RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7629
(468 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 = 64.6 bits (158), Expect = 1e-12
Identities = 28/91 (30%), Positives = 41/91 (45%), Gaps = 5/91 (5%)
Query: 313 HIYTDGSLINPEDGAGAGIFCELFSFYKR---LGTFTTNFDGEIAAIKIALLQILNRTNQ 369
IYTDGS + E GAG R LG + + FD E+ AI AL L +
Sbjct: 1 VIYTDGSKL--EGRTGAGFAIVRKGTISRSYKLGPYCSVFDAELLAILEALQLALREGRR 58
Query: 370 FERAVILSDSKAAIQSITNCSEDPSIKHNKR 400
+ I SDS+AA++++ + + R
Sbjct: 59 ARKITIFSDSQAALKALRSPRSSSPLVLRIR 89
>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 = 51.1 bits (123), Expect = 8e-08
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 7/81 (8%)
Query: 314 IYTDGSLI-NPEDGAGAGI---FCE--LFSFYKRL-GTFTTNFDGEIAAIKIALLQILNR 366
+YTDG+ N GA AG F + +RL G TN E+ A+ AL I
Sbjct: 2 VYTDGACRGNGRSGARAGYGVYFGPGHPRNVSERLPGPPQTNQRAELRAVIHALRLIKEV 61
Query: 367 TNQFERAVILSDSKAAIQSIT 387
+ VI +DS+ + +T
Sbjct: 62 GEGLTKLVIATDSEYVVNGVT 82
>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 = 45.8 bits (109), Expect = 3e-06
Identities = 25/109 (22%), Positives = 42/109 (38%), Gaps = 9/109 (8%)
Query: 315 YTDGS-LINPEDGAGAGIFCE-----LFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTN 368
TDGS NP G+ + LF+ + TN + E+ A+ AL L+
Sbjct: 1 NTDGSCKGNPGPAGAGGVLRDHEGAWLFAGSLSIPA-ATNNEAELLALLEALELALD--L 57
Query: 369 QFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKKWQQILNTH 417
++ +I +DSK + I + S+ + K+ I H
Sbjct: 58 GLKKLIIETDSKYVVDLINSWSKGWKKNNLLLWDILLLLSKFIDIRFEH 106
>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 = 44.2 bits (105), Expect = 1e-05
Identities = 28/111 (25%), Positives = 42/111 (37%), Gaps = 21/111 (18%)
Query: 314 IYTDGSLI--NPEDGAGAGIFCELFSFYKRLGTFTTNFDGEIAAIKIALLQILNRTNQFE 371
+YTDGS GAG K L TTN E+ A+ AL + +
Sbjct: 6 VYTDGSCNGNPGPGGAGYVTD-GGKQRSKPLP-GTTNQRAELLALIEALEALSG-----Q 58
Query: 372 RAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKK---WQQILNTHDI 419
+ I +DS+ I ITN ++E + K W+ + H +
Sbjct: 59 KVNIYTDSQYVIGGITN---------GWPTKSESKPIKNEIWELLQKKHKV 100
>gnl|CDD|223405 COG0328, RnhA, Ribonuclease HI [DNA replication, recombination, and
repair].
Length = 154
Score = 40.8 bits (96), Expect = 3e-04
Identities = 26/115 (22%), Positives = 42/115 (36%), Gaps = 21/115 (18%)
Query: 312 LHIYTDG-SLINPEDGAGAGIFCELFSFYKRLG-------TFTTNFDGEIAAIKIALLQI 363
+ I+TDG L NP G + Y TTN E+ A+ AL +
Sbjct: 4 VEIFTDGACLGNPGPGGWGAVL-----RYGDGEKELSGGEGRTTNNRAELRALIEAL-EA 57
Query: 364 LNRTNQFERAVILSDSKAAIQSITNCSEDPSIKHNKRLRNEGQGKK----WQQIL 414
L + + +DSK ++ IT K N + + K W+++
Sbjct: 58 L-KELGACEVTLYTDSKYVVEGITRWIVKW--KKNGWKTADKKPVKNKDLWEELD 109
>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 = 32.1 bits (74), Expect = 0.24
Identities = 23/84 (27%), Positives = 35/84 (41%), Gaps = 15/84 (17%)
Query: 312 LHIYTDGS-LINPEDGA-GAGIFC-----ELFSFYKRLGTFTTNFDGEIAAIKIALLQIL 364
+ IYTDG+ L NP G A + EL TTN E+ A+++ L
Sbjct: 2 ITIYTDGACLGNPGPGGWAAILRYGDHEKELSGGEAG----TTNNRMEL----TAVIEAL 53
Query: 365 NRTNQFERAVILSDSKAAIQSITN 388
+ ++ +DS+ I IT
Sbjct: 54 EALKEPCPVLLYTDSQYVINGITK 77
>gnl|CDD|223338 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and
metabolism].
