RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5725
(117 letters)
>gnl|CDD|218368 pfam04992, RNA_pol_Rpb1_6, RNA polymerase Rpb1, domain 6. 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 6, represents a mobile module of the RNA
polymerase. Domain 6 forms part of the shelf module.
This family appears to be specific to the largest
subunit of RNA polymerase II.
Length = 187
Score = 132 bits (335), Expect = 1e-40
Identities = 44/68 (64%), Positives = 57/68 (83%)
Query: 25 GVRELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGE 84
GVRELL++ V+V G+D LSK+A ENATLLF+ L+RSTL +K V E YRL+ EAF+W++GE
Sbjct: 120 GVRELLDRLVVVRGDDPLSKEAQENATLLFKILLRSTLASKRVLEEYRLNKEAFDWVLGE 179
Query: 85 IENRFQQA 92
IE+RF QA
Sbjct: 180 IESRFNQA 187
>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 = 84.6 bits (210), Expect = 1e-20
Identities = 24/39 (61%), Positives = 32/39 (82%)
Query: 71 YRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109
YRL+ EAF+W++GEIE RF ++ PGEMVG +AAQS+G
Sbjct: 1 YRLNKEAFDWILGEIETRFNRSLVHPGEMVGTIAAQSIG 39
>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 = 77.3 bits (191), Expect = 6e-18
Identities = 25/82 (30%), Positives = 44/82 (53%)
Query: 28 ELLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAENYRLSSEAFEWLVGEIEN 87
+L +K I + L +TLLF+ L+RS + +K V +S+A + +
Sbjct: 86 KLEKKFKIDLNDVLLLLSEFSLSTLLFEILLRSGIESKRVRSELTCNSKAGVCFLCYGRD 145
Query: 88 RFQQAQCAPGEMVGALAAQSLG 109
+++++ PGE VG +AAQS+G
Sbjct: 146 KYRRSLVEPGEAVGIIAAQSIG 167
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 39.4 bits (93), Expect = 1e-04
Identities = 15/42 (35%), Positives = 25/42 (59%)
Query: 68 AENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109
E +L+ E E ++ E+ + ++ PGE VG +AAQS+G
Sbjct: 30 LEERKLTEEEVEEIIEEVVREYLRSLVEPGEAVGVVAAQSIG 71
>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 = 37.2 bits (87), Expect = 6e-04
Identities = 11/22 (50%), Positives = 17/22 (77%)
Query: 88 RFQQAQCAPGEMVGALAAQSLG 109
++ +A+ PG VGA+AAQS+G
Sbjct: 1 KYMRAKVEPGTAVGAIAAQSIG 22
>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 = 36.8 bits (86), Expect = 9e-04
Identities = 11/22 (50%), Positives = 16/22 (72%)
Query: 88 RFQQAQCAPGEMVGALAAQSLG 109
++ ++ PGE VG LAAQS+G
Sbjct: 1 KYMRSLVEPGEAVGLLAAQSIG 22
>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 = 36.5 bits (85), Expect = 0.001
Identities = 14/43 (32%), Positives = 25/43 (58%)
Query: 67 VAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109
V + + L+ E ++ E+ + ++ PGE VG +AAQS+G
Sbjct: 10 VLKEHGLTLSEAEEIIKEVLREYLRSLIEPGEAVGIVAAQSIG 52
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 33.6 bits (77), Expect = 0.013
Identities = 14/43 (32%), Positives = 25/43 (58%)
Query: 67 VAENYRLSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109
+ LS + +E ++ I +++A+ P E VG +AAQS+G
Sbjct: 152 AMKKKELSDDEYEEILRRIREEYERARVDPYEAVGIVAAQSIG 194
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 32.6 bits (74), Expect = 0.034
Identities = 13/37 (35%), Positives = 22/37 (59%)
Query: 73 LSSEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109
++ E E ++ E+ + + A P E VG +AAQS+G
Sbjct: 33 VTEEMVEEIIDEVVSAYLNALVEPYEAVGIVAAQSIG 69
>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 = 31.9 bits (73), Expect = 0.041
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 67 VAENYRLS-SEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLG 109
+ +S E + ++ +E + ++ PGE VG +AAQS+G
Sbjct: 13 TVKKREISDKEELDEIIKRVEEEYLRSLIDPGEAVGIVAAQSIG 56
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 32.3 bits (73), Expect = 0.045
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 4/87 (4%)
Query: 29 LLEKCVIVAGEDQLSKQANENATLLFQCLVRSTLCTKLVAE---NYRLSSEAFEWLVGEI 85
++EK I SK E + + L KL+A+ L + E + E
Sbjct: 908 IIEKQKIEDRGKGASKDEIEELAKEYTKTFNANL-PKLLADAIHGAELKEDELEAICAEG 966
Query: 86 ENRFQQAQCAPGEMVGALAAQSLGTST 112
+ F++A+ PG+ +G ++AQS+
Sbjct: 967 KEGFEKAKVEPGQAIGIISAQSIAEPG 993
>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 = 28.9 bits (65), Expect = 0.42
Identities = 10/13 (76%), Positives = 11/13 (84%)
Query: 97 GEMVGALAAQSLG 109
GE VG LAAQS+G
Sbjct: 1 GEAVGVLAAQSIG 13
>gnl|CDD|181983 PRK09603, PRK09603, bifunctional DNA-directed RNA polymerase subunit
beta/beta'; Reviewed.
