RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11389
(73 letters)
>gnl|CDD|187700 cd09276, Rnase_HI_RT_non_LTR, non-LTR RNase HI domain of reverse
transcriptases. Ribonuclease H (RNase H) is classified
into two families, type 1 (prokaryotic RNase HI,
eukaryotic RNase H1 and viral RNase H) and type 2
(prokaryotic RNase HII and HIII, and eukaryotic RNase
H2). Ribonuclease HI (RNase HI) is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. RNase H is widely present
in various organisms, including bacteria, archaea and
eukaryotes. RNase HI has also been observed as an
adjunct domain to the reverse transcriptase gene in
retroviruses, long-term repeat (LTR)-bearing
retrotransposons and non-LTR retrotransposons. RNase HI
in LTR retrotransposons perform degradation of the
original RNA template, generation of a polypurine tract
(the primer for plus-strand DNA synthesis), and final
removal of RNA primers from newly synthesized minus and
plus strands. The catalytic residues for RNase H
enzymatic activity, three aspartatic acids and one
glutamatic acid residue (DEDD), are unvaried across all
RNase H domains. The position of the RNase domain of
non-LTR and LTR transposons is at the carboxyl terminal
of the reverse transcriptase (RT) domain and their RNase
domains group together, indicating a common evolutionary
origin. Many non-LTR transposons have lost the RNase
domain because their activity is at the nucleus and
cellular RNase may suffice; however LTR retotransposons
always encode their own RNase domain because it requires
RNase activity in RNA-protein particles in the
cytoplasm. RNase H inhibitors have been explored as an
anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 128
Score = 34.5 bits (80), Expect = 0.001
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 20 HCGIKGNEIVDVAAR 34
H GI+GNE D A+
Sbjct: 110 HSGIEGNERADRLAK 124
>gnl|CDD|215695 pfam00075, RNase_H, RNase H. RNase H digests the RNA strand of an
RNA/DNA hybrid. Important enzyme in retroviral
replication cycle, and often found as a domain
associated with reverse transcriptases. Structure is a
mixed alpha+beta fold with three a/b/a layers.
Length = 126
Score = 28.0 bits (63), Expect = 0.25
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 20 HCGIKGNEIVDVAAR 34
H GI GNE+ D A+
Sbjct: 108 HSGIPGNELADKLAK 122
>gnl|CDD|220003 pfam08752, Gamma-COP, Coatomer gamma subunit appendage domain.
COPI-coated vesicles function in retrograde transport
from the Golgi to the ER, and in intra-Golgi transport.
This domain corresponds to the coatomer gamma subunit
appendage domain. It contains a protein-protein
interaction site and a second proposed binding site that
interacts with the alpha, beta,epsilon COPI subcomplex.
Length = 269
Score = 28.0 bits (63), Expect = 0.35
Identities = 6/19 (31%), Positives = 11/19 (57%)
Query: 53 FVASLMNSEWQSQWDNVPN 71
F+ L +++ WD +PN
Sbjct: 156 FIQPLRVGNFKAAWDELPN 174
>gnl|CDD|218636 pfam05557, MAD, Mitotic checkpoint protein. This family consists
of several eukaryotic mitotic checkpoint (Mitotic arrest
deficient or MAD) proteins. The mitotic spindle
checkpoint monitors proper attachment of the bipolar
spindle to the kinetochores of aligned sister chromatids
and causes a cell cycle arrest in prometaphase when
failures occur. Multiple components of the mitotic
spindle checkpoint have been identified in yeast and
higher eukaryotes. In S.cerevisiae, the existence of a
Mad1-dependent complex containing Mad2, Mad3, Bub3 and
Cdc20 has been demonstrated.
Length = 722
Score = 27.2 bits (60), Expect = 0.68
Identities = 10/27 (37%), Positives = 12/27 (44%)
Query: 38 NATPLNLCTPEDFKPFVASLMNSEWQS 64
LNL TP+D + L N E Q
Sbjct: 329 QDIGLNLRTPDDLSRRIVVLQNEELQL 355
>gnl|CDD|233796 TIGR02242, tail_TIGR02242, phage tail protein domain. This model
describes a region of sequence similarity shared by a
number of uncharacterized proteins in bacterial
genomes, including Geobacter sulfurreducens PCA,
Mesorhizobium loti, Streptomyces coelicolor A3(2),
Gloeobacter violaceus PCC 7421, and Myxococcus xanthus.
In all cases, the genomic region resembles a phage tail
region, based on tentative identifications of
neighboring genes. A region of this domain resembles a
region of TIGR01634, another phage tail protein model
[Mobile and extrachromosomal element functions,
Prophage functions].
Length = 130
Score = 25.9 bits (57), Expect = 1.7
Identities = 7/32 (21%), Positives = 12/32 (37%), Gaps = 2/32 (6%)
Query: 36 PTNATPLNLCTPEDFKPFVASLMNSEWQSQWD 67
P P P F F+A + + + + D
Sbjct: 39 PDYFDPET--APAPFLDFLAQWLGNPFDDELD 68
>gnl|CDD|117265 pfam08692, Pet20, Mitochondrial protein Pet20. Pet20 is a
mitochondrial protein which is thought to play a role in
the correct assembly/maintenance of mitochondrial
components.
Length = 137
Score = 25.7 bits (56), Expect = 1.7
Identities = 7/18 (38%), Positives = 12/18 (66%)
Query: 54 VASLMNSEWQSQWDNVPN 71
+S M E+ +W+NVP+
Sbjct: 104 SSSAMGMEFYPEWENVPS 121
>gnl|CDD|225106 COG2195, PepD, Di- and tripeptidases [Amino acid transport and
metabolism].
