RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11391
(112 letters)
>gnl|CDD|219782 pfam08292, RNA_pol_Rbc25, RNA polymerase III subunit Rpc25. Rpc25
is a strongly conserved subunit of RNA polymerase III
and has homology to Rpa43 in RNA polymerase I, Rpb7 in
RNA polymerase II and the archaeal RpoE subunit. Rpc25
is required for transcription initiation and is not
essential for the elongating properties of RNA
polymerase III.
Length = 121
Score = 100 bits (252), Expect = 5e-29
Identities = 41/85 (48%), Positives = 54/85 (63%), Gaps = 3/85 (3%)
Query: 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFT 61
V+LGFF+DI IPP+ L +PS FDE+EQ WVWE+D E +L+ D G++I+FRV SE+F
Sbjct: 21 VSLGFFDDIFIPPDNLPEPSEFDEEEQAWVWEYDEE---TELYFDVGEEIRFRVESEIFV 77
Query: 62 ETSPISCPDIHDGAPGSEVDTPKIP 86
+ P S A E D K P
Sbjct: 78 DVKPTSPELAESLADSEEEDDEKKP 102
>gnl|CDD|129540 TIGR00448, rpoE, DNA-directed RNA polymerase (rpoE), archaeal and
eukaryotic form. This family seems to be confined to
the archea and eukaryotic taxa and are quite dissimilar
to E.coli rpoE [Transcription, DNA-dependent RNA
polymerase].
Length = 179
Score = 40.2 bits (94), Expect = 4e-05
Identities = 13/64 (20%), Positives = 27/64 (42%), Gaps = 6/64 (9%)
Query: 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFT 61
V+LG F+ + + +D KE + + + +D GDK++ R+ +
Sbjct: 99 VSLGPFDGLFHVSQVTDDYCYYDPKESALIGK------ETKKVLDEGDKVRARIVALSLK 152
Query: 62 ETSP 65
+ P
Sbjct: 153 DRRP 156
>gnl|CDD|224020 COG1095, RPB7, DNA-directed RNA polymerase, subunit E'
[Transcription].
Length = 183
Score = 32.7 bits (75), Expect = 0.018
Identities = 13/64 (20%), Positives = 23/64 (35%), Gaps = 6/64 (9%)
Query: 2 VTLGFFEDILIPPEGLQQPSRFDEKEQVWVWEFDNEGDKHDLFMDPGDKIKFRVTSELFT 61
V +G D L+ + D E+ V G++ + GDK++ R+
Sbjct: 99 VRIGPL-DGLVHVSQIMDD-YIDYDEKNKVLI----GEETKRVLKVGDKVRARIVGVSLK 152
Query: 62 ETSP 65
P
Sbjct: 153 SRRP 156
>gnl|CDD|198376 cd07810, FGGY_D-XK_2, D-xylulose kinases, subgroup 2; members of
the FGGY family of carbohydrate kinases. This subgroup
is predominantly composed of bacterial D-xylulose
kinases (XK, also known as xylulokinase; EC 2.7.1.17).
They share high sequence similarity with Escherichia
coli xylulokinase (EcXK), which catalyzes the
rate-limiting step in the ATP-dependent phosphorylation
of D-xylulose to produce D-xylulose 5-phosphate (X5P)
and ADP. EcXK exists as a dimer. Each monomer consists
of two large domains separated by an open cleft that
forms an active site. This model includes both the
N-terminal domain, which adopts a ribonuclease H-like
fold, and the structurally related C-terminal domain.
The presence of Mg2+ or Mn2+ might be required for
catalytic activity. Members of this subgroup belong to
the FGGY family of carbohydrate kinases.
Length = 490
Score = 28.5 bits (64), Expect = 0.73
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 5/54 (9%)
Query: 17 LQQPSRFDEKEQVWVWEFDNEG---DKHDLFMDPGDKIKFRVTSELFTETSPIS 67
L P F + WV E NE D+ M PGD I ++T E+ T S +S
Sbjct: 128 LNSPGNFTASKLAWVKE--NEPEVFDRIAKIMLPGDYIAMKLTGEVTTTKSGLS 179
>gnl|CDD|218747 pfam05786, Cnd2, Condensin complex subunit 2. This family consists
of several Barren protein homologues from several
eukaryotic organisms. In Drosophila Barren (barr) is
required for sister-chromatid segregation in mitosis.
barr encodes a novel protein that is present in
proliferating cells and has homologues in yeast and
human. Mitotic defects in barr embryos become apparent
during cycle 16, resulting in a loss of PNS and CNS
neurons. Centromeres move apart at the
metaphase-anaphase transition and Cyclin B is degraded,
but sister chromatids remain connected, resulting in
chromatin bridging. Barren protein localises to
chromatin throughout mitosis. Colocalisation and
biochemical experiments indicate that Barren associates
with Topoisomerase II throughout mitosis and alters the
activity of Topoisomerase II. It has been suggested that
this association is required for proper chromosomal
segregation by facilitating the decatenation of
chromatids at anaphase. This family forms one of the
three non-structural maintenance of chromosomes (SMC)
subunits of the mitotic condensation complex along with
Cnd1 and Cnd3.
Length = 719
Score = 27.8 bits (62), Expect = 1.5
Identities = 9/52 (17%), Positives = 14/52 (26%)
Query: 33 EFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPISCPDIHDGAPGSEVDTPK 84
D + D F D + + E S DI + P+
Sbjct: 557 GADGDDDDDGPFDDAAEMLSDPSDGEPGASASDAGGADILTYIETELIGAPR 608
>gnl|CDD|178547 PLN02962, PLN02962, hydroxyacylglutathione hydrolase.