Length = 485
Score = 32.2 bits (74), Expect = 0.65
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 18/59 (30%)
Query: 182 TGAVKTTPINAMYAL--------TQNQSLSDIIEQQALTTYEKLTRLPNNNFWTTYKED 232
TGA A+ AL + + L++ + + T E L RLP Y++
Sbjct: 364 TGA-------AVVALGNDYTGLFSNDDELANQLLAASEETGEPLWRLP---LHEEYRKQ 412
>gnl|CDD|240225 PTZ00004, PTZ00004, actin-2; Provisional.
Length = 378
Score = 29.7 bits (67), Expect = 3.3
Identities = 25/97 (25%), Positives = 43/97 (44%), Gaps = 13/97 (13%)
Query: 105 GPKAYSFISSIKKGQTSVNKPFSHNG-RSISDSKKIASIFNTFYTSKYNIP-KHEVLLTT 162
G +A K+G ++ P H + D +KI +TFY P +H VLLT
Sbjct: 56 GDEAQD-----KRGILTLKYPIEHGIVTNWDDMEKIWH--HTFYNELRVAPEEHPVLLTE 108
Query: 163 S----KTNKQKIEKVQNEALRLVTGAVKTTPINAMYA 195
+ K N++K+ ++ E + V + ++YA
Sbjct: 109 APLNPKANREKMTQIMFETHNVPAMYVAIQAVLSLYA 145
>gnl|CDD|237924 PRK15206, PRK15206, long polar fimbrial protein LpfD; Provisional.
Length = 359
Score = 28.8 bits (64), Expect = 6.4
Identities = 27/75 (36%), Positives = 32/75 (42%), Gaps = 5/75 (6%)
Query: 117 KGQTS--VNKPFSHNGRSISDSKKIASIFNTFYTSKYN-IPKHEVLLTTSKTNKQKIEKV 173
KG S + PF G SI S KI +F T S YN IP V ++ S T Q E
Sbjct: 163 KGHLSLYILHPFV--GESIIPSTKIMDLFGTKKPSVYNSIPAASVYISGSITVPQGCELS 220
Query: 174 QNEALRLVTGAVKTT 188
L + G K T
Sbjct: 221 SGSTLEIPFGEFKAT 235
>gnl|CDD|235409 PRK05325, PRK05325, hypothetical protein; Provisional.
Length = 401
Score = 28.6 bits (65), Expect = 7.4
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 5/26 (19%)
Query: 297 MALETINTRYPSDDWLHIY----TDG 318
+ALE I RYP +W +IY +DG
Sbjct: 297 LALEIIEERYPPAEW-NIYAFQASDG 321
>gnl|CDD|223417 COG0340, BirA, Biotin-(acetyl-CoA carboxylase) ligase [Coenzyme
metabolism].
Length = 238
Score = 28.0 bits (63), Expect = 8.4
Identities = 14/69 (20%), Positives = 25/69 (36%), Gaps = 5/69 (7%)
Query: 17 KEFCELLQSAAKLSIPRGKTKRFNYFWNKKLSVLKSERNAARKRAEKSNLLSDTVEWRKR 76
+F ++ Q A L + R + L+ L E ++ + WR R
Sbjct: 131 PDFEDIGQPATSLQEEGEEIDR-----EELLAKLLKELEKYLRQFLREGFAPILARWRAR 185
Query: 77 AAILKKEIN 85
+ L KE+
Sbjct: 186 SLSLGKEVR 194
>gnl|CDD|233794 TIGR02239, recomb_RAD51, DNA repair protein RAD51. This eukaryotic
sequence family consists of RAD51, a protein involved in
DNA homologous recombination and repair. It is similar
in sequence the exclusively meiotic recombinase DMC1
(TIGR02238), to archaeal families RadA (TIGR02236) and
RadB (TIGR02237), and to bacterial RecA (TIGR02012).
Length = 316
Score = 28.2 bits (63), Expect = 9.6
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 3/54 (5%)
Query: 129 NGRSISDSKKIA-SIFNTFYTSKYNIPKHEVLLTTSKTNKQKIEKVQNEALRLV 181
NG + +D KK+ + +T + Y PK + LL ++ K +K+ EA +LV
Sbjct: 7 NGITAADIKKLQEAGLHTVESVAY-APKKQ-LLEIKGISEAKADKILAEAAKLV 58
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
0.315 0.130 0.371
Gapped
Lambda K H
0.267 0.0694 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 23,119,691
Number of extensions: 2222305
Number of successful extensions: 1879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1872
Number of HSP's successfully gapped: 26
Length of query: 468
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 368
Effective length of database: 6,502,202
Effective search space: 2392810336
Effective search space used: 2392810336
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: 61 (27.3 bits)