RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy15450
(659 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 = 106 bits (268), Expect = 2e-27
Identities = 49/185 (26%), Positives = 74/185 (40%), Gaps = 60/185 (32%)
Query: 203 IFTDGSKTSESVASAFYDTQNKNSGTFKLQNFATIFTAEAFAILQALKYASSIKEKEAGY 262
I+TDGSK + F
Sbjct: 2 IYTDGSKLEGRTGAGF-------------------------------------------- 17
Query: 263 CKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKEN--EVIIITD 320
+R+ S ++KL + ++F AE AIL+AL+ ++ I +D
Sbjct: 18 --AIVRKGTI--------SRSYKLGPYCSVFDAELLAILEALQLALREGRRARKITIFSD 67
Query: 321 SKSCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLA 380
S++ L+ L++ + S L+L I KA+ L + VR WV GH+GI GNE DRLA
Sbjct: 68 SQAALKALRSPR----SSSPLVLRIRKAIRELANHGVKVRLHWVPGHSGIEGNERADRLA 123
Query: 381 KETAR 385
KE A+
Sbjct: 124 KEAAK 128
>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 = 70.8 bits (174), Expect = 9e-15
Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 7/98 (7%)
Query: 288 NFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFK 347
T AE A+++AL+ +S K V I TDS+ + + N + + +I++
Sbjct: 36 PGTTNQRAELLALIEALEALSGQK---VNIYTDSQYVIGGITNGWPTKSESKPIKNEIWE 92
Query: 348 ALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
L V WV GH+GI GNE D+LAK+ A
Sbjct: 93 LLQK----KHKVYIQWVPGHSGIPGNELADKLAKQGAS 126
>gnl|CDD|187704 cd09280, RNase_HI_eukaryote_like, Eukaryotic RNase H is longer and
more complex than their prokaryotic counterparts and
unlike prokaryote, RNase H are essential in higher
eukaryote. 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). RNase H is
an endonuclease that cleaves the RNA strand of an
RNA/DNA hybrid in a sequence non-specific manner. 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 is widely present in various organisms,
including bacteria, archaea and eukaryote 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. Eukaryotic RNase H is
longer and more complex than in prokaryotes. Almost all
eukaryotic RNase HI have highly conserved regions at the
N-terminal called hybrid binding domain (HBD). It is
speculated that the HBD contributes to binding the
RNA/DNA hybrid. Prokaryotes and some single-cell
eukaryotes do not require RNase H for viability, but
RNase H is essential in higher eukaryotes. RNase H
knockout mice lack mitochondrial DNA replication and die
as embryos.
Length = 150
Score = 67.2 bits (165), Expect = 3e-13
Identities = 39/105 (37%), Positives = 59/105 (56%), Gaps = 14/105 (13%)
Query: 295 AEAFAILQALKYVSSIKEN--EVIIITDSK---SCLEK-----LKNTSK-SNGNP-SH-- 340
AE A++ AL+ + + E +++I TDS+ + + + KN K S G P ++
Sbjct: 46 AELRAVIHALRLIKEVGEGLTKLVIATDSEYVVNGVTEWIPKWKKNGWKTSKGKPVANKD 105
Query: 341 LILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
LI ++ K L L+E I V+F V GH+GI GNE DRLAK+ A
Sbjct: 106 LIKELDKLLEELEERGIRVKFWHVPGHSGIYGNEEADRLAKKGAD 150
>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 = 62.8 bits (153), Expect = 6e-12
Identities = 35/95 (36%), Positives = 48/95 (50%), Gaps = 8/95 (8%)
Query: 290 ATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKAL 349
AT AE A+L+AL+ + ++II TDSK ++ + + SK + L+ DI L
Sbjct: 37 ATNNEAELLALLEALELALDLGLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLL 96
Query: 350 SHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETA 384
S I +RF V GNE DRLAKE A
Sbjct: 97 SKF----IDIRFEHVPRE----GNEVADRLAKEAA 123
>gnl|CDD|187702 cd09278, RNase_HI_prokaryote_like, RNase HI family found mainly in
prokaryotes. Ribonuclease H (RNase H) is classified
into two evolutionarily unrelated 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). RNase H is an endonuclease that
cleaves the RNA strand of an RNA/DNA hybrid in a
sequence non-specific manner. 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.