Length = 251
Score = 27.5 bits (61), Expect = 1.6
Identities = 13/28 (46%), Positives = 17/28 (60%), Gaps = 3/28 (10%)
Query: 38 GDKHDLFMDPGDKIKFRVTSELFTETSP 65
G K DLF++PGDKI F +L+ E
Sbjct: 97 GSKADLFVEPGDKIYF---GDLYLEVRA 121
>gnl|CDD|235966 PRK07207, PRK07207, ribonucleotide-diphosphate reductase subunit
alpha; Validated.
Length = 965
Score = 26.8 bits (60), Expect = 2.6
Identities = 14/36 (38%), Positives = 16/36 (44%), Gaps = 14/36 (38%)
Query: 42 DLFMDPGDKIKFRVTSE----LFTETSPISCPDIHD 73
DLFM RV + LF SP PD+HD
Sbjct: 490 DLFMK-------RVMEDGEWTLF---SPSEVPDLHD 515
>gnl|CDD|238368 cd00717, URO-D, Uroporphyrinogen decarboxylase (URO-D) is a
dimeric cytosolic enzyme that decarboxylates the four
acetate side chains of uroporphyrinogen III (uro-III)
to create coproporphyrinogen III, without requiring any
prosthetic groups or cofactors. This reaction is
located at the branching point of the tetrapyrrole
biosynthetic pathway, leading to the biosynthesis of
heme, chlorophyll or bacteriochlorophyll. URO-D
deficiency is responsible for the human genetic
diseases familial porphyria cutanea tarda (fPCT) and
hepatoerythropoietic porphyria (HEP).
Length = 335
Score = 26.3 bits (59), Expect = 4.0
Identities = 8/22 (36%), Positives = 11/22 (50%)
Query: 6 FFEDILIPPEGLQQPSRFDEKE 27
F DIL+P E + F E +
Sbjct: 64 IFSDILVPLEAMGMDVEFVEGK 85
>gnl|CDD|233423 TIGR01464, hemE, uroporphyrinogen decarboxylase. This model
represents uroporphyrinogen decarboxylase (HemE), which
converts uroporphyrinogen III to coproporphyrinogen
III. This step takes the pathway toward protoporphyrin
IX, a common precursor of both heme and chlorophyll,
rather than toward precorrin 2 and its products
[Biosynthesis of cofactors, prosthetic groups, and
carriers, Heme, porphyrin, and cobalamin].
Length = 338
Score = 25.7 bits (57), Expect = 6.5
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 7 FEDILIPPEGLQQPSRFDEKE 27
F DIL+P + L F E +
Sbjct: 68 FSDILVPLQALGLDVEFVEGK 88
>gnl|CDD|240448 cd13425, Peptidase_G1_like, Peptidases of the G1 family and
homologs that might lack peptidase activity. Some
members of this family had been classified earlier as
carboxyl peptidases insensitive to pepstatin, and the
family has also been called the eqolisin family, due to
the fact that the conserved catalytic dyad of the
family consists of a glutamate (E) and glutamine (Q)
residue. The family is found in fungi and bacteria.
This family also includes homologous uncharacterized
proteins that might lack peptidase activity.
Length = 195
Score = 25.4 bits (55), Expect = 7.1
Identities = 7/35 (20%), Positives = 11/35 (31%)
Query: 32 WEFDNEGDKHDLFMDPGDKIKFRVTSELFTETSPI 66
W NE ++ PGD ++ V
Sbjct: 65 WGPKNEKFTYNKGFRPGDTVQXTVYKTSSGNGRAT 99
>gnl|CDD|188093 TIGR00864, PCC, polycystin cation channel protein. The Polycystin
Cation Channel (PCC) Family (TC 1.A.5) Polycystin is a
huge protein of 4303aas. Its repeated leucine-rich (LRR)
segment is found in many proteins. It contains 16
polycystic kidney disease (PKD) domains, one LDL-receptor
class A domain, one C-type lectin family domain, and
16-18 putative TMSs in positions between residues 2200
and 4100. Polycystin-L has been shown to be a cation
(Na+, K+ and Ca2+) channel that is activated by Ca2+. Two
members of the PCC family (polycystin 1 and 2) are
mutated in autosomal dominant polycystic kidney disease,
and polycystin-L is deleted in mice with renal and
retinal defects. Note: this model is restricted to the
amino half for technical reasons.
Length = 2740
Score = 25.4 bits (55), Expect = 7.9
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 3/46 (6%)
Query: 70 DIHDGAPGSEVDTPKIPYSY---GYYSLAVLRTQLLSPVRFQHVVT 112
D DG+ G + D P+ + Y G Y + V + L+S +
Sbjct: 2078 DFGDGSAGQDTDEPRAEHEYLHPGDYRVQVNASNLVSFFSAHAEIN 2123
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 0.140 0.438
Gapped
Lambda K H
0.267 0.0473 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,949,836
Number of extensions: 496501
Number of successful extensions: 383
Number of sequences better than 10.0: 1
Number of HSP's gapped: 381
Number of HSP's successfully gapped: 23
Length of query: 112
Length of database: 10,937,602
Length adjustment: 76
Effective length of query: 36
Effective length of database: 7,566,698
Effective search space: 272401128
Effective search space used: 272401128
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: 53 (24.8 bits)