RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10407
(210 letters)
>gnl|CDD|187698 cd09274, RNase_HI_RT_Ty3, Ty3/Gypsy family of RNase HI in long-term
repeat retroelements. 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 widely present in various organisms,
including bacteria, archaea and eukaryotes. RNase HI
has also been observed as adjunct domains to the reverse
transcriptase gene in retroviruses, in 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.
Phylogenetic patterns of RNase HI of LTR retroelements
is classified into five major families, Ty3/Gypsy,
Ty1/Copia, Bel/Pao, DIRS1 and the vertebrate
retroviruses. Ty3/Gypsy family widely distributed among
the genomes of plants, fungi and animals. RNase H
inhibitors have been explored as an anti-HIV drug target
because RNase H inactivation inhibits reverse
transcription.
Length = 121
Score = 72.9 bits (180), Expect = 7e-17
Identities = 25/57 (43%), Positives = 34/57 (59%), Gaps = 5/57 (8%)
Query: 95 TDNKALVTLFGEDKAVPMLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPL 151
TD+K+L L + + RL RW L+L FD+ I+Y+ G + VADALSRLP
Sbjct: 70 TDHKSLKYLLTKKDL-----NPRLARWLLLLQEFDFEIEYRPGKENVVADALSRLPE 121
>gnl|CDD|187690 cd06222, RNase_H, RNase H is an endonuclease that cleaves the RNA
strand of an RNA/DNA hybrid in a sequence non-specific
manner. 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 widely present in various organisms,
including bacteria, archaea and eukaryotes. 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 residues and have the same catalytic
mechanism and functions in cells. RNase H is involved in
DNA replication, repair and transcription. One of the
important functions of RNase H is to remove Okazaki
fragments during DNA replication. RNase H inhibitors
have been explored as an anti-HIV drug target because
RNase H inactivation inhibits reverse transcription.
Length = 123
Score = 33.5 bits (77), Expect = 0.026
Identities = 18/119 (15%), Positives = 32/119 (26%), Gaps = 21/119 (17%)
Query: 48 GRISCGGVMLMIHKKYFSQPVPGSPVEMGCCTN--------------SLHFKYIHCSLNE 93
G GGV+ + + + TN +L +
Sbjct: 11 GPAGAGGVLRDHEGAWLF----AGSLSIPAATNNEAELLALLEALELALDLGLKKLIIE- 65
Query: 94 ATDNKALVTLFGEDKAVP-MLSSARLQRWSLILSNFDYSIKYKKGTQIPVADALSRLPL 151
TD+K +V L + L+ D ++ VAD L++
Sbjct: 66 -TDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEHVPREGNEVADRLAKEAA 123
>gnl|CDD|212564 cd11674, lambda-1, inner capsid protein lambda-1 or VP3. The
reovirus inner capsid protein lambda-1 displays
nucleoside triphosphate phosphohydrolase (NTPase),
RNA-5'-triphosphatase (RTPase), and RNA helicase activity
and may play a role in the transcription of the virus
genome, the unwinding or reannealing of double-stranded
RNA during RNA synthesis. The RTPase activity constitutes
the first step in the capping of RNA, resulting in a
5'-diphosphorylated RNA plus-strand. lambda1 is an
Orthoreovirus core protein, VP3 is the homologous core
protein in Aquareoviruses.
Length = 1166
Score = 31.3 bits (71), Expect = 0.38
Identities = 20/83 (24%), Positives = 30/83 (36%), Gaps = 17/83 (20%)
Query: 67 PVPGS-PVEMG-CCTNSLHFKYIHCSLNE-----ATDNKALVTLFGEDKAVPMLSSARLQ 119
PVP P+ YI + N +T+ + T FG D ++P L+
Sbjct: 1072 PVPFLMPIPQDHNVITGRRVHYIWATENNDGSLFSTNAASPATAFGPDVSIP------LE 1125
Query: 120 RWSLILSNFDYSIKYKKGTQIPV 142
RW L + Y Q+P
Sbjct: 1126 RWP-ALVDPAYRP---GTNQLPA 1144
>gnl|CDD|119411 cd00206, snake_toxin, Snake toxin domain, present in short and
long neurotoxins, cytotoxins and short toxins, and in
other miscellaneous venom peptides. The toxin acts by
binding to the nicotinic acetylcholine receptors in the
postsynaptic membrane of skeletal muscles and
preventing the binding of acetylcholine, thereby
blocking the excitation of muscles. This domain
contains 60-75 amino acids that are fixed by 4-5
disulfide bridges and is nearly all beta sheet; it
exists as either monomers or dimers.