Length = 2890
Score = 28.0 bits (62), Expect = 1.5
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 96 PGEMVGALAAQSLG 109
PGE VG +AAQS+G
Sbjct: 2276 PGEAVGVVAAQSIG 2289
>gnl|CDD|149597 pfam08599, Nbs1_C, DNA damage repair protein Nbs1. This C
terminal region of the DNA damage repair protein Nbs1
has been identified to be necessary for the binding of
Mre11 and Tel1.
Length = 65
Score = 26.3 bits (58), Expect = 1.5
Identities = 15/28 (53%), Positives = 18/28 (64%)
Query: 66 LVAENYRLSSEAFEWLVGEIENRFQQAQ 93
LVA N R +SE EWL EIE + Q A+
Sbjct: 27 LVAHNRRKNSELEEWLRQEIEEQNQSAR 54
>gnl|CDD|236611 PRK09672, PRK09672, phage exclusion protein Lit; Provisional.
Length = 305
Score = 25.5 bits (56), Expect = 6.9
Identities = 9/42 (21%), Positives = 14/42 (33%)
Query: 75 SEAFEWLVGEIENRFQQAQCAPGEMVGALAAQSLGTSTYFPF 116
S A WL+ + E + + G + L Q L
Sbjct: 198 SYATNWLLSKSEKYAPSKKRSVGIAIALLFLQELELENKSCG 239
>gnl|CDD|234794 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 25.4 bits (57), Expect = 8.6
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 97 GEMVGALAAQSLG 109
GE VG +AAQS+G
Sbjct: 879 GEAVGVIAAQSIG 891
>gnl|CDD|216584 pfam01580, FtsK_SpoIIIE, FtsK/SpoIIIE family. FtsK has extensive
sequence similarity to wide variety of proteins from
prokaryotes and plasmids, termed the FtsK/SpoIIIE
family. This domain contains a putative ATP binding
P-loop motif. It is found in the FtsK cell division
protein from E. coli and the stage III sporulation
protein E SpoIIIE, which has roles in regulation of
prespore specific gene expression in B. subtilis. A
mutation in FtsK causes a temperature sensitive block in
cell division and it is involved in peptidoglycan
synthesis or modification. The SpoIIIE protein is
implicated in intercellular chromosomal DNA transfer.
Length = 201
Score = 25.0 bits (55), Expect = 9.8
Identities = 8/24 (33%), Positives = 12/24 (50%)
Query: 67 VAENYRLSSEAFEWLVGEIENRFQ 90
VA + + A LV E+E R+
Sbjct: 96 VATDPEDALSALRALVAEMERRYA 119
>gnl|CDD|214368 CHL00117, rpoC2, RNA polymerase beta'' subunit; Reviewed.
Length = 1364
Score = 25.3 bits (56), Expect = 9.9
Identities = 8/13 (61%), Positives = 10/13 (76%)
Query: 97 GEMVGALAAQSLG 109
GE VG +A QS+G
Sbjct: 315 GEAVGIIAGQSIG 327
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 0.132 0.376
Gapped
Lambda K H
0.267 0.0641 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,629,468
Number of extensions: 454796
Number of successful extensions: 321
Number of sequences better than 10.0: 1
Number of HSP's gapped: 321
Number of HSP's successfully gapped: 26
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
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 (21.8 bits)
S2: 53 (24.4 bits)