RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy6966
(155 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 = 49.9 bits (120), Expect = 8e-08
Identities = 15/31 (48%), Positives = 21/31 (67%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
++E VLGIEA RK++ KE+ V+ F G Y
Sbjct: 296 IVEIFEVLGIEAARKALLKELRNVISFDGSY 326
>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 = 43.1 bits (102), Expect = 2e-05
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 3/56 (5%)
Query: 102 EGTWIHDPLYGLRGGVILDYH--LLVLETTIVLGIEAVRKSVEKEMNTVLQFYGLY 155
EG + + L+G + D + E LGIEA R S+ E+ V +F G+Y
Sbjct: 356 EGNNLQA-VMRLQGVIDNDKTYSNDIREMLKKLGIEAARDSILLEIRNVFKFDGIY 410
>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 = 31.8 bits (73), Expect = 0.10
Identities = 10/21 (47%), Positives = 16/21 (76%)
Query: 133 GIEAVRKSVEKEMNTVLQFYG 153
GIEA R+++ KE++ V + YG
Sbjct: 206 GIEAARRAIVKEISNVFKVYG 226
>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 = 31.8 bits (73), Expect = 0.12
Identities = 10/30 (33%), Positives = 19/30 (63%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154
++E VLGIEA R ++ E+ ++ +G+
Sbjct: 191 IMEVEKVLGIEAARSTIINEIQYTMKSHGM 220
>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 = 31.2 bits (71), Expect = 0.18
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 131 VLGIEAVRKSVEKEMNTVLQFYGL 154
VLGIEA R ++ +E+ L+ GL
Sbjct: 259 VLGIEAARNAIIEEIKRTLEEQGL 282
>gnl|CDD|182059 PRK09752, PRK09752, adhesin; Provisional.
Length = 1250
Score = 31.2 bits (70), Expect = 0.20
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 44 PSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPL 76
PSPP P P+ P P P+P+P P+
Sbjct: 921 PSPPDPDPTPDPDPTPDPDPTPDPEPTPAYQPV 953
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 31.0 bits (71), Expect = 0.22
Identities = 11/24 (45%), Positives = 16/24 (66%)
Query: 131 VLGIEAVRKSVEKEMNTVLQFYGL 154
VLGIEA R ++ +E+ L+ GL
Sbjct: 271 VLGIEAARNAIIEEIKNTLEEQGL 294
>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 = 29.5 bits (67), Expect = 0.57
Identities = 11/24 (45%), Positives = 15/24 (62%)
Query: 131 VLGIEAVRKSVEKEMNTVLQFYGL 154
VLGIEA R ++ E+ L+ GL
Sbjct: 254 VLGIEAARNAIINEIKRTLEEQGL 277
>gnl|CDD|218191 pfam04652, DUF605, Vta1 like. Vta1 (VPS20-associated protein 1) is
a positive regulator of Vps4. Vps4 is an ATPase that is
required in the multivesicular body (MVB) sorting
pathway to dissociate the endosomal sorting complex
required for transport (ESCRT). Vta1 promotes correct
assembly of Vps4 and stimulates its ATPase activity
through its conserved Vta1/SBP1/LIP5 region.
Length = 315
Score = 29.7 bits (67), Expect = 0.58
Identities = 13/56 (23%), Positives = 16/56 (28%)
Query: 33 NAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVSHPLDLHPS 88
+ SP P P S S PP + + P P T S P
Sbjct: 188 PSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAP 243
Score = 26.6 bits (59), Expect = 6.5
Identities = 13/60 (21%), Positives = 16/60 (26%)
Query: 13 SPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDPSPF 72
+ S + P P PS PP P + PP P P P
Sbjct: 180 ASASPSDPPSSSPGVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPG 239
Score = 26.2 bits (58), Expect = 9.3
Identities = 10/67 (14%), Positives = 15/67 (22%)
Query: 5 HPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPY 64
P + + LP + P S +P P + PP
Sbjct: 193 GVPSFPSPPEDPSSPSDSSLPPAPSSFQSDTPPPSPESPTNPSPPPGPAAPPPPPVQQVP 252
Query: 65 IRPDPSP 71
P
Sbjct: 253 PLSTAKP 259
>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 = 28.2 bits (63), Expect = 1.2
Identities = 10/25 (40%), Positives = 16/25 (64%)
Query: 131 VLGIEAVRKSVEKEMNTVLQFYGLY 155
LGIEA R+++ +E+ VL G+
Sbjct: 56 ALGIEAARETIIREIQKVLASQGVS 80
>gnl|CDD|173687 cd05596, STKc_ROCK, Catalytic domain of the Protein
Serine/Threonine Kinase, Rho-associated coiled-coil
containing protein kinase. Serine/Threonine Kinases
(STKs), Rho-associated coiled-coil containing protein
kinase (ROCK) subfamily, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The ROCK subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. ROCK is also referred to as Rho-associated
kinase or simply as Rho kinase. It contains an
N-terminal extension, a catalytic kinase domain, and a
long C-terminal extension, which contains a coiled-coil
region encompassing a Rho-binding domain (RBD) and a
pleckstrin homology (PH) domain. ROCK is auto-inhibited
by the RBD and PH domain interacting with the catalytic
domain. It is activated via interaction with Rho GTPases
and is involved in many cellular functions including
contraction, adhesion, migration, motility,
proliferation, and apoptosis. The ROCK subfamily
consists of two isoforms, ROCK1 and ROCK2, which may be
functionally redundant in some systems, but exhibit
different tissue distributions. Both isoforms are
ubiquitously expressed in most tissues, but ROCK2 is
more prominent in brain and skeletal muscle while ROCK1
is more pronounced in the liver, testes, and kidney.