Length = 64
Score = 27.8 bits (62), Expect = 0.93
Identities = 11/40 (27%), Positives = 15/40 (37%), Gaps = 6/40 (15%)
Query: 61 KKYFSQPVPGSPVEMGC---CTNSLHFKYIHCSLNEATDN 97
KK + G +E GC C +Y+ C TD
Sbjct: 26 KKSWKDTPRGVRIERGCAATCPKVKPGEYVTCC---TTDK 62
>gnl|CDD|215268 PLN02487, PLN02487, zeta-carotene desaturase.
Length = 569
Score = 28.6 bits (64), Expect = 2.5
Identities = 12/34 (35%), Positives = 20/34 (58%), Gaps = 3/34 (8%)
Query: 174 DKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVVKI 207
DK++ +V + V +PS + L T+ +VVKI
Sbjct: 465 DKIVEKVHKQVLELFPSSRGLEV---TWSSVVKI 495
>gnl|CDD|184922 PRK14958, PRK14958, DNA polymerase III subunits gamma and tau;
Provisional.
Length = 509
Score = 28.2 bits (62), Expect = 3.6
Identities = 22/64 (34%), Positives = 32/64 (50%), Gaps = 8/64 (12%)
Query: 88 HCSLNEATDNKALVTLFGEDKAVPMLSSARLQRWSLILS-NFDYSIKYK-----KGTQIP 141
CSL E TDN+ + L + K P+L ++R S LS +F+ +I K T+ P
Sbjct: 404 QCSLKELTDNRLYLMLNPKQK--PLLQQKHIERISEALSEHFNRTITVKIDISNHQTETP 461
Query: 142 VADA 145
A A
Sbjct: 462 AALA 465
>gnl|CDD|241233 cd00836, FERM_C-lobe, FERM domain C-lobe. The FERM domain has a
cloverleaf tripart structure (FERM_N, FERM_M, FERM_C/N,
alpha-, and C-lobe/A-lobe, B-lobe, C-lobe/F1, F2, F3).
The C-lobe/F3 within the FERM domain is part of the PH
domain family. The FERM domain is found in the
cytoskeletal-associated proteins such as ezrin, moesin,
radixin, 4.1R, and merlin. These proteins provide a link
between the membrane and cytoskeleton and are involved
in signal transduction pathways. The FERM domain is also
found in protein tyrosine phosphatases (PTPs), the
tyrosine kinases FAK and JAK, in addition to other
proteins involved in signaling. This domain is
structurally similar to the PH and PTB domains and
consequently is capable of binding to both peptides and
phospholipids at different sites.
Length = 91
Score = 26.2 bits (58), Expect = 6.1
Identities = 11/47 (23%), Positives = 18/47 (38%), Gaps = 7/47 (14%)
Query: 160 LGLTAN-IIINSTRKDKVLSRVMEYVKHGWPSVKNLSCDKKTFHTVV 205
LG++ I + L WP ++ +S KKTF +
Sbjct: 18 LGVSLEGISVLDDNTGNPL------TLFRWPEIRKISFSKKTFTIEI 58
>gnl|CDD|223977 COG1048, AcnA, Aconitase A [Energy production and conversion].
Length = 861
Score = 27.3 bits (61), Expect = 7.5
Identities = 9/26 (34%), Positives = 14/26 (53%), Gaps = 3/26 (11%)
Query: 172 RKDKVLSRVMEYVKHGWPSVKNLSCD 197
RK V+ + +E+ G P V +LS
Sbjct: 264 RKKGVVGKFVEFF--G-PGVASLSLA 286
>gnl|CDD|237816 PRK14788, PRK14788, lipoprotein signal peptidase; Provisional.
Length = 200
Score = 26.5 bits (59), Expect = 9.6
Identities = 9/25 (36%), Positives = 16/25 (64%), Gaps = 1/25 (4%)
Query: 45 FLDGRISCGGVMLMI-HKKYFSQPV 68
D IS G ++L++ +KK F +P+
Sbjct: 175 IADSAISIGVILLLLFNKKAFPEPL 199
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
0.321 0.137 0.418
Gapped
Lambda K H
0.267 0.0655 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,458,892
Number of extensions: 944171
Number of successful extensions: 632
Number of sequences better than 10.0: 1
Number of HSP's gapped: 631
Number of HSP's successfully gapped: 11
Length of query: 210
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 117
Effective length of database: 6,812,680
Effective search space: 797083560
Effective search space used: 797083560
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 (21.9 bits)
S2: 57 (25.9 bits)