Length = 139
Score = 62.1 bits (152), Expect = 1e-11
Identities = 29/100 (29%), Positives = 46/100 (46%), Gaps = 21/100 (21%)
Query: 299 AILQALKYVSSIKEN-EVIIITDSKSCLE---------KLKNTSKSNGNP---SHLILDI 345
A+++AL+ ++KE V++ TDS+ + K ++G P L ++
Sbjct: 48 AVIEALE---ALKEPCPVLLYTDSQYVINGITKWIHGWKKNGWKTADGKPVKNVDLWQEL 104
Query: 346 FKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
L+ Q V + WV+GHAG GNE D LA A
Sbjct: 105 DALLAKHQ-----VTWHWVKGHAGHPGNERADELANAAAD 139
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 57.4 bits (139), Expect = 1e-09
Identities = 32/100 (32%), Positives = 51/100 (51%), Gaps = 10/100 (10%)
Query: 295 AEAFAILQALKYVSSIKENEVIIITDSKSCLE---------KLKNTSKSNGNPSHLILDI 345
AE A+++AL+ + + EV + TDSK +E K ++ P D+
Sbjct: 46 AELRALIEALEALKELGACEVTLYTDSKYVVEGITRWIVKWKKNGWKTADKKPV-KNKDL 104
Query: 346 FKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKETAR 385
++ L L + + V + WV+GHAG NE D+LA+E AR
Sbjct: 105 WEELDELLKRHELVFWEWVKGHAGHPENERADQLAREAAR 144
>gnl|CDD|187697 cd09273, RNase_HI_RT_Bel, Bel/Pao 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 eukaryote. 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. Bel/Pao family has been described only in
metazoan genomes. RNase H inhibitors have been explored
as an anti-HIV drug target because RNase H inactivation
inhibits reverse transcription.
Length = 135
Score = 49.2 bits (118), Expect = 4e-07
Identities = 38/149 (25%), Positives = 54/149 (36%), Gaps = 35/149 (23%)
Query: 252 ASSIKEKEAGYCKVSIRESLWIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIK 311
SS K AGY V+ + L I S AE A+++AL+
Sbjct: 6 GSSFVRK-AGYAVVTGPDVLEIATLPYGTSAQ----------RAELIALIRALELAKGKP 54
Query: 312 ENEVIIITDSK-----------SCLEKLKNTSKSNGNPSHLILDIFKALSHLQEWNISVR 360
N I TDS E+ T K + LIL + KA+ + V
Sbjct: 55 VN---IYTDSAYAFGILHALETIWKERGFLTGKPIAL-ASLILQLQKAIQRPKP----VA 106
Query: 361 FIWVRGHAG-----IAGNEAVDRLAKETA 384
I +R H+G GN D+ A++ A
Sbjct: 107 VIHIRAHSGLPGPLALGNARADQAARQAA 135
>gnl|CDD|205634 pfam13456, RVT_3, Reverse transcriptase-like. This domain is found
in plants and appears to be part of a retrotransposon.
Length = 88
Score = 44.9 bits (107), Expect = 5e-06
Identities = 21/91 (23%), Positives = 43/91 (47%), Gaps = 8/91 (8%)
Query: 291 TIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLEKLKNTSKSNGNPSHLILDIFKALS 350
+ AEA A+L+ L+ + +I+ +DS+ +++++ ++ + L+ +I K L
Sbjct: 1 SPLEAEAEALLEGLQLALELGIRRLIVESDSQLVVQQIQGEYEARSRLAALLREIRKLLK 60
Query: 351 HLQEWNISVRFIWVRGHAGIAGNEAVDRLAK 381
++SV + R N D LAK
Sbjct: 61 KF--DSVSVSHVP-R-----ECNRVADALAK 83
>gnl|CDD|178927 PRK00203, rnhA, ribonuclease H; Reviewed.