Studies in knockout mice result in different phenotypes,
suggesting that the two isoforms do not compensate for
each other during embryonic development.
Length = 370
Score = 28.6 bits (64), Expect = 1.5
Identities = 19/52 (36%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 77 TGVSHPLDLHPSVLLLEGTTGSYGPEGTWIHDPLYGLRGGVILDYHLLVLET 128
T V P + P VL +G G YG E W GV L Y +LV +T
Sbjct: 202 TAVGTPDYISPEVLKSQGGDGYYGRECDW-------WSVGVFL-YEMLVGDT 245
>gnl|CDD|237864 PRK14950, PRK14950, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 585
Score = 28.6 bits (64), Expect = 1.5
Identities = 17/82 (20%), Positives = 22/82 (26%), Gaps = 5/82 (6%)
Query: 6 PLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYI 65
P P++ P P T A + TP P P P
Sbjct: 366 PQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPP---RPVAPP-- 420
Query: 66 RPDPSPFILPLTGVSHPLDLHP 87
P LT + P+D P
Sbjct: 421 VPHTPESAPKLTRAAIPVDEKP 442
>gnl|CDD|237854 PRK14898, PRK14898, DNA-directed RNA polymerase subunit A'';
Provisional.
Length = 858
Score = 28.7 bits (64), Expect = 1.6
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154
++E VLGIEA R ++ EM L+ GL
Sbjct: 735 IIEIQEVLGIEAARNAIINEMMNTLEQQGL 764
>gnl|CDD|223021 PHA03247, PHA03247, large tegument protein UL36; Provisional.
Length = 3151
Score = 28.4 bits (63), Expect = 2.0
Identities = 16/62 (25%), Positives = 19/62 (30%)
Query: 10 PPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTPYIRPDP 69
P P + P + T L P +PP P P PP P P P
Sbjct: 2878 PARPPVRRLARPAVSRSTESFALPPDQPERPPQPQAPPPPQPQPQPPPPPQPQPPPPPPP 2937
Query: 70 SP 71
P
Sbjct: 2938 RP 2939
>gnl|CDD|237853 PRK14897, PRK14897, unknown domain/DNA-directed RNA polymerase
subunit A'' fusion protein; Provisional.
Length = 509
Score = 27.5 bits (61), Expect = 3.4
Identities = 13/30 (43%), Positives = 17/30 (56%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154
++E VLGIEA R ++ E LQ GL
Sbjct: 389 IIEIATVLGIEAARNAIIHEAKRTLQEQGL 418
>gnl|CDD|184940 PRK14977, PRK14977, bifunctional DNA-directed RNA polymerase A'/A''
subunit; Provisional.
Length = 1321
Score = 27.7 bits (61), Expect = 3.4
Identities = 11/30 (36%), Positives = 17/30 (56%)
Query: 125 VLETTIVLGIEAVRKSVEKEMNTVLQFYGL 154
E LGIEA R ++ E+ ++L+ GL
Sbjct: 1196 CFEIAGTLGIEAARNAIFNELASILEDQGL 1225
>gnl|CDD|215301 PLN02546, PLN02546, glutathione reductase.
