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 32 YVNDIHYM--ASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVADYMT 80
+ H + G EA + ++ E++ V+ G+ ++ +H+ ++ MT
Sbjct: 52 RKINPHDLLRIKFLGPEAVQKYLVEEIQKVYRSQGVNINDKHIEIIVRQMT 102
>gnl|CDD|183829 PRK12921, PRK12921, 2-dehydropantoate 2-reductase; Provisional.
Length = 305
Score = 26.4 bits (59), Expect = 6.7
Identities = 8/42 (19%), Positives = 16/42 (38%), Gaps = 4/42 (9%)
Query: 74 LVADYMTHSEFDLIIMVSKSWMLDEVKSTTARSVTPACEPNS 115
+ FDL+I+ K++ LD + P ++
Sbjct: 59 ITDPEELTGPFDLVILAVKAYQLDAA----IPDLKPLVGEDT 96
>gnl|CDD|213903 TIGR04290, meth_Rta_06860, methyltransferase, Rta_06860 family.
Members of this family are methyltransferases that mark
a widely distributed large conserved gene neighborhood
of unknown function. It appears most common in soil and
rhizosphere bacteria.
Length = 226
Score = 26.2 bits (58), Expect = 7.3
Identities = 18/47 (38%), Positives = 22/47 (46%), Gaps = 7/47 (14%)
Query: 27 DLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLS 73
DL+ V DI A Y IE R R V GI+ DPR+L+
Sbjct: 47 DLSGWSVLDIGCNAGFYSIEMKRRGAGR-------VLGIDSDPRYLA 86
>gnl|CDD|182863 PRK10954, PRK10954, periplasmic protein disulfide isomerase I;
Provisional.
Length = 207
Score = 26.2 bits (58), Expect = 7.8
Identities = 8/26 (30%), Positives = 14/26 (53%), Gaps = 4/26 (15%)
Query: 1 METNGKHLLKTDGINV----NYISQY 22
M NGK+++ G++ Y+ QY
Sbjct: 171 MFVNGKYMVNNQGMDTSSMDVYVQQY 196
>gnl|CDD|233710 TIGR02074, PBP_1a_fam, penicillin-binding protein, 1A family.
Bacterial that synthesize a cell wall of peptidoglycan
(murein) generally have several transglycosylases and
transpeptidases for the task. This family consists of
bifunctional transglycosylase/transpeptidase
penicillin-binding proteins (PBP). In the
Proteobacteria, this family includes PBP 1A but not the
paralogous PBP 1B (TIGR02071). This family also includes
related proteins, often designated PBP 1A, from other
bacterial lineages [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan].
Length = 531
Score = 26.5 bits (59), Expect = 7.8
Identities = 10/21 (47%), Positives = 14/21 (66%)
Query: 31 LYVNDIHYMASTYGIEAANRV 51
LY+N I++ YGIEAA +
Sbjct: 98 LYLNRIYFGNGAYGIEAAAQF 118
>gnl|CDD|211993 TIGR04270, Rama_corrin_act, methylamine methyltransferase
corrinoid protein reductive activase. Members of this
family occur as paralogs in species capable of
generating methane from mono-, di-, and
tri-methylamine. Members include RamA (Reductive
Activation of Methyltransfer, Amines) from
Methanosarcina barkeri MS (DSM 800). Member proteins
have two C-terminal motifs with four Cys each, likely
to bind one 4Fe-4S cluster per motif.
Length = 535
Score = 26.3 bits (58), Expect = 8.0
Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 2/37 (5%)
Query: 40 ASTYGIEAANRVIIREVKNVFAVYGIEVDPRHLSLVA 76
A YG E A+ +I+ V + A ++V +S A
Sbjct: 47 AINYGQEVAHGLIVEAVNRLIA--ALDVPLEEVSRFA 81
>gnl|CDD|153087 cd01678, PFL1, Pyruvate formate lyase 1. Pyruvate formate lyase
catalyzes a key step in anaerobic glycolysis, the
conversion of pyruvate and CoenzymeA to formate and
acetylCoA. The PFL mechanism involves an unusual radical
cleavage of pyruvate in which two cysteines and one
glycine form radicals that are required for catalysis.
PFL has a ten-stranded alpha/beta barrel domain that is
structurally similar to those of all three
ribonucleotide reductase (RNR) classes as well as
benzylsuccinate synthase and B12-independent glycerol
dehydratase.
Length = 738
Score = 26.2 bits (58), Expect = 8.3
Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 10/61 (16%)
Query: 22 YRHLLD-LNKLYV---NDIHYMASTYGIEAANRVII-REVKNVFAVYGIEVDPRHLSLVA 76
Y +D L YV N IHYM Y EA + +V+ A +GI LS+ A
Sbjct: 466 YDKSMDWLADTYVNALNIIHYMHDKYAYEALQMALHDTDVRRTMA-FGIA----GLSVAA 520
Query: 77 D 77
D
Sbjct: 521 D 521
>gnl|CDD|221783 pfam12807, eIF3_p135, Translation initiation factor eIF3 subunit
135. Translation initiation factor eIF3 is a
multi-subunit protein complex required for initiation
of protein biosynthesis in eukaryotic cells. The
complex promotes ribosome dissociation, the binding of
the initiator methionyl-tRNA to the 40 S ribosomal
subunit, and mRNA recruitment to the ribosome. The
protein product from TIF31 genes in yeast is p135 which
associates with the eIF3 but does not seem to be
necessary for protein translation initiation.
Length = 169
Score = 25.8 bits (57), Expect = 8.8
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 10/66 (15%)
Query: 8 LLKTDGINVNYISQYRHLLDLNKLYVNDIHYMASTYGIEAANRVIIREVKNVFAVYGIEV 67
LL GIN+ Y+ + L ++ + + +I R K++ Y V
Sbjct: 16 LLHRRGINMRYLGKVAKLASKRLPHLKRL----------CVSEMIARAAKHILRTYLRGV 65
Query: 68 DPRHLS 73
LS
Sbjct: 66 PAPDLS 71
>gnl|CDD|235067 PRK02759, PRK02759, bifunctional phosphoribosyl-AMP
cyclohydrolase/phosphoribosyl-ATP pyrophosphatase
protein; Reviewed.
Length = 203
Score = 25.9 bits (58), Expect = 9.0
Identities = 7/27 (25%), Positives = 20/27 (74%)
Query: 115 SHHDVKKIEFKKQNKILPLVLQNSLTG 141
+ +++++F K + ++P ++Q++LTG
Sbjct: 1 TEQQIEELDFDKNDGLIPAIVQDALTG 27
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 0.134 0.388
Gapped
Lambda K H
0.267 0.0818 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,768,093
Number of extensions: 685521
Number of successful extensions: 614
Number of sequences better than 10.0: 1
Number of HSP's gapped: 614
Number of HSP's successfully gapped: 41
Length of query: 154
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 65
Effective length of database: 6,990,096
Effective search space: 454356240
Effective search space used: 454356240
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: 55 (24.8 bits)