Length = 150
Score = 44.8 bits (107), Expect = 2e-05
Identities = 12/27 (44%), Positives = 17/27 (62%)
Query: 358 SVRFIWVRGHAGIAGNEAVDRLAKETA 384
+++ WV+GHAG NE D LA+ A
Sbjct: 114 QIKWHWVKGHAGHPENERCDELARAGA 140
>gnl|CDD|238827 cd01650, RT_nLTR_like, RT_nLTR: Non-LTR (long terminal repeat)
retrotransposon and non-LTR retrovirus reverse
transcriptase (RT). This subfamily contains both non-LTR
retrotransposons and non-LTR retrovirus RTs. RTs
catalyze the conversion of single-stranded RNA into
double-stranded DNA for integration into host
chromosomes. RT is a multifunctional enzyme with
RNA-directed DNA polymerase, DNA directed DNA polymerase
and ribonuclease hybrid (RNase H) activities.
Length = 220
Score = 44.2 bits (105), Expect = 7e-05
Identities = 21/63 (33%), Positives = 37/63 (58%), Gaps = 2/63 (3%)
Query: 45 DNNILPMEQRGCLEGATGCKDLLMLDKIITEDCKKKYKNLSVAWIDLLKAYDNCPHEWMV 104
+ NILP Q G G D ++L + + E K+K K+L + ++D KA+D+ HE+++
Sbjct: 45 EENILP-NQFGFRPGR-STTDAILLLREVIEKAKEKKKSLVLVFLDFEKAFDSVDHEFLL 102
Query: 105 KVI 107
K +
Sbjct: 103 KAL 105
>gnl|CDD|75628 PRK06548, PRK06548, ribonuclease H; Provisional.
Length = 161
Score = 41.7 bits (97), Expect = 3e-04
Identities = 35/122 (28%), Positives = 58/122 (47%), Gaps = 15/122 (12%)
Query: 272 WIFDTQNKNSGTFKLKNFATIFTAEAFAILQALKYVSSIKENEVIIITDSKSCLE----- 326
W D +SG + + AT AE A+ + L + + ++I++DSK +
Sbjct: 25 WYVDENTWDSGGW---DIATNNIAELTAVRELL-IATRHTDRPILILSDSKYVINSLTKW 80
Query: 327 ----KLKNTSKSNGNPSHLILDIFKALSHLQEWNISVRFIWVRGHAGIAGNEAVDRLAKE 382
K++ K++G P L +I + + L E N ++R WV H G NEA D LA++
Sbjct: 81 VYSWKMRKWRKADGKPV-LNQEIIQEIDSLME-NRNIRMSWVNAHTGHPLNEAADSLARQ 138
Query: 383 TA 384
A
Sbjct: 139 AA 140
>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 = 40.9 bits (97), Expect = 3e-04
Identities = 11/27 (40%), Positives = 17/27 (62%)
Query: 356 NISVRFIWVRGHAGIAGNEAVDRLAKE 382
I + F+ V+ H+G NE D+LAK+
Sbjct: 105 KIKISFVKVKAHSGDKYNELADKLAKK 131
>gnl|CDD|236334 PRK08719, PRK08719, ribonuclease H; Reviewed.
Length = 147
Score = 33.3 bits (76), Expect = 0.14
Identities = 13/27 (48%), Positives = 15/27 (55%)
Query: 359 VRFIWVRGHAGIAGNEAVDRLAKETAR 385
V V H+GI GNEA D LA+ A
Sbjct: 120 VEVEKVTAHSGIEGNEAADMLAQAAAE 146
>gnl|CDD|206693 cd04108, Rab36_Rab34, Rab GTPase families 34 (Rab34) and 36
(Rab36). Rab34/Rab36 subfamily. Rab34, found primarily
in the Golgi, interacts with its effector,
Rab-interacting lysosomal protein (RILP). This enables
its participation in microtubular
dynenin-dynactin-mediated repositioning of lysosomes
from the cell periphery to the Golgi. A Rab34 (Rah)
isoform that lacks the consensus GTP-binding region has
been identified in mice. This isoform is associated with
membrane ruffles and promotes macropinosome formation.