Length = 558
Score = 26.8 bits (59), Expect = 5.9
Identities = 14/52 (26%), Positives = 20/52 (38%)
Query: 9 LPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPH 60
LP +S + + + L R L L S S P P T S+ + H
Sbjct: 5 LPSTSKLTSSPSLQTLYRKLPLRLPLPSSSSSSHLPLPKTLTRLSSPRPLSH 56
>gnl|CDD|215153 PLN02271, PLN02271, serine hydroxymethyltransferase.
Length = 586
Score = 26.7 bits (59), Expect = 6.3
Identities = 15/32 (46%), Positives = 17/32 (53%), Gaps = 8/32 (25%)
Query: 14 PYSCTS------TPLILPRTTHLILNAHSPSG 39
PYSCTS T L+LP I+ SPSG
Sbjct: 220 PYSCTSANFAVYTGLLLPGDR--IMGLDSPSG 249
>gnl|CDD|233508 TIGR01649, hnRNP-L_PTB, hnRNP-L/PTB/hephaestus splicing factor
family. Included in this family of heterogeneous
ribonucleoproteins are PTB (polypyrimidine tract binding
protein ) and hnRNP-L. These proteins contain four RNA
recognition motifs (rrm: pfam00067).
Length = 481
Score = 26.7 bits (59), Expect = 6.5
Identities = 19/78 (24%), Positives = 22/78 (28%), Gaps = 10/78 (12%)
Query: 26 RTTHLILNAHSPSGIRSY-----PSPPTPHPSSTSKGPPHWTPYIRPDPSPFILPLTGVS 80
R L PS P P GPPH P R P+ PL
Sbjct: 206 RQRQPALLGQHPSSYGHDGYSSHGGPLAPLAGGDRMGPPHGPPS-RYRPAYEAAPLAPAI 264
Query: 81 ----HPLDLHPSVLLLEG 94
SVL++ G
Sbjct: 265 SSYGPAGGGPGSVLMVSG 282
>gnl|CDD|184927 PRK14963, PRK14963, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 504
Score = 26.7 bits (59), Expect = 6.6
Identities = 18/68 (26%), Positives = 25/68 (36%), Gaps = 1/68 (1%)
Query: 4 LHPLILPPSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPPHWTP 63
L L PS + + P P LN +RS S PT ++ P + P
Sbjct: 339 LLALGGAPSEGVAAVAPPAPAPADLTQRLNRLEK-EVRSLRSAPTAAATAAGAPLPDFDP 397
Query: 64 YIRPDPSP 71
R P+P
Sbjct: 398 RPRGPPAP 405
>gnl|CDD|148150 pfam06372, Gemin6, Gemin6 protein. This family consists of several
mammalian Gemin6 proteins. The exact function of Gemin6
is unknown but it has been found to form part of the
pfam06003 complex. The SMN complex plays a key role in
the biogenesis of spliceosomal small nuclear
ribonucleoproteins (snRNPs) and other ribonucleoprotein
particles.
Length = 169
Score = 25.8 bits (56), Expect = 8.0
Identities = 12/32 (37%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 8 ILPPSSPYSCTST-PLILPRTTHLILNAHSPS 38
I PP +P +C S+ +IL R LI S
Sbjct: 137 IDPPYAPENCRSSNEIILQRIQDLIQGHLSAE 168
>gnl|CDD|218181 pfam04621, ETS_PEA3_N, PEA3 subfamily ETS-domain transcription
factor N terminal domain. The N terminus of the PEA3
transcription factors is implicated in transactivation
and in inhibition of DNA binding. Transactivation is
potentiated by activation of the Ras/MAP kinase and
protein kinase A signalling cascades. The N terminal
region contains conserved MAP kinase phosphorylation
sites.
Length = 336
Score = 26.4 bits (58), Expect = 8.1
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 11 PSSPYSCTSTPLILPRTTHLILNAHSPSGIRSYPSPPTPHPSSTSKGPP 59
P +P S +P+ P+ T L P S PSP TP P+ + PP
Sbjct: 132 PPTPPSTPCSPVN-PQETVRQLQPSGPLSNSSPPSPHTPLPNQSPLPPP 179
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 0.140 0.450
Gapped
Lambda K H
0.267 0.0647 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,310,536
Number of extensions: 771581
Number of successful extensions: 1023
Number of sequences better than 10.0: 1
Number of HSP's gapped: 970
Number of HSP's successfully gapped: 99
Length of query: 155
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 66
Effective length of database: 6,990,096
Effective search space: 461346336
Effective search space used: 461346336
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 (21.6 bits)
S2: 55 (25.1 bits)