Length = 414
Score = 25.4 bits (56), Expect = 3.0
Identities = 12/32 (37%), Positives = 13/32 (40%), Gaps = 5/32 (15%)
Query: 9 SYLRYLSNPICHCGIKG-----NEIVDVAARN 35
S LR I H GI+G EI A N
Sbjct: 157 SVLREKHPEIPHGGIRGGFSPDEEIGGRGAAN 188
>gnl|CDD|187701 cd09277, RNase_HI_bacteria_HBD, Bacterial RNase HI containing a
hybrid binding domain (HBD) at the N-terminus.
Ribonuclease H (RNase H) enzymes are divided into two
major families, Type 1 and Type 2, based on amino acid
sequence similarities and biochemical properties. RNase
H is an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner in the
presence of divalent cations. RNase H is involved in
DNA replication, repair and transcription. RNase H is
widely present in various organisms, including bacteria,
archaea and eukaryotes and most prokaryotic and
eukaryotic genomes contain multiple RNase H genes.
Despite the lack of amino acid sequence homology, Type 1
and type 2 RNase H share a main-chain fold and steric
configurations of the four acidic active-site (DEDD)
residues and have the same catalytic mechanism and
functions in cells. One of the important functions of
RNase H is to remove Okazaki fragments during DNA
replication. Prokaryotic RNase H varies greatly in
domain structures and substrate specificities.
Prokaryotes and some single-cell eukaryotes do not
require RNase H for viability. Some bacteria
distinguished from other bacterial RNase HI in the
presence of a hybrid binding domain (HBD) at the
N-terminus which is commonly present at the N-termini of
eukaryotic RNase HI. It has been reported that this
domain is required for dimerization and processivity of
RNase HI upon binding to RNA-DNA hybrids.
Length = 133
Score = 25.2 bits (56), Expect = 3.1
Identities = 7/16 (43%), Positives = 9/16 (56%)
Query: 20 HCGIKGNEIVDVAARN 35
H G K NE+ D A+
Sbjct: 116 HSGDKYNELADKLAKK 131
>gnl|CDD|173724 cd06606, STKc_MAPKKK, Catalytic domain of the Protein
Serine/Threonine Kinase, Mitogen-Activated Protein
Kinase Kinase Kinase. Serine/threonine kinases (STKs),
mitogen-activated protein kinase (MAPK) kinase kinase
(MAPKKK) subfamily, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
MAPKKK 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. MAPKKKs (MKKKs or MAP3Ks) are also called
MAP/ERK kinase kinases (MEKKs) in some cases. They
phosphorylate and activate MAPK kinases (MAPKKs or MKKs
or MAP2Ks), which in turn phosphorylate and activate
MAPKs during signaling cascades that are important in
mediating cellular responses to extracellular signals.
This subfamily is composed of the Apoptosis
Signal-regulating Kinases ASK1 (or MAPKKK5) and ASK2 (or
MAPKKK6), MEKK1, MEKK2, MEKK3, MEKK4, as well as plant
and fungal MAPKKKs. Also included in this subfamily are
the cell division control proteins Schizosaccharomyces
pombe Cdc7 and Saccharomyces cerevisiae Cdc15.
Length = 260
Score = 25.2 bits (56), Expect = 3.2
Identities = 11/19 (57%), Positives = 11/19 (57%), Gaps = 1/19 (5%)
Query: 11 LRYL-SNPICHCGIKGNEI 28
L YL SN I H IKG I
Sbjct: 114 LAYLHSNGIVHRDIKGANI 132
>gnl|CDD|162945 TIGR02604, Piru_Ver_Nterm, putative membrane-bound dehydrogenase
domain. All proteins that score above the trusted
cutoff score of 45 to this model are large proteins of
either Pirellula sp. 1 or Verrucomicrobium spinosum.
These proteins all contain, in addition to this domain,
several hundred residues of highly variable sequence,
and then a well-conserved C-terminal domain (TIGR02603)
that features a putative cytochrome c-type heme binding
motif CXXCH. The membrane-bound L-sorbosone
dehydrogenase from Acetobacter liquefaciens
(Gluconacetobacter liquefaciens) (SP|Q44091) is
homologous to this domain but lacks additional sequence
regions shared by members of this family and belongs to
a different clade of the larger family of homologs. It
and its closely related homologs are excluded from the
this model by scoring between the trusted (45) and
noise (18) cutoffs.
Length = 367
Score = 25.1 bits (55), Expect = 3.5
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 29 VDVAARNPTNATPLNLCTPEDFKPFVA 55
V + A P P+ +C E + +VA
Sbjct: 4 VTLFAAEPLLRNPIAVCFDERGRLWVA 30
>gnl|CDD|220919 pfam10974, DUF2804, Protein of unknown function (DUF2804). This is
a family of proteins with unknown function.
Length = 333
Score = 24.9 bits (55), Expect = 4.3
Identities = 10/37 (27%), Positives = 15/37 (40%), Gaps = 1/37 (2%)
Query: 19 CHCGIKGNEI-VDVAARNPTNATPLNLCTPEDFKPFV 54
KG + D+ P + PL +CTP + F
Sbjct: 127 VDLFGKGKGLEADLELDLPPGSEPLAVCTPTGYNGFT 163
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
0.317 0.133 0.432
Gapped
Lambda K H
0.267 0.0766 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,663,939
Number of extensions: 255487
Number of successful extensions: 220
Number of sequences better than 10.0: 1
Number of HSP's gapped: 220
Number of HSP's successfully gapped: 11
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
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: 53 (24.1 bits)