Rab36 has been mapped to human chromosome 22q11.2, a
region that is homozygously deleted in malignant
rhabdoid tumors (MRTs). However, experimental
assessments do not implicate Rab36 as a tumor suppressor
that would enable tumor formation through a
loss-of-function mechanism. GTPase activating proteins
(GAPs) interact with GTP-bound Rab and accelerate the
hydrolysis of GTP to GDP. Guanine nucleotide exchange
factors (GEFs) interact with GDP-bound Rabs to promote
the formation of the GTP-bound state. Rabs are further
regulated by guanine nucleotide dissociation inhibitors
(GDIs), which facilitate Rab recycling by masking
C-terminal lipid binding and promoting cytosolic
localization. Most Rab GTPases contain a lipid
modification site at the C-terminus, with sequence
motifs CC, CXC, or CCX. Lipid binding is essential for
membrane attachment, a key feature of most Rab proteins.
Length = 170
Score = 31.0 bits (70), Expect = 1.3
Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 7/67 (10%)
Query: 371 AGNEAVDRLAKETARGTDALNPYPIPVQDVRAVTDMQHEIQWRENVMSQNNNKGLFYKNL 430
AG E +A RG A+ I V D+ V ++H QW E+ + +N+ + L
Sbjct: 57 AGQERFKCIASTYYRGAQAI----IIVFDLTDVASLEHTRQWLEDALKENDPSSVL---L 109
Query: 431 FTITDKK 437
F + KK
Sbjct: 110 FLVGTKK 116
>gnl|CDD|213306 cd05940, FATP_FACS, Fatty acid transport proteins (FATP) play dual
roles as fatty acid transporters and its activation
enzymes. Fatty acid transport protein (FATP) transports
long-chain or very-long-chain fatty acids across the
plasma membrane. FATPs also have fatty acid CoA
synthetase activity, thus playing dual roles as fatty
acid transporters and its activation enzymes. At least
five copies of FATPs are identified in mammalian cells.
This family also includes prokaryotic FATPs. FATPs are
the key players in the trafficking of exogenous fatty
acids into the cell and in intracellular fatty acid
homeostasis.
Length = 444
Score = 31.1 bits (71), Expect = 2.0
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 5/34 (14%)
Query: 597 LPLYGNFFTAIWFLYLGVACCLAAGACVVIRTYF 630
LPLY + A L +G + LAAGA + +R F
Sbjct: 129 LPLYHS--NA---LTVGWSSALAAGASLALRRKF 157
>gnl|CDD|183259 PRK11652, emrD, multidrug resistance protein D; Provisional.
Length = 394
Score = 30.3 bits (69), Expect = 3.5
Identities = 14/41 (34%), Positives = 18/41 (43%), Gaps = 12/41 (29%)
Query: 597 LPLYGNFFTAIWF-----------LYLGVACCLAAGACVVI 626
LP+ FF A WF ++ V CCL AG + I
Sbjct: 251 LPIPAAFFGA-WFAGRPNKRFSTLMWQSVICCLLAGLLMWI 290
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 0.135 0.416
Gapped
Lambda K H
0.267 0.0797 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 32,742,591
Number of extensions: 3145431
Number of successful extensions: 2390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 2380
Number of HSP's successfully gapped: 25
Length of query: 659
Length of database: 10,937,602
Length adjustment: 103
Effective length of query: 556
Effective length of database: 6,369,140
Effective search space: 3541241840
Effective search space used: 3541241840
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: 62 (27.5 bits)